Information on EC 2.7.7.7 - DNA-directed DNA polymerase

Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Mark a special word or phrase in this record:
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)


The expected taxonomic range for this enzyme is: Eukaryota

EC NUMBER
COMMENTARY
2.7.7.7
-
RECOMMENDED NAME
GeneOntology No.
DNA-directed DNA polymerase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism; mechanism of polymerase translocation along templates; overview: basic mechanism of replicative DNA polymerases alpha and delta
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism of exonuclease activity
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
binding mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
modelling and simulation of the reaction mechanism, detailed overview
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
nucleotidyl-transfer reaction mechanism, intermediate structures and energy profiles, overview
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
reaction mechanism
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
reaction and kinetic mechanism, overview
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
mechanism
Sulfolobus solfataricus MT4
-
-
deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
nucleotidyl group transfer
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Metabolic pathways
-
Purine metabolism
-
Pyrimidine metabolism
-
SYSTEMATIC NAME
IUBMB Comments
deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed)
Catalyses DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time. Cannot initiate a chain de novo. Requires a primer, which may be DNA or RNA. See also EC 2.7.7.49 RNA-directed DNA polymerase.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
3'–5'-exonuclease
O29753
-
ABO4/POL2a/TIL1
-
-
Afu polymerase
O29753
-
B-family replicative DNA polymerase
-
-
beta type DNA polymerase
-
-
Bst DNA polymerase
-
-
Bst DNA polymerase
Geobacillus stearothermophilus Donc
-
-
-
CpDNApolI
Chlamydia pneumoniae AR39
-
-
-
Dbh DNA polymerase
-, P96022
-
Dbh polymerase
-
-
Dbh polymerase
P96022
-
ddNTP-sensitive DNA polymerase
-
-
deoxynucleate polymerase
-
-
-
-
deoxyribonucleate nucleotidyltransferase
-
-
-
-
deoxyribonucleic acid duplicase
-
-
-
-
deoxyribonucleic acid polymerase
-
-
-
-
deoxyribonucleic duplicase
-
-
-
-
deoxyribonucleic polymerase
-
-
-
-
deoxyribonucleic polymerase I
-
-
-
-
DinB DNA polymerase
-
-
DinB homologue
-
-
DNA deoxynucleotidyltransferase
B6E9X1
-
DNA deoxynucleotidyltransferase
Geobacillus kaue NB
B6E9X1
-
-
DNA duplicase
-
-
-
-
DNA nucleotidyltransferase
-
-
-
-
DNA nucleotidyltransferase (DNA-directed)
-
-
-
-
DNA pol
-
-
DNA pol B1
Sulfolobus solfataricus P1, Sulfolobus solfataricus P2
-
-
-
DNA Pol lambda
-
-
DNA pol NI
P13382
-
DNA pol NI
Saccharomyces cerevisiae BY4742
P13382
-
-
DNA pol Y1
Sulfolobus solfataricus P1, Sulfolobus solfataricus P2
-
-
-
DNA polmerase beta
-
-
-
-
DNA polymerase
-
-
-
-
DNA polymerase
-
-
DNA polymerase
-
-
DNA polymerase
-
-
DNA polymerase
-
-
DNA polymerase
-
-
DNA polymerase
-
-
DNA polymerase
-
-
DNA polymerase
P26811, P95979, Q07635
-
DNA polymerase
Q97W02
-
DNA polymerase
P26811, P95979, Q07635
-
-
DNA polymerase
Q97W02
;
-
DNA polymerase
-
-
DNA polymerase
C7AIP4
-
DNA polymerase
A0SXL5
-
DNA polymerase
-
-
DNA polymerase
-
-
DNA polymerase 1
O50607
-
DNA polymerase 1
Sulfurisphaera ohwakuensis TA-1T
O50607
-
-
DNA polymerase 2
-
-
DNA polymerase 4
Q97W02
-
DNA polymerase alpha
-
-
-
-
DNA polymerase alpha
-
-
DNA polymerase alpha
-
-
DNA polymerase alpha
-
-
DNA polymerase B
-
-
DNA polymerase B1
P26811
-
DNA polymerase B1
Sulfolobus solfataricus MT4
P26811
-
-
DNA polymerase B1
-
;
-
DNA polymerase B2
Q9P9N2
-
DNA polymerase B2
Sulfurisphaera ohwakuensis TA-1T
Q9P9N2
-
-
DNA polymerase B3
Q9P9N1
-
DNA polymerase B3
Sulfurisphaera ohwakuensis TA-1T
Q9P9N1
-
-
DNA polymerase beta
-
-
DNA polymerase beta
Q6DRD3
-
DNA polymerase beta
-
-
DNA polymerase beta
-
-
DNA polymerase D
-
-
DNA polymerase D
-
-
DNA polymerase Dbh
Q4JB80
-
DNA polymerase delta
A0MA44
-
DNA polymerase delta
-
-
DNA polymerase delta
-
-
DNA polymerase delta
-
-
DNA polymerase Dpo4
-
-
DNA polymerase Dpo4
-, Q97W02
-
-
DNA polymerase epsilon
-
-
DNA polymerase epsilon
-
-
DNA polymerase epsilon
-
-
DNA polymerase eta
-
-
DNA polymerase eta
-
-
DNA polymerase eta
Q9Y253
-
DNA polymerase eta
-
-
DNA polymerase eta
-
-
DNA polymerase gamma
-
-
-
-
DNA polymerase gamma
-
-
DNA polymerase I
-
-
-
-
DNA polymerase I
-
-
DNA polymerase I
Chlamydia pneumoniae AR39
-
-
-
DNA polymerase I
-
-
DNA polymerase I
-
Klenow fragment
DNA polymerase I
-
-
DNA polymerase I
B6E9X1
-
DNA polymerase I
Geobacillus kaue NB
B6E9X1
-
-
DNA polymerase I
-
-
DNA polymerase I
P0CL76
-
DNA polymerase I
-
-
DNA polymerase I
O59610
-
DNA polymerase I
-
-
DNA polymerase II
-
-
-
-
DNA polymerase II
Q9V2F3 and Q9V2F4
-
DNA polymerase III
-
-
-
-
DNA polymerase III
-
-
DNA polymerase III
-
-
DNA polymerase III
P95979
-
DNA polymerase III
P95979
-
-
DNA polymerase III
-
-
DNA polymerase III epsilon subunit
-
3'-to-5' proofreading exonuclease of the holoenzyme
DNA polymerase III epsilon subunit
Escherichia coli JH39
-
3'-to-5' proofreading exonuclease of the holoenzyme
-
DNA polymerase iota
-
member of the Y-family of specialised polymerases that displays a 5'-deoxyribose phosphate lyase activity
DNA polymerase iota
-
-
DNA polymerase IV
-
-
DNA polymerase IV
A0QR77
-
DNA polymerase IV
-
-
DNA polymerase IV
-
-
DNA polymerase IV
-
-
DNA polymerase IV
P96022
-
DNA polymerase IV
-, P96022, Q97W02
-
-
DNA polymerase kappa
-
-
DNA polymerase kappa
-
-
DNA polymerase lambda
-
-
DNA polymerase mu
-
-
DNA polymerase mu
-
-
DNA polymerase ny
-
-
DNA polymerase pyrococcus kodakaraensis
-
-
DNA polymerase theta
-
-
DNA polymerase X
-
-
DNA polymerase X
-
-
-
DNA polymerase X
-
-
DNA polymerase zeta
-
-
DNA polymerases B
-
-
DNA polymerases D
-
-
DNA primase-polymerase
Q54324
bifunctional enzyme
DNA replicase
-
-
-
-
DNA replicase
-
-
DNA replication polymerase
-
-
DNA-dependent DNA polymerase
-
-
-
-
DNA-dependent DNA polymerase
-
-
DNA-dependent DNA polymerase
Chlamydia pneumoniae AR39
-
-
-
DNA-dependent DNA polymerase
-
-
DP1Pho
O57863 and O57861
small subunit
DP2Pho
O57863 and O57861
large subunit
Dpo1
P26811
;
-
Dpo2
Q07635
-
-
Dpo3
P95979
;
-
Dpo4
-, P96022, Q97W02
-
-
Dpo4-like enzyme
Q2FA65
-
Dpo4-like enzyme
Q2FA64
-
Dpo4-like enzyme
Q2FA62
-
Dpo4-like enzyme
Q2FA66
-
Dpo4-like enzyme
Q2FA63
-
duplicase
-
-
-
-
error-prone DNA polymerase
P96022
-
error-prone DNA polymerase X
-
-
family B-type DNA polymerase
-
-
family B-type DNA polymerase
Q29Y55
-
HSV 1 POL
-
-
K4 polymerase
E2RWL8
-
K4 polymerase
Thermotoga petrophila K4
E2RWL8
-
-
K4pol
Thermotoga petrophila K4
-
-
-
K4PolI
E2RWL8
-
K4PolI
Thermotoga petrophila K4
E2RWL8
-
-
kDNA replication protein
-
-
KF(exo-)
-
3'->5'-exonuclease-deficient Klenow fragment of DNA polymerase I
Klenow fragment
-
-
-
-
Klenow fragment
-
-
Klenow fragment
-
of DNA polymerase I
Klenow fragment
-
the Klenow fragment of Escherichia coli DNA polymerase I houses catalytic centers for both polymerase and 3'-5' exonuclease activities
Klenow fragment
-
-
Klenow-like DNA polymerase I
-
-
lesion-bypass DNA polymerase
-
-
M1 DNA polymerase
K4Q1U9
-
M1 DNA polymerase
Thermus thermophilus M1
K4Q1U9
-
-
M1pol
K4Q1U9
-
M1pol
Thermus thermophilus M1
K4Q1U9
-
-
MacDinB-1
Q8TIW3
-
MA_4027
Q8TIW3
locus name
Miranda pol beta protein
-
-
mitochondrial DNA polymerase
-
-
mitochondrial DNA polymerase
-
-
mtDNA polymerase NI
P13382
-
mtDNA polymerase NI
Saccharomyces cerevisiae BY4742
P13382
-
-
mtDNA replicase
-
-
Neq DNA polymerase
-
-
non-replicative DNA polymerase III
-
-
nucleotidyltransferase, deoxyribonucleate
-
-
-
-
OsPOLP1
-
-
Pfu
-
a family B DNA polymerase
PH0121
O57863 and O57861
gene name, large subunit
PH0123
O57863 and O57861
gene name, small subunit
phi29 DNA polymerase
-
phi29 DNApol is included in the B family (eukaryotic-type) of DNA-dependent DNA polymerases
phi29 DNApol
-
-
pol alpha
-
isozyme
pol alpha
-
-
pol alpha
-
isozyme
pol alpha
-
isozyme
pol beta
-
-
pol beta
Q6DRD3
-
pol beta
-
isoform
pol beta
-
isozyme
pol beta
-
has both polymerase and deoxyribose phosphate lyase activities
pol beta
-
-
pol delta
-
isozyme
pol delta
-
isozyme
POl epsilon
-
isozyme
POl epsilon
-
isozyme
Pol eta
-
isoform
Pol eta
Q9Y253
-
Pol eta
-
-
Pol gamma
-
-
-
-
Pol gamma
-
isozyme
Pol I
-
isozyme
Pol I
-
isozyme
Pol I
-
-
Pol I
P0CL76
-
Pol I
C7AIP4
-
Pol II
-
isozyme
Pol II
Q9V2F3 and Q9V2F4
-
Pol II
P81409
-
pol III
Escherichia coli JH39
-
-
-
pol iota
-
-
pol iota
-
isoform
pol iota
-
-
pol kappa
-
-
pol kappa
-
isoform
pol kappa
-
isozyme
pol kappaDELTAC
-
truncated form of isozyme pol kappa
Pol lambda
-
isozyme
Pol lambda
-
X family DNA polymerase
Pol lambda
-
-
Pol mu
-
-
Pol mu
-
isozyme
pol NI
Saccharomyces cerevisiae BY4742
P13382
-
-
Pol ny
-
-
Pol theta
-
isozyme
Pol theta
-
-
pol Vent (exo-)
-
-
Pol zeta
-
isozyme
Pol-beta
-
-
POL1
P13382
gene name
POL1
Saccharomyces cerevisiae BY4742
P13382
gene name
-
POL2a
-
catalytic subunit of DNA polymerase epsilon
Pol3
-
subunit of DNA polymerase delta
Pol31
-
subunit of DNA polymerase delta
PolB
-
replicative DNA polymerase
polD
-
replicative DNA polymerase
POLD4
-
smallest subunit of DNA polymerase delta
POLdelta1
A0MA44
catalytic subunit of the DNA polymerase delta
PolDPho
O57863 and O57861
-
POLG
-
-
PolH
-
product of the xeroderma pigmentosum variant (XPV) gene
PolH
Q9Y253
-
PolH
-
-
polI
B6E9X1
-
polI
Geobacillus kaue NB
B6E9X1
-
-
Polkappa
-
-
poly iota
-
-
polymerase alpha catalytic subunit A
P13382
-
polymerase alpha catalytic subunit A
Saccharomyces cerevisiae BY4742
P13382
-
-
polymerase III
-
-
Pwo DNA polymerase
P61876
-
Pwo DNA polymerase
Pyrococcus woesei DSM 3773
P61876
-
-
R2 polymerase
-
-
R2 reverse transcriptase
-
capable of efficiently utilizing single-stranded DNA as a template
Rec1
-
-
repair polymerase
-
-
replicative DNA polymerase
-
-
reverse transcriptase
-
-
Saci_0554
Q4JB80
-
Saci_0554
Q4JB80
locus name
Saci_0554
Q4JB80
; locus name
-
sequenase
-
-
-
-
Sso DNA pol B1
-
-
Sso DNA polymerase Y1
-
-
Sso DNApol
P26811
-
Sso DNApol
Sulfolobus solfataricus MT4
P26811
-
-
SSO0552
P26811
locus name
SSO0552
P26811
locus name
-
SSO2448
Q97W02
gene name
SSO2448
Q97W02
gene name; locus name; locus name; locus name; locus name; locus name; locus name
-
SsoDpo1
P26811
-
SsoDpo1
P26811
-
-
Szi DNA polymerase
Q29Y55
-
T4 DNA polymerase
-
-
T7 DNA polymerase
-
-
Taq DNA polymerase
-
-
-
-
Taq DNA polymerase
-
-
Taq Pol I
-
-
-
-
Taq polymerase
-
-
Tca DNA polymerase
-
-
-
-
translesion DNA polymerase
-
-
translesion DNA polymerase
-
-
-
translesion DNA synthesis polymerase
-
-
translesion polymerase Dpo4
-
-
translesion polymerase Dpo4
-
-
-
UL30/UL42
-
-
UmuD'2C
-
free DNA polymerase V
UmuD'2C-RecA-ATP
-
active form of DNA polymerase V
X family DANN polymerase
-
-
Y-family DNA polymerase eta
-
-
additional information
-
the enzyme belongs to the DNA polymerase Y family
additional information
-
the enzyme belongs to the DNA polymerase Y-family
additional information
-
the enzyme belongs to the Y-family polymerases
additional information
-
the enzyme belongs to the Y-family polymerases and is a member of the RAD30A subfamily
additional information
-
the enzyme is a Y-family DNA polymerase
additional information
Q97W02
the enzyme belongs to the Y-family polymerases
CAS REGISTRY NUMBER
COMMENTARY
9012-90-2
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
-
A0MA44
UniProt
Manually annotated by BRENDA team
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
Manually annotated by BRENDA team
calf
-
-
Manually annotated by BRENDA team
polymerase alpha
-
-
Manually annotated by BRENDA team
polymerase alpha; polymerase delta; polymerase epsilon
-
-
Manually annotated by BRENDA team
strain AR39
-
-
Manually annotated by BRENDA team
Chlamydia pneumoniae AR39
strain AR39
-
-
Manually annotated by BRENDA team
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
Manually annotated by BRENDA team
enzyme overexpressed in Escherichia coli
-
-
Manually annotated by BRENDA team
Escherichia coli infected with
-
-
Manually annotated by BRENDA team
mutator and antimutator strains
-
-
Manually annotated by BRENDA team
Escherichia coli infected with
-
-
Manually annotated by BRENDA team
Escherichia coli infected with
-
-
Manually annotated by BRENDA team
DNA polymerase V
-
-
Manually annotated by BRENDA team
K12; pol III
-
-
Manually annotated by BRENDA team
pol I; pol II; pol III
-
-
Manually annotated by BRENDA team
pol III
-
-
Manually annotated by BRENDA team
strain JH39
-
-
Manually annotated by BRENDA team
strains JM109, TOP10, TOP10F, and DH5alpha
-
-
Manually annotated by BRENDA team
Escherichia coli JH39
strain JH39
-
-
Manually annotated by BRENDA team
Escherichia coli K12
K12
-
-
Manually annotated by BRENDA team
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
Manually annotated by BRENDA team
isolated from hot springs in Gönen and Hisaralan, Turkey, gene polA
UniProt
Manually annotated by BRENDA team
Geobacillus kaue NB
isolated from hot springs in Gönen and Hisaralan, Turkey, gene polA
UniProt
Manually annotated by BRENDA team
Geobacillus stearothermophilus Donc
ATCC12980D-5
-
-
Manually annotated by BRENDA team
Herpes simplex virus
-
-
-
Manually annotated by BRENDA team
Herpes simplex virus
HeLa cells infected with
-
-
Manually annotated by BRENDA team
Herpes simplex virus
type I DNA polymerase
-
-
Manually annotated by BRENDA team
-
P06746
UniProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
Manually annotated by BRENDA team
gene POLG
-
-
Manually annotated by BRENDA team
gene POLN
-
-
Manually annotated by BRENDA team
synonym: Micrococcus lysodeikticus
-
-
Manually annotated by BRENDA team
river loach
-
-
Manually annotated by BRENDA team
mouse strains defective in specialized DNA polymerases are used for studying their function
-
-
Manually annotated by BRENDA team
two family Y DNA polymerases Rv1537 and Rv3056
UniProt
Manually annotated by BRENDA team
cherry salmon
-
-
Manually annotated by BRENDA team
Philothamnus punctatus
green shrub snake
-
-
Manually annotated by BRENDA team
strain PAO1, gene dinB
-
-
Manually annotated by BRENDA team
identical to strain KT2440, gene dinB
-
-
Manually annotated by BRENDA team
small subunit polB: Q9V2F3, large subunit polC: Q9V2F4
Q9V2F3 and Q9V2F4
SwissProt
Manually annotated by BRENDA team
Pyrococcus abyssi Orsay
-
-
-
Manually annotated by BRENDA team
DNA polymerase II large subunit
SwissProt
Manually annotated by BRENDA team
P81412: DP1, small subunit. P81409: DP2, large subunit
P81412 and P81409
SwissProt
Manually annotated by BRENDA team
O57863: small subunit, O57861: large subunit
O57863 and O57861
-
Manually annotated by BRENDA team
Pyrococcus horikoshii OT-3
-
SwissProt
Manually annotated by BRENDA team
Pyrococcus woesei DSM 3773
-
UniProt
Manually annotated by BRENDA team
common frog
-
-
Manually annotated by BRENDA team
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta. Enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent polymerase, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
Manually annotated by BRENDA team
Ruellia sp.
petunia, Mitchell
-
-
Manually annotated by BRENDA team
DNA polymerase delta overproduced in Escherichia coli
-
-
Manually annotated by BRENDA team
gene MIP1 encoding DNA pol gamma, and gene POL1 encoding DNA polymerase alpha catalytic subunit A
UniProt
Manually annotated by BRENDA team
Saccharomyces cerevisiae BY4742
gene MIP1 encoding DNA pol gamma, and gene POL1 encoding DNA polymerase alpha catalytic subunit A
UniProt
Manually annotated by BRENDA team
Sulfolobus solfataricus MT4
-
SwissProt
Manually annotated by BRENDA team
Sulfolobus solfataricus MT4
strain MT4
-
-
Manually annotated by BRENDA team
Sulfolobus solfataricus P1
-
-
-
Manually annotated by BRENDA team
Sulfurisphaera ohwakuensis TA-1T
-
SwissPro
Manually annotated by BRENDA team
Sulfurisphaera ohwakuensis TA-1T
-
UniProt
Manually annotated by BRENDA team
Testudines agrionemys
Horsfield’s terrapin
-
-
Manually annotated by BRENDA team
Thermococcus celer DSM 2476
-
SwissProt
Manually annotated by BRENDA team
strain KOD1
SwissProt
Manually annotated by BRENDA team
strain DSM 15227
UniProt
Manually annotated by BRENDA team
Thermococcus pacificus DSM 10394
-
-
-
Manually annotated by BRENDA team
Thermococcus peptonophilus DSM 10343
-
-
-
Manually annotated by BRENDA team
strain ATCC BAA-394, DSM 14981
UniProt
Manually annotated by BRENDA team
Thermococcus waiotapuensis DSM 12768
-
UniProt
Manually annotated by BRENDA team
Thermotoga petrophila K4
-
-
-
Manually annotated by BRENDA team
Thermotoga petrophila K4
-
UniProt
Manually annotated by BRENDA team
high-level expression
-
-
Manually annotated by BRENDA team
strain INValphaF' of Escherichia coli transformed with the pTaq plasmid containing the Taq gene expressed under control of the tac promoter
-
-
Manually annotated by BRENDA team
strain YT1
-
-
Manually annotated by BRENDA team
Thermus aquaticus INValphaF
strain INValphaF' of Escherichia coli transformed with the pTaq plasmid containing the Taq gene expressed under control of the tac promoter
-
-
Manually annotated by BRENDA team
Thermus aquaticus YT1
strain YT1
-
-
Manually annotated by BRENDA team
strain GH24
-
-
Manually annotated by BRENDA team
Thermus caldophilus GH24
strain GH24
-
-
Manually annotated by BRENDA team
strain Z05
-
-
Manually annotated by BRENDA team
Thermus sp. Z05
strain Z05
-
-
Manually annotated by BRENDA team
isolated from a hot spring at Kagoshima, Japan
UniProt
Manually annotated by BRENDA team
strain HB8
-
-
Manually annotated by BRENDA team
Thermus thermophilus B35
-
-
-
Manually annotated by BRENDA team
Thermus thermophilus M1
isolated from a hot spring at Kagoshima, Japan
UniProt
Manually annotated by BRENDA team
DNA polymerase A, a gamma-like DNA polymerase
-
-
Manually annotated by BRENDA team
crested newt
-
-
Manually annotated by BRENDA team
group C adenovirus 5 and group B adenovirus 35 ATCC prototype strains
-
-
Manually annotated by BRENDA team
temerature-sensitive adenoviruses Ad5ts36 and Ad5ts146
-
-
Manually annotated by BRENDA team
HeLa cells infected with
-
-
Manually annotated by BRENDA team
5 cellular DNA template-dependent DNA polymerases are encoded by distinct genes: polymerase alpha, i.e. pol I, polymerase beta, only in vertebrates, polymerase gamma, required for mitochondrial DNA replication but encoded in the nucleus, polymerase delta, enzymes in mammalian cell contain tightly associated 3'-5'-exonuclease activities, 2 forms: proliferating cell nuclear antigen-dependent and a proliferating cell nuclear antigen-independent, also called DNA polymerase delta II, now named DNA polymerase epsilon, polymerase epsilon, tightly associated 3'-5'-exonuclease activity, formerly named DNA polymerase delta II
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
evolution
-
human DNA polymerase lambda is a member of the DNA polymerase X family
evolution
B6E9X1
DNA polymerase I belongs to the DNA polymerase family A, all the functionally important regions in the polymerase active site of Geobacillus kaue polI are conserved, phylogenetic analysis, evolutionary relationship of diverse Geobacillus species, overview
evolution
-
the enzyme belongs to the DNA polymerase family A
evolution
K4Q1U9
the enzyme belongs to the DNA polymerase family A
evolution
-
the enzyme belongs to the DNA polymerase family B
evolution
E2RWL8, -
K4PolI is a family A DNA polymerase, phylogenetic tree
evolution
-
the enzyme belongs to the DNA polymerase Y-family, phylogenetic analysis
evolution
Q6DRD3
compared to mammalian pol betas, the Danio rerio enzyme contains a P63D amino acid substitution. This substitution lies in a hairpin sequence within an 8-kDa domain, likely to be important in DNA binding
evolution
-
the catalytic subunits Pol1, Pol2 and Pol3 or isozymes pol alpha, pol epsilon, and pol delta are phylogenetically related, and belong to the class B DNA polymerases. The B subunits are all essential and share a phosphodiesterase-like and oligosaccharide binding domain. Eukaryotes contain a fourth class B DNA polymerase, Pol zeta, which is the major enzyme responsible for mutagenesis in response to DNA damage
evolution
-
DNA polymerase ny is a conserved family A DNA polymerase
evolution
Geobacillus kaue NB
-
DNA polymerase I belongs to the DNA polymerase family A, all the functionally important regions in the polymerase active site of Geobacillus kaue polI are conserved, phylogenetic analysis, evolutionary relationship of diverse Geobacillus species, overview
-
evolution
Thermotoga petrophila K4
-
K4PolI is a family A DNA polymerase, phylogenetic tree; the enzyme belongs to the DNA polymerase family A
-
evolution
Thermus thermophilus M1
-
the enzyme belongs to the DNA polymerase family A
-
malfunction
-
class switch recombination is normal in mice deficient for pols theta and eta
malfunction
-
cell lines downregulating poliota exhibit hypersensitivity to DNA damage induced by hydrogen peroxide or menadione but not to ethylmethane sulfonate, UVC or UVA, extracts from cells downregulating poliota show reduced base excision repair activity
malfunction
-
Pol beta-deficient spermatocytes are defective in meiotic chromosome synapsis and undergo apoptosis during prophase I, Pol beta-deficient seminferous tubules have few germ cells, Pol beta-deficient spermatocytes do not progress through meiosis, Pol beta-deficient mice are fertile
malfunction
-
the depletion of Pol eta or Pol kappa elevates DNA damage associated with non-plasmid pULCtrl formed at the human c-MYC promoter
malfunction
-
depletion of Pol eta from undamaged human cells affects cell cycle progression (G2/M and proliferative defects) and the rate of cell proliferation and results in increased spontaneous chromosome breaks and common fragile site expression with the activation of ATM-mediated DNA damage checkpoint signaling
malfunction
-
mutations in or altered expression of Pol gamma coupled with oxidative damage to mitochondrial DNA may be involved in Parkinson disease and Alzheimer disease
malfunction
-
abo4 mutants show early flowering and reduced expression of flowering locus C and increased expression of flowering locus T with changing histone H3 modifications
malfunction
Q9Y253
DNA polymerase eta-deficient cells show strong activation of downstream DNA damage responses including ataxia-telangiectasia mutated and Rad3-related protein signaling and accumulate strand breaks as result of replication fork collapse
malfunction
-
abolished catalytic activity of mutant enzyme in the presence of two metal ions, Mg2+ and Mn2+, overview
malfunction
-
silencing of each polymerase, of mitochondrial DNA polymerases IB, IC, and ID, is lethal, resulting in kDNA loss, persistence of prereplication DNA monomers, and collapse of the mitochondrial membrane potential. Kinetics of kDNA loss during DNA polymerase silencing, overview
malfunction
-
enhanced fidelity of base selection by a polymerase active site can result in impaired lesion bypass and delayed replication fork progression
malfunction
-
more than 150 different point mutations in POLG, the gene encoding the human mitochondrial DNA polymerase gamma, cause a broad spectrum of childhood and adult onset diseases. Disorders associated with POLG mutations include: 1. myocerebrohepatopathy spectrum disorder 2. Alpers syndrome 3. ataxia neuropathy spectrum disorder 4. myoclonus epilepsy myopathy sensory ataxia 5. autosomal recessive progressive external ophthalmoplegia 6. autosomal dominant progressive external ophthalmoplegia. Also, alteration of the (CAG)10 repeat in the 2nd exon of POLG is implicated in male infertility
malfunction
-
weakened Fe-S cluster binding efficiency of CysA mutant proteins, caused by a lack of polymerase complex stabilization by Pol31, even though this subunit interacts primarily with the CysB region, overexpression of Pol31 results in a 4 to 8fold higher 55Fe binding to both wild-type and CysA mutant Pol3-CTDs. Depletion of the cysteine desulfurase Nfs1 by growth on glucose of the galactose-regulatable strain Gal-NFS1 almost completely abolishes Fe binding to the polymerases, and depletion of the CIA machinery components Nbp35 and Nar1 in regulatable yeast strains abrogates Fe-S cluster formation on the polymerases
metabolism
-
high levels of DNA polymerases of the X family might cause genomic instability
physiological function
-
Pol beta is a DNA polymerase specific to base excision repair that also possesses lyase activity capable of severing the phosphoester bond on the 3' carbon of the abasic ribose
physiological function
-
the interaction between DNA polymerase eta and MLH1 is involved in DNA replication, MutSalpha can interact with Poleta through MutLalpha
physiological function
-
POLD4 is required for the in vitro pol delta activity, and functions in cell proliferation and maintenance of genomic stability of human cells
physiological function
-
DNA polymerase iota is also capable of error-free nucleotide incorporation opposite the bulky major groove adduct N-(deoxyguanosin-8-yl)-2-acetyl-aminofluorene
physiological function
-
pol theta has no major involvement in somatic hypermutation
physiological function
-
Poleta may be involved in induction of various types of mutations through the erroneous and efficient incorporation of oxidized dNTPs into DNA
physiological function
-
human poliota protects cells from oxidative damage, poliota binds to chromatin after oxidative damage
physiological function
-
poliota uniquely replicates DNA with a constrained active site, creating shorter C1'-C1' strand distances, with the finger domain projecting the template base out towards the solvent-accessible major groove and stabilizing a mismatched G base through H-bonding
physiological function
-
DNA polymerase epsilon and the histone H3 acetylase, Rtt109, are required for the formation/maintenance of this histone-depleted region and for the recruitment of the transcription factors to the tRNA
physiological function
-
DNA polymerase beta is critical for mouse meiotic synapsis, Pol beta is required at a very early step in the processing of meiotic double-strand breaks, at or before the removal of SPO11 from double-strand break ends and the generation of the 3' single-stranded tails necessary for subsequent strand exchange
physiological function
-
Trypanosoma cruzi overexpressing Poleta is more resistant to treatment with hydrogen peroxide compared to nontransfected cells, does not increase its resistance to UV-light (with or without caffeine) or cisplatin, and is also unable to restore growth after treatment with zeocin or gamma irradiation
physiological function
-
DNA polymerase eta is a limiting factor for A:T mutations in immunglobulin genes and contributes to antibody affinity maturation in germinal center B cells
physiological function
-
the presence of 5'->3' exonuclease activity in DNA polymerase can replace mismatched base pairs with the correct nucleotide, DNA polymerase possesses 3'->5' exonuclease activity
physiological function
-
phi29 DNA polymerase is fully responsible for viral DNA replication
physiological function
-
polymerase alpha (p70-p180 or p49-p58-p70-p180 complex) extends herpes primase-synthesized RNA primers much more efficiently than herpes polymerase
physiological function
-
DNA polymerase epsilon with 3'-5' proofreading exonuclease activity bypasses only the model abasic site during processive synthesis and cannot reinitiate DNA synthesis
physiological function
-
involvement of deinococcal polymerase X in DNA-damage tolerance, possibly by contributing to DNA double-strand break repair and base excision repair
physiological function
-
both Pol eta and Pol kappa prevent genomic instability occurring at natural DNA sequences capable of forming unusual secondary structures in human cells
physiological function
-
human DNA polymerase eta modulates susceptibility to skin cancer by promoting translesion DNA synthesis past sunlight-induced cyclobutane pyrimidine dimers
physiological function
-
DNA polymerases have abortive DNA synthesis upon encountering apurinic/apyrimidinic sites. Under running start conditions, polB can incorporate in front of the damage and even replicate to the full-length oligonucleotides containing a specific apurinic/apyrimidinic site, but only when present at a molar excess. Conversely, bypassing activity of polD is strictly inhibited
physiological function
-
Polkappa efficiently bypasses 8-oxoguanine lesions, Polkappa increases Trypanosoma cruzi resistance to high doses of gamma irradiation and zeocin and can catalyse DNA synthesis within recombination intermediates
physiological function
-
Pol alpha catalyses initiation of chromosomal DNA replication at origins and at Okazaki fragments on the lagging strand, Pol beta participates in base-excision repair, Pol gamma catalyses mitochondrial DNA synthetic processes, Pol delta participates in lagging-strand synthesis, and Pol epsilon has a role in the synthesis of the leading strand of chromosomal DNA, Pol eta functions in bypass UV lesions,Pol iota, Pol kappa, and Pol zeta function in bypass synthesis, Pol lambda functions in base excision repair, Pol mu functions in non-homologous end joining, Pol theta functions in DNA repair, and DNA polymerase Rec1 incorporates dC opposite abasic sites. Pol beta can be classified as a tumour suppressor
physiological function
-
ABO4/POL2a/TIL1 is involved in DNA repair
physiological function
-
DNA polymerase eta confers UV resistance by catalyzing translesion synthesis past UV photoproducts
physiological function
Q9Y253
DNA polymerase eta is a key protein in translesion synthesis in human cells, it is a low-fidelity enzyme when copying undamaged DNA but can carry out error-free translesion synthesis at sites of UV-induced dithymine cyclobutane pyrimidine dimmers. DNA polymerase eta plays an important role in preventing genome instability after UV- and cisplatin-induced DNA damage
physiological function
-
Dpo3 is a potential player in the proper maintenance of the archaeal genome
physiological function
-
Dbh DNA polymerase has multiple functions affecting the stability of the Sulfolobus genome, suppressing certain mutations at particular sites and promoting other mutations elsewhere
physiological function
-
DNA Pol lambda has a backup role for DNA Pol beta in base-excision repair
physiological function
A0QR77, -
error-prone DNA polymerases belonging to the Y-family in mycobacteria do not participate in adaptive mutagenesis, in contrast to the representatives of theis faamily in other prokaryotes. Escherichia coli gene dinB homologues in mycobacteria code for nonfunctional molecules that are devoid of enzyme activity
physiological function
-
most damage-induced mutagenesis in Escherichia coli is dependent on pol V Pol V has intrinsically weak DNA polymerase activity, but its catalytic activity can be stimulated in vitro in the presence the beta-processivity clamp, RecA protein bound to ssDNA, and single-stranded-binding (SSB) protein. Processivity of pol V in the presence of accessory factors, overview
physiological function
-
the parasite's single mitochondrion contains a unique catenated mitochondrial DNA network called kinetoplast DNA (kDNA) that is composed of minicircles and maxicircles. Three kDNA replication proteins (mitochondrial DNA polymerases IB, IC, and ID) are required for bloodstream form parasite viability
physiological function
P81412 and P81409
replicative DNA polymerase
physiological function
-
the enzyme plays an essential role in DNA replication, repair, and recombination
physiological function
-
3'-> 5'-exonucleolytic proofreading activity
physiological function
-
the DNA polymerase catalyzes efficient and accurate translesion synthesis past cis-syn cyclobutane pyrimidine dimers, as well as 7,8-dihydro-8-oxoguanine and isomers of thymine glycol induced by reactive oxygen species
physiological function
-
pol gamma is absolutely essential for mitochondrial DNA replication and repair
physiological function
-
DNA polymerase beta from Trypanosoma cruzi is involved in kinetoplast DNA replication and repair of oxidative lesions, Tcpolbeta is involved in oxidative stress response, Tcpolbeta overexpression improves epimastigote survival in presence of H2O2
physiological function
-
three eukaryotic DNA replicative polymerases, Pol alpha, Pol delta, and Pol epsilon, are involved in chromosomal DNA replication. RNA/DNA primers synthesized by Pol alpha/primase are elongated by Pol delta and/or Pol epsilon. Pol delta requires the DNA sliding clamp, proliferating cell nuclear antigen, PCNA, for highly processive enzyme activity
physiological function
-
DNA polymerase III, an enzyme complex consisting of ten subunits, is responsible for genome duplication
physiological function
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis
physiological function
-
DNA damage that eludes cellular repair pathways can arrest the replication machinery and stall the cell cycle. This damage can be bypassed by the Y-family DNA polymerases
physiological function
-
involvement of deinococcal polymerase X in DNA-damage tolerance, possibly by contributing to DNA double-strand break repair and base excision repair
-
physiological function
Sulfolobus solfataricus P1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis
-
physiological function
-
Dpo3 is a potential player in the proper maintenance of the archaeal genome; the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis
-
metabolism
-
the pol gamma holoenzyme functions in conjunction with the mitochondrial DNA helicase and the mitochondrial SSB to form the minimal replication apparatus
additional information
-
nine residues, Tyr326, Leu329, Gln384, Lys387, Phe388, Met408, Asn422, Tyr438, and Phe451, are predicted to be involved in DNA/RNA distinction
additional information
-
binding and recognition of the correct dNTP, the recombinant enzyme performs several small steps like local conformational changes involving active site residues, reorganization of Mg2+-coordinating ligands, and proton transfer
additional information
-
structural, kinetic and thermodynamic basis for the extraordinary accuracy of high-fidelity DNA polymerases, overview. The changes in enzyme structure following nucleotide binding govern the fate of the bound nucleotide, and the conformational change plays an essential role in establishing enzyme selectivity, conformational coupling between enzyme structure and fidelity, modeling of the universal mechanism: while the correct substrate induces a structure to facilitate catalysis, the wrong substrate induces a structure to slow catalysis and promote substrate release. Two-step sequence for nucleotide binding, two metal ion mechanism, nucleotide binds to the enzyme as an Mg-dNTP-2 complex, overview
additional information
-
the incorporation of 8-oxo-dGTP and 3'-azido-3'-deoxythymidine 5'-triphosphate by the human mitochondrial DNA polymerase provides an exception to the general rule that diphosphate release is fast. Analysis of the burst kinetics during incorporation of 8-oxo-dGTP shows that the amplitude of the burst is dependent upon the nucleotide concentration, diphosphate release is extremely slow following the incorporation of 3'-azido-3'-deoxythymidine 5'-triphosphate. The reversible chemistry and slow release of diphosphate decreases the specificity constant for the incorporation of 3'-azido-3'-deoxythymidine 5'-triphosphate and 8-oxo-dGTP. Brownian ratchet model, overview
additional information
-
the error frequency of the enzyme does not change significantly when the temperature is raised from 22°C to 72°C
additional information
-
three aspartic acid residues D378, D380 and D531 form the catalytic carboxylate triad in pol E. Amino acid residues D378 and D531 are mainly responsible for the binding of metal chelated substrate dNTP, while D380 is solely responsible for the chemical step of phosphodiester bond formation
additional information
-
the DNA polymerase V is comprised by the UmuD'2C protein complex. Pol V activity depends on the beta-clamp and gamma-clamp loaders UmuC and UmuD'2, overview
additional information
-
replicative DNA polymerases use a complex, multistep mechanism for efficient and accurate DNA replication, kinetics and conformational dynamics by single-molecule Förster resonance energy transfer techniques, overview. The replicative polymerase can bind to DNA in at least three conformations, corresponding to an open and closed conformation of the finger domain as well as a conformation with the DNA substrate bound to the exonuclease active site of PolB1. PolB1 can transition between these conformations without dissociating from a primer-template DNA substrate. The closed conformation is promoted by a matched incoming dNTP but not by a mismatched dNTP and that mismatches at the primer-template terminus lead to an increase in the binding of the DNA to the exonuclease site
additional information
E2RWL8, -
structure modeling of K4 polymerase, overview
additional information
-
the enzyme contains domains for binding ubiquitin and proliferating cell nuclear antigen
additional information
-
the holoenzyme of pol gamma consists of a catalytic subunit and a dimeric form of its accessory subunit, interaction of the accessory subunit with the pol gamma catalytic subunit enhances the processivity bx 50fold and the DNA binding properties of the catalytic subunit. The catalytic subunit is a 140 kDa enzyme, i.e. p140, that contains an N-terminal exonuclease domain connected by a linker region to a C-terminal polymerase domain and has DNA polymerase, 3'->5' exonuclease and 5' dRP lyase activities. The accessory subunit is a 55 kDa protein, i.e. p55, required for tight DNA binding and processive DNA synthesis
additional information
-
physiological importance of the two different metal cofactors, the [4Fe-4S] cluster in CysB and Zn2+ in CysA, in the stabilization of DNA polymerase interactions with different accessory proteins essential for processive DNA synthesis at the replication fork. CysA is an important determinant for proliferating cell nuclear antigen binding
additional information
Thermotoga petrophila K4
-
nine residues, Tyr326, Leu329, Gln384, Lys387, Phe388, Met408, Asn422, Tyr438, and Phe451, are predicted to be involved in DNA/RNA distinction; structure modeling of K4 polymerase, overview
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2'-deoxyguanosine triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
2-aminopurine-2'-deoxy-D-ribose 5'-triphosphate + DNAn
diphosphate + ?
show the reaction diagram
-
-
-
-
?
2-hydroxy-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase eta incorporates 2-hydroxy-2'-deoxyadenosine 5'-triphosphate opposite template G during DNA synthesis
-
-
?
2-thio-dCTP + DNAn
?
show the reaction diagram
-
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2’-deoxyribofuranosid-5’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
5-methyl-dCTP + DNAn
?
show the reaction diagram
-
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2’-deoxyribofuranosid-5’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
7-deaza-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
show the reaction diagram
-
-
-
-
?
8-bromo-dATP + DNAn
?
show the reaction diagram
-
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2’-deoxyribofuranosid-5’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
8-hydroxy-2'-deoxyguanosine 5'-triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase eta incorporates 8-hydroxy-2'-deoxyguanosine 5'-triphosphate opposite template A and slightly opposite template C during DNA synthesis
-
-
?
8-oxo-dATP + DNAn
?
show the reaction diagram
-
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2’-deoxyribofuranosid-5’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
dATP + DNAn
?
show the reaction diagram
-
-
-
-
?
dATP + DNAn
?
show the reaction diagram
-
-
-
-
?
dATP + DNAn
?
show the reaction diagram
-
-
-
-
?
dATP + DNAn
?
show the reaction diagram
-
-
-
-
?
dATP + DNAn
?
show the reaction diagram
Q07635
-
-
-
?
dATP + DNAn
?
show the reaction diagram
-
Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
-
-
?
dATP + DNAn
?
show the reaction diagram
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
dATP + DNAn
?
show the reaction diagram
-
in addition to the correct insertion of dATP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dATP + DNAn
?
show the reaction diagram
-
-
-
-
?
dATP + DNAn
?
show the reaction diagram
Q07635
-
-
-
?
dATP + DNAn
?
show the reaction diagram
-
-
-
-
?
dATP + DNAn
?
show the reaction diagram
-
in addition to the correct insertion of dATP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dATP + DNAn
?
show the reaction diagram
-
-
-
-
?
dATP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
dATP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
dATP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
with activated calf thymus DNA
-
-
?
dATP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
with labeled 20/33-mer primer-template duplex DNA
-
-
?
dATP + DNAn
diphosphate + ?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
Q07635
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-methyl-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2’-deoxyribofuranosid-5’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
Q07635
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-methyl-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2’-deoxyribofuranosid-5’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
dCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
dCTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
with activated calf thymus DNA
-
-
?
deoxxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the phosphoryl transfer step may be rate limiting for the non-cognate nucleotide incorporation by the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P19821
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P00582
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P28340
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q9UNA4
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P46957
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P61875
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-, 3822
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-, 3822
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q97W02
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Herpes simplex virus
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Herpes simplex virus
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Herpes simplex virus
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Ruellia sp.
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P74918
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P77933
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P03156
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q97W02
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Triturus cristatus, Testudines agrionemys, Philothamnus punctatus
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
C7AIP4
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
A0SXL5
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
A0MA44
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q9Y253
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q54324
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P13382
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
E2RWL8, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
K4Q1U9
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
O57863 and O57861, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P81409
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q6DRD3
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-, Q2FA65
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA63, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA66, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA62
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA64, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q29Y55
calf thymus DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P74918
PI-TfuI recognizes a minimal sequence of 16 base pairs, PI-TfuII requires a sequence of 21 base pairs, both enzymes have endonuclease activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity and 5'--3' activity, phage T7-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, identical to RTHI nuclease
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
nicked duplex is no substrate of phage T4-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
enzyme has two exonuclease 3'--5' degradative activities: an exonuclease activity and an inorganic diphosphate-dependent degradative activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' and 5'--3' activity activity, phage T5-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
no exonuclease 5'--3' activity: pol II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
highly stereospecific, polymerase alpha, beta and epsilon incorporate only natural beta-D-dNTPs, L-dNTPs are no substrate
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
can initiate polymer synthesis de novo, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
template specificity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
template specificity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
template specificity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
template specificity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol epsilon
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
single strands, pol I, but not pol II and III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
44kDa C-terminal fragment has no exonuclease activity, reduced efficiency with Mn2+ and reduced capacity to initiate terminal protein-primed DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
preferentially removes purines opposite an abasic site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA substrate: gapped duplex or single-stranded 5'-ends smaller than 100 nucleotides, pol I, pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P03156
RNase H domain degrades RNA component of RNA-DNA hybrids
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
wild-type enzyme, but not the truncated form has exonuclease 5'--3' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
no exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
single-stranded 5'-ends greater than 100 nucleotides, pol I, but not pol II and pol III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase gamma also has proofreading activity with an RNA template, reverse transcriptase activity and incorporates ribonucleotide triphosphates into a DNA primer
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease activity associated with the replicative polymerase is contained within the epsilon subunit
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
phage T5-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time, cannot initiate a chain de novo, requires a primer which may be DNA or RNA
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol I
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
mechanical tension on DNA controls speed and direction of DNA polymerase motor
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease activity utilizes both, ssDNA and melted dsDNA templates, mismatched basepair is preferred over a correct basepair, removes an incorrect base incorporated opposite a template lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
template specificity, enzyme overexpressed in E. coli
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5', phage T4-induced DNA polymerase
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 3'--5', phage T4-induced DNA polymerase
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
specific preference for five base pairs, relatively low catalytic activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
beta-polymerase can copy a synthetic ribohomopolymer such as (A)n*(dT)12 as well as the corresponding deoxyribohomopolymer (dA)n*(dT)12 or activated DNA, alpha-polymerase utilizes the deoxyribohomopolymer (dA)n*dT12-18 eight times better than (A)n*dT12
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
template specificity of polymerase II
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
nicked duplex is no substrate of polymerase I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
nicked duplex is no substrate of pol II and III of E. coli
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
enzyme also has RNAse H/exonuclease 5'--3' activity, enzyme prefers RNA/DNA substrate over DNA/DNA duplex
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
nicked duplex, as poly d(A-T), pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
template specificity polymerase I, II and III
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
interaction of polymerases with template-primers containing chemically modified or damaged bases
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
can not initiate polymer synthesis de novo: pol II and III, exonuclease 5'--3' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 5'--3' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 5'--3' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 5'--3' activity, pol I
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease 5'--3' activity, pol I
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
incorporates alpha-D-dNTPs and beta-D-dNTPs, L-dNTPs are no substrate
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
primed single strands
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
template specificity of DNA polymerase epsilon
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
fidelity of DNA replication
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
natural substrate is gapped DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
physiological role of pol I
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase I plays a role in repair of chromosomal damage
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
physiological role of pol I and pol III
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
overview: functional role of mammalian DNA polymerases
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase alpha: role in DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase beta: role in DNA repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
physiological role of pol I, II and pol III
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
enzyme is active only in cells at meiotic prophase, in somatic cells it is in an inactive state
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
pol III can repair short gaps created by nuclease in duplex DNA, for efficient replication of the long, single-stranded templates pol III requires auxiliary subunits
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase III: role in replication of chromosomal DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase II: role in DNA repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase III is necessary for DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
role in DNA gap repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease activity contributes to the avoidance of alkylation mutations
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
phage T4 DNA polymerase is essential for initiation and maintenance of viral DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase V is involved in translesion synthesis and mutagenesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Pol lambda plays a role in the short-patch base excision repair rather than contributes to the long-patch base excision repair pathway
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
role in non-homologous end joining of double strand breaks, perhaps including those with damaged ends, possible role for pol IV in base excision repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
beta sliding clamp plays an essential role in pol V-dependent translesion DNA synthesis in vivo
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase lambda possesses the ability to synthesise in vitro short fragments of DNA in the absence of a primer-template or even a primer or a template. Amino acid Phe506 of poly lambda is essential for the de novo synthesis, DNA polymerase mu possesses the ability to synthesize in vitro short fragments of DNA in the absence of a primer-template or even a primer or a template. Amino acid Phe506 of poly lambda is essential for the de novo synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase V is involved in translesion synthesis and mutagenesis. Two factors are essential for efficient Pol V-mediated lesion bypass: 1. a DNA substrate onto which the beta-clamp is stably loaded and 2. an extended single-stranded RecA/ATP filament assembled downstream from the lesion site. For efficient bypass, Pol V needs to interact simultaneously with the beta-clamp and the 3' tip of the RecA filament
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
in addition to a slow and distributive DNA polymerase activity, Pol mu possesses a weak strand-displacement activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Phi29 DNA polymerase belongs to the family B DNA polymerases able to start replication by protein-priming
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Pol eta effectively bypasses N2-methylguanine, N2-ethylguanine, N2-isobutylguanine, N2-benzylguanine, and N2-CH2(2-naphthyl)guanine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Pol lambda is unable to catalyze strand displacement synthesis using nicked DNA, although this enzyme efficiently incorporates a dNMP into a one-nucleotide gap
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
preference for poly(dA)/oligo(dT)10:1 as a template primer and has high processivity for DNA synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
several dTTP analoges bearing a photoreactive 2-nitro-5-azidobenzoyl group attached at position 5 of uracil through linkers of various lengths, are substrates in the elongation reaction of the 5'-32P-labeled primer-template complex. The incorporation of the analogs into the 3' primer end did not impede further elongation of the chain in the presence of natural dNTP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme contains a double strand-dependent 3'-5' proofreading exonuclease activity, but lacks any 5'-3' exonuclease activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme has intrinsic 5'-2-deoxyribose-5-phosphate lyase activity. Pol IV has low processivity and can fill short gaps in DNA. The gap-filling activity of pol IV is not enhanced by a 5'-phosphate on the downstream primer but is stimulated by a 5'-terminal synthetic abasic site. Pol IV incorporates rNTPs into DNA with high efficiency relative to dNTPs. Pol IV is highly inaccurate, with an unusual error specificity indicating the ability to extend primer termini with limited homology
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
wild-type Pfu-Pol makes about one mistake for every 1000000 bases incorporated, wild-type variant Pfu-Pol(exo-)(D473F)is 60fold less accurate
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase iota may play a limited and error-prone role in translesion synthesis across the N2-guanine adducts (possibly medium sized adducts up to N2-benzylguanine) due to the low polymerization rates and high error rates
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
double-stranded DNA property of DNA polymerase epsilon is required for epigenetic silencing at telomeres
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
OsPOLP1 might be involved in a repair pathway similar to long-patch base excision repair. Possible role of POLPs in plastidial DNA replication and repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
a fast fluorescence transition corresponding to conformational closing, and a slow fluorescence transition matching the rate of single-nucleotide incorporation. This transition represents a conformational event after chemistry, likely subdomain reopening
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
a fast fluorescence transition corresponding to conformational closing, and a slow fluorescence transition matching the rate of single-nucleotide incorporation. This transition represents a conformational event after chemistry, likely subdomain reopening. Rotation of the Arg258 side chain is not rate-limiting in the overall kinetic pathway of Pol beta, yet is kinetically significant in subdomain reopening
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P04415
bacteriohage T4 and bacteriophage RB69 replicative DNA polymerases exhibit differing abilities to form various base pairs. Formation of Watson-Crick base pairs occurs at similar rates between the two proteins but the incoming nucleotides are bound less tightly by RB69 DNA polymerase. Incorporation of an A opposite furan by T4 DNA polymerase is more rapid than for RB69 DNA polymerase with the two proteins having similar binding constants for the incoming dATP. An A:C mismatch is formed almost equally well by both proteins, while a significant difference exists when a T:T mismatch is formed
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase mu could be involved in the repair of a DSB subset when resolution of junctions requires some gap filling
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
downstream strand and its 5'-phosphate moiety are critical to the polymerase efficiency of the enzyme. Nucleotide-gapped DNA substrates containing a 1,2-dideoxyribose-5-phosphate moiety (a 2-deoxyribose-5-phosphate mimic) moderately decrease the polymerase efficiency by 3.4fold
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
inefficient and error-prone bypass across bulky N2-guanine DNA adducts. Effectively bypasses N2-methylguanine and N2-ethylguanine, partially bypasses N2-isobutylguanine and N2-benzylguanine, and is blocked at N2-CH2(2-naphthyl)guanine, N2-CH2(9-anthracenyl)guanine, and N2-CH2(6-benzo[a]pyrenyl)guanine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
no detectable 3' exonuclease activity. CpDNApolI-dependent DNA synthesis is performed using DNA templates carrying different lesions. DNAs containing 2'-deoxyuridine (dU), 2'-deoxyinosine (dI) or 2'-deoxy-8-oxo-guanosine (8-oxo-dG) served as templates as effectively as unmodified DNAs for CpDNApolI. Furthermore, the CpDNApolI can bypass natural apurinic/apyrimidinic sites (AP sites), deoxyribose (dR), and synthetic AP site tetrahydrofuran (THF). CpDNApolI can incorporate any dNMPs opposite both of deoxyribose and tetrahydrofuran with the preference to dAMP-residue. CpDNApolI preferentially extends primer with 3'-dAMP opposite deoxyribose during DNA synthesis, however all four primers with various 3'-end nucleosides (dA, dT, dC, and dG) opposite THF can be extended by CpDNApolI. Efficiently bypassing of AP sites by CpDNApolI is hypothetically attributed to lack of 3' exonuclease activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
OsPOLP1 efficiently catalyzed strand displacement on nicked DNA with a 5'-deoxyribose phosphate
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
poly(dA)/oligo(dT)10:1. 2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate can be incorporated on both templates but only by the Y505A mutant enzyme. N-(Benzyloxycarbonyl)-4-aminobutyl triphosphate can be incorporated by DNA pol lambda either wild type or the Y505A mutant, opposite to an abasic site only. Incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymmerase lambda wild type is 22fold higher opposite an abasic site than on the intact template. DNA polymerase lambda wild type incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate 2.2fold more frequently than dCTP opposite the lesion. The DNA polymerase lambda Y505A mutant shows a 5.3fold preference for dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate incorporation opposite the lesion, poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase gamma is required for replication of mitochondrial DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
R2-RT is capable of efficiently utilizing single-stranded DNA (ssDNA) as a template. The processivity of the enzyme on ssDNA templates is higher than its processivity on RNA templates. This finding suggests that R2-RT is also capable of synthesizing the second DNA strand during retrotransposition
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Sso DNA pol B1 recognizes the presence of uracil and hypoxanthine in the template strand and stalls synthesis 3–4 bases upstream of this lesion (read-ahead function). Sso DNA pol Y1 is able to synthesize across these and other lesions on the template strand. Sso DNA pol B1 physically interacts with DNA pol Y1. The region of DNA pol B1 responsible for this interaction has been mapped in the central portion of the polypeptide chain (from the amino acid residue 482 to 617)
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
T4 DNA polymerase can remove two incorrect nucleotides under single turnover conditions, which includes presumed exonuclease-to-polymerase and polymerase-to-exonuclease active site switching steps and proofreading reactions that initiate in the polymerase active center are not intrinsically processive
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the effects of varied DNA substrate size on the synthesis of DNA by the high fidelity T7 DNA polymerase: the T7 enzyme is highly sensitive in kinetic efficiency to size changes across this analog series. The T7 enzyme shows a strong dependence on substrate size and shows a preference for smaller substrates
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the flexibility on the template side of the Dbh active site allows for a consistent location of the incoming dNTP regardless of whether or not it is correctly paired with its templating partner. Contact of the dNTP sugar with the Phe12 steric gate side chain is maintained in all circumstances with the result that Dbh shows stringent discrimination against ribonucleotides but does not use the steric gate side chain as a discriminator against nascent mispairs
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
two proton transfers in the transition state for nucleotidyl transfer
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
two proton transfers occur in the transition state for nucleotidyl-transfer reactions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P42489
use of damaged DNA and dNTP substrates by the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
wild-type DinB inserts deoxycytidine opposite N2-furfuryl-dG with 10–15fold greater catalytic proficiency than opposite undamaged dG
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
with template guanine and Watson-Crick paired dCTP as the nascent base pair. Water-mediated and substrate-assisted mechanism: the initial proton transfer to the R-phosphate of the substrate via a bridging crystal water molecule is the rate-limiting step, the nucleotidyl-transfer step is associative with a metastable pentacovalent phosphorane intermediate, and the diphosphate leaving is facilitated by a highly coordinated proton relay mechanism through mediation of water which neutralizes the evolving negative charge. The conserved carboxylates, which retain their liganding to the two Mg2+ ions during the reaction process, are found to be essential in stabilizing transition states. This water-mediated and substrate-assisted mechanism takes specific advantage of the unique structural features of this low-fidelity lesion-bypass Y-family polymerase, which has a more spacious and solvent-exposed active site than replicative and repair polymerases
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the Klenow fragment of DNA polymerase I is able to dimerize on a DNA primer/template. Dimerization is favored when the first molecule is bound in the polymerizing mode, but disfavored when it is bound in the editing mode. Self-association of the polymerase may play an important role in coordinating high-fidelity DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine, a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene. The diol epoxide (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[ a]pyrene reacts largely, but not exclusively, with the exocyclic amino group of guanine to produce the major 10S (+) trans-anti-BP-N2-dG adduct, that is bypassed by Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
mechanism of purine-purine mispair formation, substrate specificity and binding structure, the kpol/Kd dNTP values for the insertion of dATP and dGTP opposite 7-deazaadenine and 7-deazaguanine are decreased over 10fold with respect to those of the unmodified nucleotides during formation of purine-purine mispairs. In addition, the rate of incorporation of 1-deaza-dATP opposite guanine is decreased 5fold. Dpo4 holds the incoming dNTP in the normal anti conformation while allowing the template nucleotide to change conformations to allow reaction to occur. This result may be functionally relevant in the replication of damaged DNA in that the polymerase may allow the template to adopt multiple configurations, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q97W02
nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in DNA polymerase IV, 5'-slippage mechanism: the dATP can be inserted opposite the T on the 5' side of the adduct G1*, in which the unadducted G2, rather than G1*, is skipped, to produce a -1 deletion, molecular modeling and dynamics simulations, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
substrate is a 44-mer DNA template containing a site-specific cisplatin-d(GpG) adduct, Dpo4 is able to bypass a single, site-specifically placed cisplatin-d(GpG) adduct, although, the incorporation efficiency of dCTP opposite the first and second cross-linked guanine bases is decreased by 72 and 860fold, respectively, enzyme fidelity, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the nucleotidyl-transfer reaction coupled with the conformational transitions in DNA polymerases is critical for maintaining the fidelity and efficiency of DNA synthesis, correct insertion of dCTP opposite 8-oxoguanine and quantum mechanics/molecular mechanics investigation of the chemical reaction in Dpo4 reveals water-dependent pathways and requirements for active site reorganization, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine, a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene, Dpo4 bypasses 8-oxoG accurately
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase iota preferentially misincorporates nucleotides opposite thymines and halts replication at T bases
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
herpes polymerase only elongates primase-synthesized primers at least 8 nucleotides long
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
in the presence of Mg2+ or Mn2+, the POLX catalytic domain inserts dIMP, IMP and 8-oxo-dGMP opposite deoxycytosine as well as dGMP and GMP, PolX likely prefers deoxyguanine to deoxythymidine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
naturally occurring DNA structures are physiological substrates of both pol eta and pol kappa
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
phi29 DNA polymerase accomplishes sequential template-directed addition of dNMP units onto the 3'-OH group of a growing DNA chain, in addition phi29 DNApol catalyses 3'-5' exonucleolysis, that is, the release of dNMP units from the 3' end of a DNA strand
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polB and polD preferentially insert dAMP opposite an apurinic/apyrimidinic site, albeit inefficiently
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme shows deoxynucleotide transferase activity, short patch DNA synthesis activity on heteropolymeric DNA substrate, 5'-deoxyribose phosphate lyase activity and base excision repair function in vitro
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
with undamaged templating purines DNA polymerase iota normally favors Hoogsteen base pairing, DNA polymerase iota can incorporate nucleotides opposite a benzo[a]pyrene-derived adenine lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
approximately 2/3 of the errors made by the enzyme are single-base substitutions, of which 58% are C->T transition. Frameshift mutations, mostly resulting from single-base deletions, account for 19% of the total errors. An exonuclease-deficient mutant of Sso pol B1 is three times as mutagenic as the wild-type enzyme, suggesting that the intrinsic proofreading function contributed only modestly to the fidelity of the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
at optimal temperature (70-75°C) a singly primed, single-stranded recombinant phage M13 DNA is efficiently replicated in ten min using a ratio of enzyme molecule to primed-template of 0.8
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
bypass of apurinic/apyrimidinic sites lacking A or G is nearly 100% mutagenic. The majority (70–80%) of bypass events are insertion of dAMP opposite the apurinic/apyrimidinic site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
in the absence of additional cofactor the enzyme is an essentially distributive enzyme that only extends primers by 1-2 nt per binding event. At high enzyme to primer/template ratios, dissociation and rebinding of the enzyme to the primer/template is robust and can lead to the synthesis of polynucleotide chains of several hundred nucleotides in length
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
modeling and molecular dynamics simulations for 2'-deoxy-8-[(1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-yl)amino]guanosine suggest that the adduct would increase the infidelity of Dpo4 and hinder translocation by the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
products of replication of polycyclic aromatic hydrocarbon-modified DNA by the translesion DNA polymerase Dpo4 are complex
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
propenal and malondialdehyde react with DNA to form adducts, including 3-(2'-deoxy-beta-D-erythro-pentofuranosyl) pyrimido[1,2-alpha]purin-10(3H)-one (M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG. To improve the understanding of the basis for M1dG-induced mutagenesis, the mechanism of translesion DNA synthesis opposite M1dG by the model Y-family polymerase Dpo4 is studied at a molecular level using kinetic and structural approaches. The enzyme can bypass the exocyclic M1dG adduct in largely an error-prone fashion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
replication bypass studies in vitro reveal that the polymerase inserts dNTPs opposite the (6S,8R,11S)-trans-4-hydroxynonenal-1,N2-dGuo adduct in a sequence-specific manner. If the template 5'-neighbor base is dCyt, the polymerase inserts primarily dGTP. If the template 5'-neighbor base is dThy, the polymerase inserts primarily dATP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
ribonucleotide discrimination by the DinB homolog (Dbh) DNA polymerase is as stringent as in other polymerases. When making a deletion error, ribonucleotide discrimination by wild-type and F12A Dbh is the same as in normal DNA synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P95690
the activated herring sperm DNA is an optimal template and gives 3times higher activity than that obtained with poly(dA)/oligo(dT). The DNA polymerase can not use templates without primer (poly(dA) and poly(dT)), even when appropriate priming ribonucleotides (UTP or ATP, respectively) are supplied. It does not accept a polyribonucleotide template (poly(rA):oligo(dT))
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme bypasses aflatoxin B1-N7-dG in an error-free manner but conducts error-prone replication past the aflatoxin B1-formamidopyrimidine adduct, including misinsertion of dATP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P96022
the enzyme is nonprocessive and can bypass an abasic site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme shows a limited decrease in catalytic efficiency (kcat/Km) for insertion of dCTP opposite a series of N2-alkylguanine templates of increasing size from (methyl (Me) to (9-anthracenyl)-Me (Anth)). Fidelity is maintained with increasing size up to (2-naphthyl)-Me (Naph). The catalytic efficiency increases slightly going from the N2-NaphG to the N2-AnthG substrate, at the cost of fidelity. A set of oligonucleotides differing only in their N2-substitution at a single G site is used in this study with Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the pre-steady-state kinetic methods is used to determine the base substitution fidelity and mismatch extension fidelity of PolB1
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the rate-constant defining Dpo4-catalyzed incorporation of dCTP is about 6-fold slower for incorporation opposite O6-MeG relative to G. The basis for the decreased rate is revealed by the crystal structure to be formation of a wobble base pairing between O6-MeG and C
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
translesion synthesis of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine lesion by the enzyme in 5'-TXG-3' and 5'-CXG-3' local sequence contexts is examined and compared to 1,N2-etheno-2'-deoxyguanosine lesions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
gamma-phosphates of the incoming dNTP, contributing to charge neutralization and alignment of the alpha-phosphate for reaction
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
PabPolD might play an important role in DNA replication likely together with PabpolB, suggesting that archaea require two DNA polymerases at the replication fork
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P81412 and P81409
the enzyme has a template-primer preference which is characteristic of a replicative DNA polymerase
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme plays an essential role in DNA replication, repair, and recombination
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
assays of Pol delta complexes on poly(dA)/oligo(dT) template/primers
DNA products synthesized by Pol delta and its subassemblies on primed M13 DNA, overview
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
both DNA polymerase D and DNA polymerases B are DNA polymerizing enzymes exclusively. DNA polymerase D has a preference for a primed template. DNA polymerase D is a primer-directed DNA polymerase independently of the primer composition whereas DNA polymerase B behaves as an exclusively DNA primer-directed DNA polymerase. Proliferating cell nuclear antigen is required for DNA polymerases D to perform efficient DNA synthesis but not DNA polymerases B. DNA polymerase D, but not DNA polymerase B, contains strand displacement activity. In the presence of PabPCNA, however, both DNA polymerases D and B show strand displacement activity. Direct interaction between DNA polymerase D and proliferating cell nuclear antigen is DNA-dependent
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
K4Q1U9
DNA-dependent DNA polymerase activity to incorporate dNTP into gapped M13mp2 DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
measurement of the incorporation of methyl-TTP into acid insoluble material. The single-stranded DNA substrate is more sensitive than the double stranded substrate. The polymerase and exonuclease domains in the family B DNA polymerases are functionally interdependent
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
PCR performance and fidelity parameters are highest in the presence of 20 mM Tris-HCl, pH 9.0, 1.5 mM MgSO4, 25 mM KCl, 10 mM (NH4)2SO4 and 40 microM of each dNTP. Under these conditions, the error rate is 0.66.10(-6) mutations/nucleotide/duplication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P81412 and P81409
replicative DNA polymerase
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
reversibility of the polymerase reaction at the level of the template with diphosphate as leaving group, not with the alternative leaving groups, overview
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
standard substrate PTJ1 and substrate PTJ2
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the carboxyl-terminal (1255–1332) of the large subunit (DP2Pho) and two regions, the 201–260 and 599–622, of the small subunit (DP1Pho) are critical for the complex formation, and probable subunit interaction of PolDPho. The amino-terminal (1–300) of DP2Pho is essential for the folding of PolDPho and is likely the oligomerization domain of PolDPho
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the DNA polymerase from Pyrococcus furiosus has the lowest error rate of any known polymerase in polymerase chain reaction amplification
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme can efficiently incorporate nucleotides opposite 8-oxoG and extend from an 8-oxoG:C base pair with a mechanism similar to that observed for the replication of undamaged DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P81409
the enzyme utilizes activated DNA as a template-primer, artificial substrate (activated poly(dA-dT)) is preferred by the enzyme. M13 single-stranded DNA primed with 17 base oligonucleotide is not a good substrate. DNA elongation ability of Pol II using a natural DNA template is much lower than that of Pol I from this organism and DNA synthesis of Pol II seems to be non-processive
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
O59610
the functional motif, K253xRxxxD259 (outside known motifs Exo I, II, and III), that is important not only for exonuclease activity but also for polymerizing activity, confirms functional interdependence between the polymerase and exonuclease domains. The short loop region, K253G254R255, probably contributes to binding to DNA substrates
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. B-family DNA polymerases from hyperthermophilic archaea recognize the presence of uracil in DNA and stall DNA synthesis. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency is substantially enhanced by the initiation of DNA synthesis. The generation of ds DNA is significantly inhibited, however, by the presence of template uracil. Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution. Single molecules of Pol B1 bind to template uracil and stall DNA synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme bypasses DNA adducts pyrrolo-deoxycytosine, dP, N6-furfuryl-deoxyadenosine, and 1,N6-ethenodeoxyadenosine in a process known as translesion synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine, the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
an abasic lesion causes Dpo4 to switch from a normal to a very mutagenic mode of replication. Incorporation upstream of the abasic lesion is replicated error-free. Once Dpo4 encounters the lesion, synthesis became sloppy, with bypass products containing a myriad of mutagenic events. Incorporation of dAMP (29%) and dCMP (53%) opposite the abasic lesion at 37°C correlates exceptionally well with our kinetic results and demonstrates two dominant bypass pathways via the A-rule and the lesion loop-out mechanism. The percentage of overall frameshift mutations increases from 71% (37°C) to 87% (75°C), an abasic lesion causes the enzyme to switch from a normal to a very mutagenic mode of replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
ATP binding to replication factor C is sufficient for loading the heterotrimeric PCNA123 [proliferating cell nuclear antigen (PCNA)] clamp onto DNA that includes a rate-limiting conformational rearrangement of the complex. ATP hydrolysis is required for favorable recruitment and interactions with the replication polymerase (PolB1) that most likely include clamp closing and dissociation of replication factor C. Surprisingly, the assembled holoenzyme complex synthesizes DNA distributively and with low processivity, unlike most other well-characterized DNA polymerase holoenzyme complexes. PolB1 repeatedly disengages from the DNA template, leaving PCNA123 behind. Interactions with a C-terminal PCNA-interacting peptide (PIP) motif on PolB1 specifically with PCNA2 are required for holoenzyme formation and continuous re-recruitment during synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
bifunctional enzyme EC 2.7.7.7/EC 3.1.11.2. The polymerization and the 3'-5' exonuclease activity of a family B DNA polymerase can be ascribed to physically distinct modules of the enzyme molecule
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Dbh polymerase is much less accurate than the classical polymerases, but it shows a remarkable tendency to skip over a template pyrimidine positioned immediately 3' to a G residue, generating a single-base deletion. The rate of incorporation of dCTP opposite a template G is about 10fold faster than for the other three dNTPs opposite their complementary partners
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
distributive enzyme but a substantial increase in the processivity was observed on poly(dA)-oligo(dT) in the presence of proliferating cell nuclear antigen (039p or 048p) and replication factor CRFC. The length of the synthesized DNA product reaches at least 200 nucleotides
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Dpo4 in most cases selects the correctly paired partner for each benzo-expanded DNA base, but with efficiency lowered by the enlarged pair size
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Dpo4 predominantly uses a template slippage deletion mechanism when replicating repetitive DNA sequences. Dpo4 stabilizes the skipped template base in an extrahelical conformation between the polymerase and the little-finger domains of the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
even at 60°C, excessive amounts of Dpo4 are needed to carry out minimal bypass of the cyclobutane pyrimidine dimers
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exclusively incorporates 8-OH-GTP opposite adenine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
GTP incorporation by the wild-type enzyme is about 1000fold slower than dGTP incorporation. The rate of GTP incorporation by the mutant enzyme F12A Dbh is 2-3fold slower than incorporation of dGTP. The enzyme makes single-base deletion errors at high frequency in particular sequence contexts
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
incorporated of 2-amino-3-methylimidazo[4,5-f]quinoline C8- and N2-dGuo adducts into the G1- and G3-positions of the NarI recognition sequence (5'-G1G2CG3CC-3'), which is a hotspot for arylamine modification. Replication of the C8-adduct at the G3-position results in two-base deletion, whereas error-free bypass and extension is observed at the G1-position. The N2-adduct is bypassed and extended when positioned at the G1-position, and the error-free product is observed. The N2-adduct at the G3-position is more blocking and is bypassed and extended only by Dpo4 to produce an errorfree product. The replication of the 2-amino-3-methylimidazo[4,5-f]quinoline-adducts of dGuo is strongly influenced by the local sequence and the regioisomer of the adduct
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
low fidelity. When copying undamaged DNA, Dpo4 is highly inaccurate for essentially all types of single base substitutions and deletions in a large number of different sequence contexts
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-, Q8TIW3
MacDinB-1 synthesizes long products (approximately 7.2 kb) in the presence of its cognate proliferating cell nuclear antigen (PCNA). MacDinB-1 works in an error-free mode to repair cyclobutane pyrimidine dimers
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
mechanism of template-independent nucleotide incorporation. Based on the efficiency ratios, Dpo4 selects nucleotides for blunt-end addition in the order of decreasing efficiency: dATP, dTTP, dCTP, dGTP, with dATP favored by five to 50fold over the other nucleotides. The first bluntend dATP incorporation is 80fold more efficient than the second, and among natural deoxynucleotides, dATP is the preferred substrate due to its stronger intrahelical base-stacking ability
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
most of the dNTP analogs with modified sugar moiety tested are shown to be specific terminating substrates for the synthesis irreversibly blocking further elongation of a nascent chain. The most powerful inhibitors are the 3'-amino derivatives of deoxy and arabino nucleoside triphosphates, while specific reverse transcriptase inhibitors, 3'-azido and 3'-methoxy derivatives of dNTP, were found to be inactive
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q07635
proliferating cell nuclear antigen facilitates DNA synthesis with Dpo3, as with Dpo1 and Dpo4, but very weakly with Dpo2. DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most processive with DNA polymerase Dpo1 in comparison to DNA polymerase Dpo3 and Dpo4. DNA lesion bypass DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most effective with DNA polymerase Dpo4 in comparison to DNA polymerase Dpo1 and Dpo3. Both Dpo2 and Dpo3, but not Dpo1, bypass hypoxanthine and 8-oxoguanine. Dpo2 and Dpo3 bypass uracil and cis-syn cyclobutane thymine dimer, respectively. DNA polymerase Dpo2 and Dpo3 possess very low DNA polymerase and 3' to 5' exonuclease activities in vitro compared with Dpo1 and Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
relative to undamaged DNA the enzyme generates far more mutations (base deletions, insertions, and substitutions) with a DNA template containing a site-specifically placed N-(deoxyguanosin-8-yl)-1-aminopyrene. Opposite N-(deoxyguanosin-8-yl)-1-aminopyrened and at an immediate downstream template position, the most frequent base substitutions are dA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
removal of the 2-amino group from the template dG (i.e. deoxyinosine) has little impact on the catalytic efficiency of either polymerase, although the misincorporation frequency is increased by an order of magnitude. Deoxyxanthosine is highly miscoding with both polymerases, and incorporation of several bases is observed. The addition of bromine or oxygen at C2 lowers the Tm further, strongly inhibits and increases the frequency of misincorporation
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
ring-opening of the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1,2-a] purin-10(3H)-one adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the binding of a correct nucleotide induces a fast and surprising DNA translocation event. All four domains of the polymerase rapidly move in a synchronized manner before and after the polymerization reaction. Repositioning of active site residues is the rate-limiting step during correct nucleotide incorporation. The motions of the polymerase and the polymerase bound DNA substrate are tightly coupled to catalysis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the conformational dynamics of the Y-family DNA polymerase Dpo4 on DNA is characterized in real time using single-molecule Förster resonance energy transfers (mFRET). Two different binary complexes consistent with DNA translocation in the polymerase active site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the DNA polymerase also shows 3'-5' exonuclease activity. The 3'–5' exonuclease activity of the DNA polymerase is important for DNA elongation with high fidelity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme binds to DNA in at least three distinct conformations. The relative frequency of each conformation can be modulated by both the identity of the primer 3' terminus and the presence of an incoming dNTP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme bypasses Pt-GG DNA (1,2-intrastrand covalent linkage, cis-Pt-1,2-d(GpG)). This is a dynamic process, in which the lesion is converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-, Q2FA65
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA63, -
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA66, -
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA62
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA64, -
the enzyme can traverse a wide variety of DNA lesions. The enzyme is moderately processive. It can substitute for Taq in polymerase chain reaction (PCR) and can bypass DNA lesions that normally block Taq
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme catalyze DNA synthesis using either activated calf thymus DNA or oligonucleotide-primed single-stranded DNA as a template
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme does not efficiently insert nucleotides opposite to the (6S,8R,11S)-1,N2-deoxyguanosine adduct, consistent with the low levels of Gua->Thy mutations. However it extends past the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair. A series of ternary (Dpo4-DNA-dNTP) structures with (6S,8R,11S)-1,N2-deoxyguanosine-adducted templates suggest that during replication, the ring-closed (6S,8R,11S)-1,N2-deoxyguanosine lesion at the active site hinders incorporation of dNTPs opposite the lesion, whereas the ring-opened form of the lesion in the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair allows for extension to full-length product
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q7LYT8
the enzyme exhibits its highest specific activity with gapped-duplex (activated) calf thymus DNA as the substrate, less activity with double-stranded salmon sperm DNA or heat-denatured double-stranded salmon sperm DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme incorporates dTTP in a 61 mer template containing pyrrolo-deoxycytosine, dP, N6-furfuryl-deoxyadenosine, and 1,N6-ethenodeoxyadenosine (translesion synthesis)
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme is able to bypass N-(deoxyguanosin-8-yl)-1-aminopyrene, but pauses strongly at two sites: opposite the lesion and immediately downstream from the lesion. Both nucleotide incorporation efficiency and fidelity decrease significantly at the pause sites, especially during extension of the bypass product. Interestingly, a 4-fold tighter inding affinity of damaged DNA to Dpo4 DNA polymerase promotes catalysis through putative interactions between the active site residues of Dpo4 and 1-aminopyrene moiety at the first pause site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme is inefficient at extending mispairs opposite a template G or T, which include, a G*T mispair expected to conform closely to Watson-Crick geometry. It is hindered in extending a G*T mismatch by a reverse wobble
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme possess a remarkable DNA stabilizing ability for maintaining weak base pairing interactions to facilitate primer extension. This thermal stabilization by Dpo1 allows for template-directed synthesis at temperatures more than 30°C above the melting temperature of naked DNA. Dpo1 elongates single stranded DNA in template-dependent and template-independent manners. Initial deoxyribonucleotide incorporation is complementary to the template. Rate-limiting steps that include looping back and annealing to the template allow for a unique template-dependent terminal transferase activity. Dpo1 also displays a competing terminal deoxynucleotide transferase activity unlike any other B-family DNA polymerase
-
-
ß
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme readily bypasses N2-methyl(Me)G and O6-MeG, but is strongly blocked at O6-benzyl(Bz)G and N2-BzG. the enzyme shows 110-, 180-, and 300fold decreases in catalytic efficiency (kcat/Km) for nucleotide insertion opposite an abasicP site, N2-MeG, and O6-MeG but 1800- and 5000fold decreases opposite O6-BzG and N2-BzG, respectively, as compared to G. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Vent (exo-) accepts nonbulky DNA lesions (e.g., N2- or O6-MeG and an AP site) as manageable substrates despite causing errorprone synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme shows little decreases opposite N2-MeG, 13fold decrease opposite N2-BzG but 260-370fold decreases opposite O6-MeG, O6-BzG, and the abasic site site as compared to G. Dpo4 favored correct C insertion opposite opposite N2-MeG, opposite O6-MeG, opposite an abasic site site and oppositeN2-BzG. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Dpo4 strongly favors minor-groove N2-alkylG lesions over major-groove or noninstructive lesions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the fidelity of Dpo4 is in the range of 0.001-0.0001. The ground-state binding affinity of correct nucleotides is 10-50-fold weaker than those of replicative DNA polymerases. The affinity of incorrect nucleotides for Dpo4 is about 2-10-fold weaker than that of correct nucleotides. The mismatched dCTP has an affinity similar to that of the matched nucleotides when it is incorporated against a pyrimidine template base flanked by a 5'-template guanine. The mismatch incorporation rates, regardless of the 5'-template base, are about 2-3 orders of magnitude slower than the incorporation rates for matched nucleotides, which is the predominant contribution to the fidelity of Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by the enzyme, with hydrogen bonding capacity being a major influence. Modifications at the C2-position of dCTP increases the selectivity for incorporation opposite O6-methylguanine without a significant loss of efficiency
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the initial enzyme/DNA/dNTP complex undergoes a rapid (18/s), reversible (21/s) conformational change, followed by relatively rapid phosphodiester bond formation (11/s) and then fast release of pyrophosphate, followed by a rate-limiting relaxation of the active conformation (2/s) and then rapid DNA release, yielding an overall steady-state kcat of less than 1/s
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the molecular dynamics simulations suggest that mismatched nucleotide insertion opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG is increased at 55°C compared with 37°C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. With the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG by Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the rate of insertion of dNTPs opposite and extension past both O2-[4-(3-pyridyl)-4-oxobut-1-yl]-thymidine and O2-methylthymidine is measured. The size of the alkyl chain only marginally affects the reactivity and the specificity of adduct bypass is very low. Dpo4 catalyzes the incorporation opposite and extension past the adducts approximately 1000fold more slowly than undamaged DNA. dA is the preferred base pair partner for O2-[4-(3-pyridyl)-4-oxobut-1-yl]-thymidine and dT is the preferred base pair partner for O2-methylthymidine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the rate of mismatched nucleotide incorporation is greater than the rate of correct dC insertion at 55 °C, whereas at 37 °C there is little selectivity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
when insertion is opposite an unmodified G, insertion of dATP or dGTP is 1000 less efficient than dCTP. For insertion opposite 8-oxoG, the order of decreasing efficiency is dCTP, dATP, dGTP, with an order of magnitude or more difference in catalytic efficiency (kcat/Km) in each pair of comparisons. The insertion of dCTP opposite G and 8-oxoG shows similar catalytic efficiency, even with differences in the trends for kcat and Km. 90fold higher incorporation efficiency of dCTP compared to dATP opposite 8-oxoG and 4fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. The 8-oxoG:C pair shows classic Watson-Crick geometry; the 8-oxoG:A pair is in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5'C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshiftevent observed in the catalytic assays
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
while showing efficient bypass, the enzyme pauses when incorporating nucleotides directly opposite and one position downstream from an abasic lesion because of a drop of several orders of magnitude in catalytic efficiency. Biphasic kinetics for incorporation indicating that Dpo4 primarily forms a nonproductive complex with DNA that converts slowly to a productive complex. These strong pause sites are mutational hot spots with the embedded lesion even affecting the efficiency of five to six downstream incorporations
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Pyrococcus abyssi Orsay
-
PCR performance and fidelity parameters are highest in the presence of 20 mM Tris-HCl, pH 9.0, 1.5 mM MgSO4, 25 mM KCl, 10 mM (NH4)2SO4 and 40 microM of each dNTP. Under these conditions, the error rate is 0.66.10(-6) mutations/nucleotide/duplication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Saccharomyces cerevisiae BY4742
P13382
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P95690
the activated herring sperm DNA is an optimal template and gives 3times higher activity than that obtained with poly(dA)/oligo(dT). The DNA polymerase can not use templates without primer (poly(dA) and poly(dT)), even when appropriate priming ribonucleotides (UTP or ATP, respectively) are supplied. It does not accept a polyribonucleotide template (poly(rA):oligo(dT))
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q4JB80
DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme shows deoxynucleotide transferase activity, short patch DNA synthesis activity on heteropolymeric DNA substrate, 5'-deoxyribose phosphate lyase activity and base excision repair function in vitro
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Geobacillus stearothermophilus Donc
-
-, standard substrate PTJ1 and substrate PTJ2
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus caldophilus GH24
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus caldophilus GH24
-
exonuclease 5'--3' activity, no exonuclease 3'--5' activity
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus thermophilus M1
K4Q1U9
-, DNA-dependent DNA polymerase activity to incorporate dNTP into gapped M13mp2 DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus thermophilus B35
-
several dTTP analoges bearing a photoreactive 2-nitro-5-azidobenzoyl group attached at position 5 of uracil through linkers of various lengths, are substrates in the elongation reaction of the 5'-32P-labeled primer-template complex. The incorporation of the analogs into the 3' primer end did not impede further elongation of the chain in the presence of natural dNTP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Sulfolobus solfataricus MT4
-
-, exonuclease 3'--5' activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermococcus pacificus DSM 10394
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermococcus peptonophilus DSM 10343
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Escherichia coli JH39
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermotoga petrophila K4
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermotoga petrophila K4
E2RWL8
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Chlamydia pneumoniae AR39
-
no detectable 3' exonuclease activity. CpDNApolI-dependent DNA synthesis is performed using DNA templates carrying different lesions. DNAs containing 2'-deoxyuridine (dU), 2'-deoxyinosine (dI) or 2'-deoxy-8-oxo-guanosine (8-oxo-dG) served as templates as effectively as unmodified DNAs for CpDNApolI. Furthermore, the CpDNApolI can bypass natural apurinic/apyrimidinic sites (AP sites), deoxyribose (dR), and synthetic AP site tetrahydrofuran (THF). CpDNApolI can incorporate any dNMPs opposite both of deoxyribose and tetrahydrofuran with the preference to dAMP-residue. CpDNApolI preferentially extends primer with 3'-dAMP opposite deoxyribose during DNA synthesis, however all four primers with various 3'-end nucleosides (dA, dT, dC, and dG) opposite THF can be extended by CpDNApolI. Efficiently bypassing of AP sites by CpDNApolI is hypothetically attributed to lack of 3' exonuclease activity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Escherichia coli K12
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus aquaticus YT1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus aquaticus INValphaF
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Sulfolobus solfataricus P1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine, the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine, DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine, exclusively incorporates 8-OH-GTP opposite adenine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the pre-steady-state kinetic methods is used to determine the base substitution fidelity and mismatch extension fidelity of PolB1
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-, translesion synthesis of the 7-(2-oxoheptyl)-1,N2-etheno-2'-deoxyguanosine lesion by the enzyme in 5'-TXG-3' and 5'-CXG-3' local sequence contexts is examined and compared to 1,N2-etheno-2'-deoxyguanosine lesions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine, the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine, DNA polymerase pol Y1 exclusively incorporates 8-OH-GTP opposite adenine. DNA polymerase pol Y1 incorporates 2-OH-dATP predominantly opposite guanine and thymine. DNA polymerase pol B1 incorporates 8-OH-GTP opposite adenine and cytosine. DNA polymerase pol B1 incorporates 2-OH-dATP opposite thymine, exclusively incorporates 8-OH-GTP opposite adenine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the molecular dynamics simulations suggest that mismatched nucleotide insertion opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG is increased at 55°C compared with 37°C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. With the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG by Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
removal of the 2-amino group from the template dG (i.e. deoxyinosine) has little impact on the catalytic efficiency of either polymerase, although the misincorporation frequency is increased by an order of magnitude. Deoxyxanthosine is highly miscoding with both polymerases, and incorporation of several bases is observed. The addition of bromine or oxygen at C2 lowers the Tm further, strongly inhibits and increases the frequency of misincorporation
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
ATP binding to replication factor C is sufficient for loading the heterotrimeric PCNA123 [proliferating cell nuclear antigen (PCNA)] clamp onto DNA that includes a rate-limiting conformational rearrangement of the complex. ATP hydrolysis is required for favorable recruitment and interactions with the replication polymerase (PolB1) that most likely include clamp closing and dissociation of replication factor C. Surprisingly, the assembled holoenzyme complex synthesizes DNA distributively and with low processivity, unlike most other well-characterized DNA polymerase holoenzyme complexes. PolB1 repeatedly disengages from the DNA template, leaving PCNA123 behind. Interactions with a C-terminal PCNA-interacting peptide (PIP) motif on PolB1 specifically with PCNA2 are required for holoenzyme formation and continuous re-recruitment during synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q07635
proliferating cell nuclear antigen facilitates DNA synthesis with Dpo3, as with Dpo1 and Dpo4, but very weakly with Dpo2. DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most processive with DNA polymerase Dpo1 in comparison to DNA polymerase Dpo3 and Dpo4. DNA lesion bypass DNA synthesis in the presence of proliferating cell nuclear antigen, replication factor C, and single-stranded binding protein is most effective with DNA polymerase Dpo4 in comparison to DNA polymerase Dpo1 and Dpo3. Both Dpo2 and Dpo3, but not Dpo1, bypass hypoxanthine and 8-oxoguanine. Dpo2 and Dpo3 bypass uracil and cis-syn cyclobutane thymine dimer, respectively. DNA polymerase Dpo2 and Dpo3 possess very low DNA polymerase and 3' to 5' exonuclease activities in vitro compared with Dpo1 and Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P96022, -
in the absence of additional cofactor the enzyme is an essentially distributive enzyme that only extends primers by 1-2 nt per binding event. At high enzyme to primer/template ratios, dissociation and rebinding of the enzyme to the primer/template is robust and can lead to the synthesis of polynucleotide chains of several hundred nucleotides in length
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q97W02
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
products of replication of polycyclic aromatic hydrocarbon-modified DNA by the translesion DNA polymerase Dpo4 are complex
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
replication bypass studies in vitro reveal that the polymerase inserts dNTPs opposite the (6S,8R,11S)-trans-4-hydroxynonenal-1,N2-dGuo adduct in a sequence-specific manner. If the template 5'-neighbor base is dCyt, the polymerase inserts primarily dGTP. If the template 5'-neighbor base is dThy, the polymerase inserts primarily dATP, the enzyme does not efficiently insert nucleotides opposite to the (6S,8R,11S)-1,N2-deoxyguanosine adduct, consistent with the low levels of Gua->Thy mutations. However it extends past the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair. A series of ternary (Dpo4-DNA-dNTP) structures with (6S,8R,11S)-1,N2-deoxyguanosine-adducted templates suggest that during replication, the ring-closed (6S,8R,11S)-1,N2-deoxyguanosine lesion at the active site hinders incorporation of dNTPs opposite the lesion, whereas the ring-opened form of the lesion in the (6S,8R,11S)-1,N2-deoxyguanosine:dCyd pair allows for extension to full-length product
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme bypasses aflatoxin B1-N7-dG in an error-free manner but conducts error-prone replication past the aflatoxin B1-formamidopyrimidine adduct, including misinsertion of dATP
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-, DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine, when insertion is opposite an unmodified G, insertion of dATP or dGTP is 1000 less efficient than dCTP. For insertion opposite 8-oxoG, the order of decreasing efficiency is dCTP, dATP, dGTP, with an order of magnitude or more difference in catalytic efficiency (kcat/Km) in each pair of comparisons. The insertion of dCTP opposite G and 8-oxoG shows similar catalytic efficiency, even with differences in the trends for kcat and Km. 90fold higher incorporation efficiency of dCTP compared to dATP opposite 8-oxoG and 4fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. The 8-oxoG:C pair shows classic Watson-Crick geometry; the 8-oxoG:A pair is in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5'C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshiftevent observed in the catalytic assays
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the rate-constant defining Dpo4-catalyzed incorporation of dCTP is about 6-fold slower for incorporation opposite O6-MeG relative to G. The basis for the decreased rate is revealed by the crystal structure to be formation of a wobble base pairing between O6-MeG and C
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme shows a limited decrease in catalytic efficiency (kcat/Km) for insertion of dCTP opposite a series of N2-alkylguanine templates of increasing size from (methyl (Me) to (9-anthracenyl)-Me (Anth)). Fidelity is maintained with increasing size up to (2-naphthyl)-Me (Naph). The catalytic efficiency increases slightly going from the N2-NaphG to the N2-AnthG substrate, at the cost of fidelity. A set of oligonucleotides differing only in their N2-substitution at a single G site is used in this study with Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-, modeling and molecular dynamics simulations for 2'-deoxy-8-[(1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-yl)amino]guanosine suggest that the adduct would increase the infidelity of Dpo4 and hinder translocation by the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme can efficiently incorporate nucleotides opposite 8-oxoG and extend from an 8-oxoG:C base pair with a mechanism similar to that observed for the replication of undamaged DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the fidelity of Dpo4 is in the range of 0.001-0.0001. The ground-state binding affinity of correct nucleotides is 10-50-fold weaker than those of replicative DNA polymerases. The affinity of incorrect nucleotides for Dpo4 is about 2-10-fold weaker than that of correct nucleotides. The mismatched dCTP has an affinity similar to that of the matched nucleotides when it is incorporated against a pyrimidine template base flanked by a 5'-template guanine. The mismatch incorporation rates, regardless of the 5'-template base, are about 2-3 orders of magnitude slower than the incorporation rates for matched nucleotides, which is the predominant contribution to the fidelity of Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
incorporated of 2-amino-3-methylimidazo[4,5-f]quinoline C8- and N2-dGuo adducts into the G1- and G3-positions of the NarI recognition sequence (5'-G1G2CG3CC-3'), which is a hotspot for arylamine modification. Replication of the C8-adduct at the G3-position results in two-base deletion, whereas error-free bypass and extension is observed at the G1-position. The N2-adduct is bypassed and extended when positioned at the G1-position, and the error-free product is observed. The N2-adduct at the G3-position is more blocking and is bypassed and extended only by Dpo4 to produce an errorfree product. The replication of the 2-amino-3-methylimidazo[4,5-f]quinoline-adducts of dGuo is strongly influenced by the local sequence and the regioisomer of the adduct
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
in addition to the correct insertion of dCTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme shows little decreases opposite N2-MeG, 13fold decrease opposite N2-BzG but 260-370fold decreases opposite O6-MeG, O6-BzG, and the abasic site site as compared to G. Dpo4 favored correct C insertion opposite opposite N2-MeG, opposite O6-MeG, opposite an abasic site site and oppositeN2-BzG. DNA polymerase Vent (exo-) from Thermococcus litoralis is as or more efficient as polymerase Dpo4 from Sulfolobus solfataricus in synthesis opposite O6-MeG and AP lesions, whereas DNA polymerase Dpo4 from Sulfolobus solfataricus is much or more efficient opposite N2-alkylGs than DNA polymerase Vent (exo-) from Thermococcus litoralis, irrespective of DNA-binding affinity. DNA polymerase Dpo4 strongly favors minor-groove N2-alkylG lesions over major-groove or noninstructive lesions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
ring-opening of the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1,2-a] purin-10(3H)-one adduct promotes error-free bypass by the Sulfolobus solfataricus DNA polymerase Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme bypasses Pt-GG DNA (1,2-intrastrand covalent linkage, cis-Pt-1,2-d(GpG)). This is a dynamic process, in which the lesion is converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Dpo4 predominantly uses a template slippage deletion mechanism when replicating repetitive DNA sequences. Dpo4 stabilizes the skipped template base in an extrahelical conformation between the polymerase and the little-finger domains of the enzyme
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
low fidelity. When copying undamaged DNA, Dpo4 is highly inaccurate for essentially all types of single base substitutions and deletions in a large number of different sequence contexts
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the rate of mismatched nucleotide incorporation is greater than the rate of correct dC insertion at 55 °C, whereas at 37 °C there is little selectivity
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
while showing efficient bypass, the enzyme pauses when incorporating nucleotides directly opposite and one position downstream from an abasic lesion because of a drop of several orders of magnitude in catalytic efficiency. Biphasic kinetics for incorporation indicating that Dpo4 primarily forms a nonproductive complex with DNA that converts slowly to a productive complex. These strong pause sites are mutational hot spots with the embedded lesion even affecting the efficiency of five to six downstream incorporations
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-, the initial enzyme/DNA/dNTP complex undergoes a rapid (18/s), reversible (21/s) conformational change, followed by relatively rapid phosphodiester bond formation (11/s) and then fast release of pyrophosphate, followed by a rate-limiting relaxation of the active conformation (2/s) and then rapid DNA release, yielding an overall steady-state kcat of less than 1/s
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme is able to bypass N-(deoxyguanosin-8-yl)-1-aminopyrene, but pauses strongly at two sites: opposite the lesion and immediately downstream from the lesion. Both nucleotide incorporation efficiency and fidelity decrease significantly at the pause sites, especially during extension of the bypass product. Interestingly, a 4-fold tighter inding affinity of damaged DNA to Dpo4 DNA polymerase promotes catalysis through putative interactions between the active site residues of Dpo4 and 1-aminopyrene moiety at the first pause site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
mechanism of template-independent nucleotide incorporation. Based on the efficiency ratios, Dpo4 selects nucleotides for blunt-end addition in the order of decreasing efficiency: dATP, dTTP, dCTP, dGTP, with dATP favored by five to 50fold over the other nucleotides. The first bluntend dATP incorporation is 80fold more efficient than the second, and among natural deoxynucleotides, dATP is the preferred substrate due to its stronger intrahelical base-stacking ability
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme is inefficient at extending mispairs opposite a template G or T, which include, a G*T mispair expected to conform closely to Watson-Crick geometry. It is hindered in extending a G*T mismatch by a reverse wobble
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the conformational dynamics of the Y-family DNA polymerase Dpo4 on DNA is characterized in real time using single-molecule Förster resonance energy transfers (mFRET). Two different binary complexes consistent with DNA translocation in the polymerase active site
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
even at 60°C, excessive amounts of Dpo4 are needed to carry out minimal bypass of the cyclobutane pyrimidine dimers
-
-
?
deoxynucleoside triphosphate + DNAn
?
show the reaction diagram
-
the enzyme can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene. An anti glycosidic torsion with C1'-exo deoxyribose conformation allows N-(deoxyguanosin-8-yl)-2-acetylaminofluorene to be Watson–Crick hydrogen-bonded with dCTP with modest polymerase perturbation, but other nucleotides are more distorting
-
-
?
deoxynucleoside triphosphate + DNAn |
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + primed M13n
diphosphate + primed M13n+1
show the reaction diagram
-
-
-
-
dGTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dGTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dGTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dGTP + DNAn
?
show the reaction diagram
Q07635
-
-
-
?
dGTP + DNAn
?
show the reaction diagram
-
Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
-
-
?
dGTP + DNAn
?
show the reaction diagram
-
in addition to the correct insertion of dGTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dGTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dGTP + DNAn
?
show the reaction diagram
Q07635
-
-
-
?
dGTP + DNAn
?
show the reaction diagram
-
in addition to the correct insertion of dGTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dGTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dGTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
with activated calf thymus DNA
-
-
?
dITP + DNAn
?
show the reaction diagram
-
-
-
-
?
DNA 21/41-mer + dTTP
? + diphosphate
show the reaction diagram
-
kinetic mechanism for DNA polymerization is proposed, the enzyme utilizes an induced-fit mechanism to select correct incoming nucleotides
-
-
?
dPTP + DNAn
?
show the reaction diagram
-
i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-beta-D-2'-deoxyribofuranosid 5'-triphosphate. dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
-
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q6DRD3
-
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
activity assay with plus-strand m13 DNA annealed to 5'-32P end-labeled primer 5'-GCTGTTGGGAAGGGCGATCG-3'
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
K4Q1U9
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
with activated calf thymus DNA
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
with labeled 20/33-mer primer-template duplex DNA
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus thermophilus M1
K4Q1U9
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus thermophilus B35
-
-
-
-
-
dTTP + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermotoga petrophila K4
-
incorporation of dTTP into poly(rA)-p(dT)45
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dTTP + DNAn
?
show the reaction diagram
Q07635
-
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
Dbh is a distributive enzyme showing a low DNA and nucleotide binding affinity along with a slow polymerization rate. DNA binding occurs in a single step, diffusion-controlled manner. The rate-limiting step of nucleotide incorporation (correct and incorrect) is the chemical step (phosphoryl transfer) and not a conformational change of the enzyme. An induced fit mechanism to select and incorporate nucleotides during DNA polymerization can not be detected for the enzyme
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
activity with poly(dA) or poly(dT) as template, minimal primers are dAMP or dTMP. Lengthening of primers by each mononucleotide increases their affinity about 2.16-fold. The affinity of the primer d(pA)gp(rib*) with a deoxyribosylurea residue at the 3'-end does not differ essentially from that of d(pA)9. Substitution of the 3'-terminal nucleotide of a complementary primer for a noncomplementary nucleotide, e.g., substitution of 3'-terminal A for C in d(pA)10 in the reaction catalyzed on poly(dT), decreases the affinity of a primer by one order of magnitude
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2’-deoxyribofuranosid-5’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
in addition to the correct insertion of dTTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dTTP + DNAn
?
show the reaction diagram
Q07635
-
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
in addition to the correct insertion of dTTP opposite the lesion, Dpo4 misincorporates dATP, dGTP, and TTP in an oligonucleotide containing a site-specific N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion. dCTP insertion opposite the N6-(2-deoxy-D-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-N-methylformamidopyrimidine lesion is only 1.4fold lower than insertion opposite an unmodified deoxyguanosine
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
-
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
dTTP incorporation is the most preferred addition opposite the N6dA-(OH)2butyl-GSH adduct, N6dA-butanetriol adduct, or unmodified dA
-
-
?
N1-methyl-2'-deoxyadenosine 5'-triphosphate + DNAn
diphosphate + ?
show the reaction diagram
-
-
-
-
?
North-methanocarba-dATP + DNAn
?
show the reaction diagram
-
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme preferentially inserts North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker compared to a South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker, the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
North-methanocarba-dATP + DNAn
?
show the reaction diagram
-
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker, the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme preferentially inserts North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker compared to a South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
poly(dA)/oligo(dT)x + n dTTP
poly(dA)/oligo(dT)x+n + n diphosphate
show the reaction diagram
P0CL76, Q9V2F3 and Q9V2F4
preferred substrate
-
-
?
rATP + DNAn
?
show the reaction diagram
-
-
-
-
?
rCTP + DNAn
?
show the reaction diagram
-
-
-
-
?
South-methanocarba-dATP + DNAn
?
show the reaction diagram
-
the role of sugar geometry during nucleotide selection is probed by the enzyme from Sulfolobus solfataricus using fixed conformation nucleotide analogues. The enzyme relatively tolerant to the substrate conformation: North-methanocarba-dATP that locks the central ring into a RNA-type (C2'-exo, North) conformation near a C3'-endo pucker or South-methanocarba-dATP that locks the central ring system into a (C3'-exo, South) conformation near a C2'-endo pucker
-
-
?
dTTP + DNAn
?
show the reaction diagram
-
dCTP and 5-methyl-dCTP are efficiently incorporated opposite a template guanine but significantly less so opposite a template O6-methylguanine. 2-thio-dCTP is efficiently inserted opposite guanine and is also incorporated opposite O6-methylguanine, to a similar extent as dCTP. Of the dNTPs assayed, dCTP, 5-Me-dCTP, and 2-thio-dCTP display the highest incorporation efficiency opposite O6-methylguanine. dTTP incorporation is favored opposite O6-methylguanine rather than opposite guanine. Hydrophobicity of the incoming dNTP appears to have little influence on the process of nucleotide selection by Dpo4, with hydrogen bonding capacity being a major influence. 8-oxo-dATP and 8-bromo-dATP are not inserted opposite O6-methylguanine and are slowly incorporated opposite guanine. dPTP (i.e. 6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one-8-b-d-2’-deoxyribofuranosid-5’-triphosphate) is incorporated opposite guanine slightly less efficiently than dCTP and is not incorporated opposite O6-methylguanine
-
-
?
additional information
?
-
-
Neq L and Neq S are needed to form the active DNA polymerase that possesses higher proofreading activity. The genetically protein splicing-processed Neq P shows the same properties as the protein trans-spliced Neq C
-
-
-
additional information
?
-
-
PolH can be up-regulated by DNA breaks induced by ionizing radiation or chemotherapeutic agents, and knockdown of PolH gives cells resistance to apoptosis induced by DNA breaks in multiple cell lines and cell types in a p53-dependent manner. PolH has a role in the DNA damage checkpoint. POlH is target of p53
-
-
-
additional information
?
-
-
lesion-bypass DNA polymerase
-
-
-
additional information
?
-
P06746
modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase
-
-
-
additional information
?
-
Q29Y55
Szi DNA polymerase possesses associated 3'-5' and 5'-3' exonuclease activities
-
-
-
additional information
?
-
-
the enzyme is responsible for mutagenesis, e.g. UV-induced, in human host cells of lungs of cystic fibrosis patients contributing to morbidity and mortality of these people, with a striking correlation between mutagenesis and the persistence of Pseudomonas aeruginosa, mechanisms of mutagenesis, enzyme regulation, overview, the enzyme is responsible for resistance to to nitrofurazone and 4-nitroquinoline-1-oxide toxification
-
-
-
additional information
?
-
-
DNA synthesis on M13Gori single-stranded phage DNA as template DNA
-
-
-
additional information
?
-
-
the enzyme causes 1-bp deletions and different base substitutions in plasmids pKTpheA56+A and pKTpheA22TAG, pKTpheA22TAA, and pKTpheA22TGA, respectively, in stationary cells, overview, Pol IV-dependent mutagenesis causes an approximately 10fold increase in the frequency of accumulation of 1-bp deletion mutations on selective plates in wild-type populations starved for more than 1 week, development of a mutant detection assay system allowing to separately detect the mutants, no effect of Pol IV on the frequency of accumulation of base substitution mutations in starving cells is observed, overview, RecA independence of Pol IV-associated mutagenesis mechanisms different from the classical RecA-dependent SOS response can elevate Pol IV-dependent mutagenesis in starving cells, overview
-
-
-
additional information
?
-
-
all pols exclusively promote misincorporation of dCMP opposite a 2'-deoxyinosine lesion during translesion synthesis, isozymes pol alpha, pol eta, and pol kappaDELTAC promote preferential incorporation of 2'-deoxycytidine monophosphate , the wrong base, opposite a 2'-deoxyinosine lesion, no incorporation of 2'-deoxythymidine monophosphate, the correct base, is observed opposite the lesion
-
-
-
additional information
?
-
-
replication cycle of Dpo4, and induced fit and translocation mechanisms, overview
-
-
-
additional information
?
-
-
the R2 polymerase can utilize both RNA and DNA templates, but the processivity of the enzyme on single stranded DNA templates is higher than its processivity on RNA templates, R2-RT is also capable of synthesizing the second DNA strand during retrotransposition
-
-
-
additional information
?
-
-
the widely used anticancer drug, cis-diamminedichloroplatinum(II), i.e. cisplatin, reacts with adjacent purine bases in DNA to form predominantly cis-[Pt(NH3)2(d(GpG)-N7(1),-N7(2))] intrastrand cross-links, DNA polymerase IV is able to perform translesion synthesis in the presence of DNA-distorting damage such as cisplatin-DNA adducts, overview
-
-
-
additional information
?
-
-
(2R,4R)-4-(2-amino-6-oxo-9H-purin-9-yl)-1,3-dioxolan-2-yl-methanol triphosphate and 2',3'-dideoxy-2',3'-didehydroguanoside triphosphate, and carbovir triphosphate are much less efficiently incorporated than the natural deoxynucleoside triphosphate dGTP
-
-
-
additional information
?
-
-
Dpo4 produces mismatch and frameshift mutations at benzo[a]pyrene-derived lesions, overview
-
-
-
additional information
?
-
-
Dpo4 utilizes an induced-fit mechanism to select correct incoming nucleotides at 37°C, overview
-
-
-
additional information
?
-
-
potential structures of purine-purine base pairs, overview
-
-
-
additional information
?
-
Q97W02
significant preferential dATP insertion, dATP can be misincorporated opposite the benzo[a]pyrene-derived N2-dG adduct, standing-start single-nucleotide insertion assays, overview
-
-
-
additional information
?
-
-
simulation model of the solvated Dpo4/DNA/8-oxoG:dCTP complex, catalytic site structure, overview
-
-
-
additional information
?
-
-
the enzyme is unable to use single stranded DNA or double stranded blunt end DNA
-
-
-
additional information
?
-
-
comparing RNA primer-templates and DNA primer templates of identical sequence show that herpes polymerase greatly prefers to elongate the DNA primer by 650-26000fold, thus accounting for the extremely low efficiency with which herpes polymerase elongates primase-synthesized primers
-
-
-
additional information
?
-
-
the catalytic efficiency of PolX is almost the same with and without dNTPs, whereas that of the domain mixture increases on the addition of dNTPs
-
-
-
additional information
?
-
-
the DNA polymerase gene of Thermococcus marinus contains an intein inserted at the pol-b site
-
-
-
additional information
?
-
-
Pol beta does incorporate size augmented thymidine analogues besides the unmodified TTP
-
-
-
additional information
?
-
-
Pol beta does not incorporate size augmented thymidine analogues, while the unmodified TTP is processed
-
-
-
additional information
?
-
-
small 4'-methyl and -ethyl modifications of the nucleoside triphosphate do not perturb Klenow fragment catalysis
-
-
-
additional information
?
-
-
the excision of the matched 3'-monophosphorylated form of 2'-deoxy-2',2'-difluorocytidine moiety by the wild type pol gamma is 55fold slower than the excision of matched 3'-dCMP
-
-
-
additional information
?
-
-
while small 4'-methyl and -ethyl modifications of the nucleoside triphosphate perturb Pol beta catalysis, extension of modified primer strands is only marginally affected
-
-
-
additional information
?
-
P95979
Dpo3 has an active exonuclease proofreading domain, it shows intrinsic exonuclease activity
-
-
-
additional information
?
-
-
simulations, based on crystal complexes of Dpo4 are performed, exploring possible transitions and mechanisms associated with Dpo4’s catalytic cycle. Dynamics simulations before the nucleotidyl-transfer reaction and simulations after the reaction are performed. Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV may accommodate lesion bypass
-
-
-
additional information
?
-
-
the DNA lesion bypass polymerase can bind up to eight base pairs of double-stranded DNA which is entirely in B-type. Thus, the DNA binding cleft of Dpo4 is flexible and can accommodate both A- and B-type oligodeoxyribonucleotide duplexes as well as damaged DNA
-
-
-
additional information
?
-
E2RWL8, -
DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
-
-
-
additional information
?
-
-
only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49
-
-
-
additional information
?
-
-
at low pH the chemical step is rate limiting for catalysis, but at high pH, a postchemistry conformational step is rate limiting due to a pH-dependent increase in the rate of nucleotidyl transfer
-
-
-
additional information
?
-
-
DNA polymerase switching mechanism by which PabPol B displaces PabPol D from proliferating cell nuclear antigen on the DNA duplex
-
-
-
additional information
?
-
-
only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, no activity with the wild-type enzyme
-
-
-
additional information
?
-
-
polymerase binds DNA containing uracil 1.5–4.5-fold more strongly than hypoxanthine
-
-
-
additional information
?
-
P0CL76, Q9V2F3 and Q9V2F4
primer ssM13 DNA is the preferred substrate
-
-
?
additional information
?
-
-
the DNA polymerase possesses a 3'->5' exonuclease activity
-
-
-
additional information
?
-
-
the enzyme also displays 3'–5'-exonuclease activity
-
-
-
additional information
?
-
H9CW54
the enzyme also posseses 3'->5' exonuclease activity
-
-
-
additional information
?
-
P81412 and P81409
the enzyme has strong 3'->5' exonucleolytic activity and has a template-primer preference which is characteristic of a replicative DNA polymerase
-
-
-
additional information
?
-
-
the mutant enzyme shows single deoxynucleotide additions with dCTP, dATP and dTTP, but not with dGTP as it results in addition of two successive base incorporations on the chosen template 2 hybridised to the DNA primer 1, thereby invalidating the single-turnover kinetic model, Michaelis-Menten mechanism, overview
-
-
-
additional information
?
-
Q7LYT8
single-strand-dependent and double-strand-dependent 3'-5' exonuclease activity and marginal 5'-3' exonuclease activity
-
-
-
additional information
?
-
Thermococcus peptonophilus DSM 10343
-
the DNA polymerase possesses a 3'->5' exonuclease activity
-
-
-
additional information
?
-
Thermotoga petrophila K4
-
only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49, only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, no activity with the wild-type enzyme
-
-
-
additional information
?
-
Thermotoga petrophila K4
E2RWL8
DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
-
-
-
additional information
?
-
Thermococcus waiotapuensis DSM 12768
H9CW54
the enzyme also posseses 3'->5' exonuclease activity
-
-
-
additional information
?
-
-
the DNA lesion bypass polymerase can bind up to eight base pairs of double-stranded DNA which is entirely in B-type. Thus, the DNA binding cleft of Dpo4 is flexible and can accommodate both A- and B-type oligodeoxyribonucleotide duplexes as well as damaged DNA
-
-
-
additional information
?
-
-
simulations, based on crystal complexes of Dpo4 are performed, exploring possible transitions and mechanisms associated with Dpo4’s catalytic cycle. Dynamics simulations before the nucleotidyl-transfer reaction and simulations after the reaction are performed. Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV may accommodate lesion bypass
-
-
-
additional information
?
-
P95979
Dpo3 has an active exonuclease proofreading domain, it shows intrinsic exonuclease activity
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P19821
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P00582
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P28340
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q9UNA4
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P46957
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P61875
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q97W02
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Herpes simplex virus
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Ruellia sp.
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P74918
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P77933
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P03156
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q97W02
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Triturus cristatus, Testudines agrionemys, Philothamnus punctatus
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P13382
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
E2RWL8, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
K4Q1U9
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P81409
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q6DRD3
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-, Q2FA65
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA63, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA66, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA62
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Q2FA64, -
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
natural substrate is gapped DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
physiological role of pol I
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase I plays a role in repair of chromosomal damage
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
physiological role of pol I and pol III
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
overview: functional role of mammalian DNA polymerases
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase alpha: role in DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase beta: role in DNA repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
physiological role of pol I, II and pol III
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
enzyme is active only in cells at meiotic prophase, in somatic cells it is in an inactive state
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase delta: with its auxiliary factor i.e. proliferating cell nuclear antigen, largely responsible for leading-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
pol III can repair short gaps created by nuclease in duplex DNA, for efficient replication of the long, single-stranded templates pol III requires auxiliary subunits
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase III: role in replication of chromosomal DNA
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
overview: physiological roles in replication and in DNA repair synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase II: role in DNA repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
polymerase III is necessary for DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
role in DNA gap repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
exonuclease activity contributes to the avoidance of alkylation mutations
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase gamma: required for mitochondrial DNA replication but encoded in the nucleus
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase alpha: with its associated primase largely responsible for lagging-strand synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
phage T4 DNA polymerase is essential for initiation and maintenance of viral DNA replication
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase V is involved in translesion synthesis and mutagenesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
Pol lambda plays a role in the short-patch base excision repair rather than contributes to the long-patch base excision repair pathway
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
role in non-homologous end joining of double strand breaks, perhaps including those with damaged ends, possible role for pol IV in base excision repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
DNA polymerase iota may play a limited and error-prone role in translesion synthesis across the N2-guanine adducts (possibly medium sized adducts up to N2-benzylguanine) due to the low polymerization rates and high error rates
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
double-stranded DNA property of DNA polymerase epsilon is required for epigenetic silencing at telomeres
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
OsPOLP1 might be involved in a repair pathway similar to long-patch base excision repair. Possible role of POLPs in plastidial DNA replication and repair
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
two representative types of lesions: (i) 7,8-dihydro-8-oxoguanine, a small, highly prevalent lesion caused by oxidative damage; and (ii) bulky lesions derived from the environmental pre-carcinogen benzo[a]pyrene. The diol epoxide (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[ a]pyrene reacts largely, but not exclusively, with the exocyclic amino group of guanine to produce the major 10S (+) trans-anti-BP-N2-dG adduct, that is bypassed by Dpo4
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
gamma-phosphates of the incoming dNTP, contributing to charge neutralization and alignment of the alpha-phosphate for reaction
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
PabPolD might play an important role in DNA replication likely together with PabpolB, suggesting that archaea require two DNA polymerases at the replication fork
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
P81412 and P81409
the enzyme has a template-primer preference which is characteristic of a replicative DNA polymerase
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme plays an essential role in DNA replication, repair, and recombination
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. B-family DNA polymerases from hyperthermophilic archaea recognize the presence of uracil in DNA and stall DNA synthesis. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency is substantially enhanced by the initiation of DNA synthesis. The generation of ds DNA is significantly inhibited, however, by the presence of template uracil. Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution. Single molecules of Pol B1 bind to template uracil and stall DNA synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the enzyme bypasses DNA adducts pyrrolo-deoxycytosine, dP, N6-furfuryl-deoxyadenosine, and 1,N6-ethenodeoxyadenosine in a process known as translesion synthesis
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine, the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Saccharomyces cerevisiae BY4742
P13382
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Geobacillus stearothermophilus Donc
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus caldophilus GH24
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus thermophilus M1
K4Q1U9
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Sulfolobus solfataricus MT4
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Escherichia coli JH39
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermotoga petrophila K4
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermotoga petrophila K4
E2RWL8
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Escherichia coli K12
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus aquaticus YT1
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Thermus aquaticus INValphaF
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
Sulfolobus solfataricus P1
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine, the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis 2-OH-dATP is predominantly incorporated opposite guanine and thymine, the Y-family DNA polymerases promote mutagenesis through the erroneous incorporation of oxidized dNTPs during DNA synthesis. 2-OH-dATP is predominantly incorporated opposite guanine and thymine
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
show the reaction diagram
-
-
-
-
?
additional information
?
-
-
Neq L and Neq S are needed to form the active DNA polymerase that possesses higher proofreading activity. The genetically protein splicing-processed Neq P shows the same properties as the protein trans-spliced Neq C
-
-
-
additional information
?
-
-
PolH can be up-regulated by DNA breaks induced by ionizing radiation or chemotherapeutic agents, and knockdown of PolH gives cells resistance to apoptosis induced by DNA breaks in multiple cell lines and cell types in a p53-dependent manner. PolH has a role in the DNA damage checkpoint. POlH is target of p53
-
-
-
additional information
?
-
-
the enzyme is responsible for mutagenesis, e.g. UV-induced, in human host cells of lungs of cystic fibrosis patients contributing to morbidity and mortality of these people, with a striking correlation between mutagenesis and the persistence of Pseudomonas aeruginosa, mechanisms of mutagenesis, enzyme regulation, overview, the enzyme is responsible for resistance to to nitrofurazone and 4-nitroquinoline-1-oxide toxification
-
-
-
additional information
?
-
-
all pols exclusively promote misincorporation of dCMP opposite a 2'-deoxyinosine lesion during translesion synthesis, isozymes pol alpha, pol eta, and pol kappaDELTAC promote preferential incorporation of 2'-deoxycytidine monophosphate , the wrong base, opposite a 2'-deoxyinosine lesion, no incorporation of 2'-deoxythymidine monophosphate, the correct base, is observed opposite the lesion
-
-
-
additional information
?
-
-
replication cycle of Dpo4, and induced fit and translocation mechanisms, overview
-
-
-
additional information
?
-
-
the R2 polymerase can utilize both RNA and DNA templates, but the processivity of the enzyme on single stranded DNA templates is higher than its processivity on RNA templates, R2-RT is also capable of synthesizing the second DNA strand during retrotransposition
-
-
-
additional information
?
-
-
the widely used anticancer drug, cis-diamminedichloroplatinum(II), i.e. cisplatin, reacts with adjacent purine bases in DNA to form predominantly cis-[Pt(NH3)2(d(GpG)-N7(1),-N7(2))] intrastrand cross-links, DNA polymerase IV is able to perform translesion synthesis in the presence of DNA-distorting damage such as cisplatin-DNA adducts, overview
-
-
-
additional information
?
-
-
comparing RNA primer-templates and DNA primer templates of identical sequence show that herpes polymerase greatly prefers to elongate the DNA primer by 650-26000fold, thus accounting for the extremely low efficiency with which herpes polymerase elongates primase-synthesized primers
-
-
-
additional information
?
-
-
the catalytic efficiency of PolX is almost the same with and without dNTPs, whereas that of the domain mixture increases on the addition of dNTPs
-
-
-
additional information
?
-
-
the DNA polymerase gene of Thermococcus marinus contains an intein inserted at the pol-b site
-
-
-
additional information
?
-
E2RWL8, -
DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
-
-
-
additional information
?
-
Thermotoga petrophila, Thermotoga petrophila K4
-
only the enzyme mutant T326A/L324A/Q384A/F388A/m4008A/Y438A shows RNA-dependent DNA polymerase activity, EC 2.7..7.49
-
-
-
additional information
?
-
Thermotoga petrophila K4
E2RWL8
DNA-dependent DNA polymerase commonly accepts DNA and dNTP and excludes RNA and rNTP, but some enzyme mutants also show RNA-dependent DNA polymerase activity as reverse transcriptases, overview. Reverse transcriptase is the enzyme that catalyzes DNA polymerization using RNA as a template, i.e. RNA-dependent DNA polymerase, see for EC 2.7.7.49
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Ca2+
Q97W02
bound to the active site, structure, overview
Ca2+
-
Ca2+ (but not Ba2+, Co2+, Cu2+, Ni2+, or Zn2+) is a cofactor for Dpo4-catalyzed polymerization with both native and 8-oxoG-containing DNA templates. Both dNTP and ddNTP are substrates of the polymerase in the presence of either Mg2+ or Ca2+. No pyrophosphorolysis occurs in the presence of Ca2+
Co2+
-
can partially replace Mg2+ in activation, optimal concentration: 2.5 mM
Fe2+
-
required, in [4Fe-4S] clusters, that are bound to the CysB motif in all yeast B family DNA polymerases, assembly of the essential Fe-S cluster is strictly dependent on the function of mitochondrial Nfs1 and cytosolic Nbp35. The C-terminal domain of the catalytic subunit binds the Fe-S cluster in the CysB motif requiring all Cys residues of motif Cysb
K+
-
optimal concentration: 0.22 mM, DNA polymerase gamma
K+
Herpes simplex virus, Homo sapiens
-
-
K+
-
100-200 mM KCl, stimulates Novikoff hepatoma DNA polymerase beta 2fold
K+
Ruellia sp.
-
stimulates
K+
-
stimulates at 50 mM, inhibition at higher concentrations
K+
-
stimulates at 10-55 mM KCl
K+
-
stimulates at 100 mM
K+
-
optimal concentration: 0.025 mM
K+
-
stimulates
K+
-
stimulates; stimulates at 100-200 mM
K+
-
5-100 mM; stimulates; stimulates at 100-200 mM
K+
-
stimulates at 125 mM, inhibition at higher concentrations
K+
-
optimal concentration for wild-type enzyme: 50 mM, optimal concentration for G418/E507Q mutant: 100 mM
K+
-
optimal concentration: 50 mM
K+
-
optimal processivity at 100-150 mM
K+
A0SXL5
over 80% of maximal activity is obtained with KCl concentrations of 50-80 mM, with a maximum at 60 mM
K+
-
pols beta, iota and zeta exhibit maximal activity under conditions of moderate KCl concentrations of 20-60 mM
KCl
-
optimal concentration is 20 mM
KCl
-
optimal concentration of 80 mM
KCl
B6E9X1
required, optimal at 85 mM
KCl
P81409
optimum: 25-150 mM
KCl
P0CL76, Q9V2F3 and Q9V2F4
optimal concentration: 40 mM; optimal concentration: 50-80 mM
KCl
Q6DRD3
activates best at 10 mM
KCl
Q7LYT8
optimum salt concentration is either 50 mM KCl or 75 mM NaCl
Mg2+
P03156
enzyme prefers Mg2+ over Mn2+
Mg2+
-
DNA polymerase alpha: increasing concentrations of Mg2+ lead to a dramatically increased affinity for poly(dT) and poly(dC) polypyrimidines, has little or no effect on the interaction of the enzyme with poly(dA); free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum, catalytic core binds primer through a Mg2+-chelate, with each of 4 Mg2+ ions acting to coordinate 2 phosphodiester groups
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
stimulates at 12 mM, DNA polymerase gamma
Mg2+
Herpes simplex virus
-
stimulates at 3 mM
Mg2+
-
stimulates at 4-8 mM
Mg2+
-
stimulates at 5-10 mM, polymerase beta
Mg2+
-
divalent cation required, Mg2+ or Mn2+; stimulates at 4 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+; optimal concentration: 6 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+; stimulates at 9 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
optimal concentration for polymerase C and N2: 10 mM, optimal concentration for polymerase N1: 20 mM
Mg2+
Ruellia sp.
-
required
Mg2+
-
required
Mg2+
-
optimal concentration: 6 mM; required
Mg2+
-
MgCl2 is the preferred cofactor compared to MnCl2, CoCl2 and NiCl2; optimal concentration: 2-4 mM; required
Mg2+
-
stimulates at 70 mM
Mg2+
-
optimal concentration: 12 mM
Mg2+
-
optimal concentration: 8 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+; optimal concentration: 5-30 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+; optimal concentration: 20-30 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+; optimal concentration: 10 mM
Mg2+
-
exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+, mutant D190A shows preference for Mn2+
Mg2+
-
higher polymerase activity with Mg2+ than with Mn2+, exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+
Mg2+
-
enzyme prefers Mn2+ over Mg2+ for RNase H activity
Mg2+
-
optimal concentration: 8 mM
Mg2+
-
enzyme prefers Mg2+ over Mn2+
Mg2+
-
enzyme prefers Mn2+ over Mg2+ for RTHI activity; enzyme prefers Mn2+ over Mg2+ for RTHI nuclease activity
Mg2+
P74918
PI-TfuI utilizes either Mg2+ or Mn2+, PI-TfuII only utilizes Mg2+
Mg2+
-
divalent cation required, optimal concentration is 5 mm
Mg2+
-
maximal activity at 8.75 mM
Mg2+
-
optimal concentration is 3 mM
Mg2+
-
DNA polymerase lambda is not able to perform de novo DNA synthesis in the absence of a metal ion activator. Synthesis of de novo DNA is much stronger with Mn2+ than with Mg2+
Mg2+
-
synthesizes DNA processively in the presence of Mn2+ and Mg2+, optimal Mg2+ concentration is 3 mM
Mg2+
Q29Y55
activates, optimal concentration is 1.5-2.5 mM
Mg2+
-
peak activity in the presence of Mg2+ is observed in the range of 0.1-0.5 mM and is significantly reduced at concentrations above 2 mM
Mg2+
-
poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
Mg2+
-
optimal processivity at 6 mM, no synthesis is observed in the absence of Mg2+
Mg2+
-
binding of Mg2+-dNTP to Pol X facilitates subsequent formation of the catalytically competent Pol X-DNA-dNTP ternary complex, Pol X prefers an ordered sequential mechanism with Mg2+-dNTP as the first substrate
Mg2+
-
DNA polymerase iota contains two catalytic Mg2+ ions in the active site
Mg2+
A0SXL5
no activity is detected in the absence of magnesium, activity is maximal between 1.5 and 3.0 mM MgCl2
Mg2+
-
highly dependent on MgCl2 in the range of 0-20 mM with maximal activity at 14 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
-
PolX has Mg2+-dependent 5'-3' DNA polymerase activity
Mg2+
-
pol zeta functions best in the presence of 1-5mM MgCl2, but exhibits dramatically lower activity in the presence of MnCl2
Mg2+
-
cofactor for both the polymerase and pyrophosphorolysis activities
Mg2+
P95690
the enzyme requires an extremely low concentration of Mg+2 cations for activity. A broad plateau is observed between 0.1 and 2 mM MgCl2. Concentrations above 2 mM are inhibitory. 20% of the activity of the plateau value is still observed even if no MgCl2 is added to the assay
Mg2+
-
highly dependent on MgCl2, with maximal activity at 14 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
B6E9X1
polI activity is absolutely dependent on the presence of divalent cations Mg2+ and Mn2+, Mn2+ cannot be replaced with Mg2+ completely, optimal at 8 mM
Mg2+
-
maximal activity at 4-10 mM Mg2+
Mg2+
-
required, substrate-like inhibition by Mg2+ occur
Mg2+
-
required, two metal ion mechanism, nucleotide binds to the enzyme as an Mg–dNTP-2 complex, overview. Mg2+ enforces tetrahedral geometry
Mg2+
-
required
Mg2+
P13382
required
Mg2+
-
highly dependent on MgCl2, with maximal activity at 12 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
H9CW54
activates
Mg2+
P0CL76, Q9V2F3 and Q9V2F4
oprtimal concentration: 15-20 mM; optimal concentration: 3 mM
Mg2+
O59610
the negative charge and the side-chain length of D259 might play a supporting role in coordinating the conserved Mg2+ to the correct position at the active center in the exonuclease domain
Mg2+
O57863 and O57861
optimal magnesium concentration is 17.5 mM
Mg2+
E2RWL8, -
required
Mg2+
Q6DRD3
activates, Mn2+ shows a 8.6fold higher catalytic efficiency than Mg2+
Mg2+
-
required
Mg2+
Q7LYT8
divalent cation required. Maximum activity is observed with 6 mM MgCl2, whereas about 50% activity is obtained with MnCl2 at its optimal concentration of 6 mM
Mg2+
-
Mg2+-dependent DNA-polymerizing activity
Mg2+
Q07635
DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+; DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+; DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+; DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+
MgCl2
P81409
optimal concentration: 10 mM
MgCl2
-
optimal concentration: 5 mM
Mn2+
P03156
enzyme prefers Mg2+ over Mn2+
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
-
Mn2+
-
stimulates at 0.5-0.6 mM, 5fold more effective than optimal Mg2+ concentration
Mn2+
Herpes simplex virus, Homo sapiens
-
-
Mn2+
-
activates DNA polymerase beta; optimal concentration: 1 mM, DNA polymerase beta
Mn2+
-
divalent cation required, Mn2+ or Mg2+; stimulates at 0.2 mM
Mn2+
-
25% of the activity with Mg2+; divalent cation required, Mn2+ or Mg2+; optimal concentration: 0.1 mM
Mn2+
-
divalent cation required, Mn2+ or Mg2+; stimulates at 0.5 mM, about a third the maximal activity with Mg2+
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
can partially replace Mg2+ in activation
Mn2+
-
can partially replace Mg2+ in activation
Mn2+
-
can partially replace Mg2+ in activation
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
divalent cation required, Mn2+ or Mg2+; stimulates at 0.4 mM
Mn2+
-
divalent cation required, Mn2+ or Mg2+; stimulates at 0.4-0.8 mM; stimulates at 0.4 mM
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+, mutant D190A shows preference for Mn2+
Mn2+
-
enzyme prefers Mn2+ over Mg2+ for RNase H activity, optimal concentration: 1.5-2.5 mM
Mn2+
-
enzyme prefers Mg2+ over Mn2+
Mn2+
-
enzyme prefers Mn2+ over Mg2+ for RTHI nuclease activity
Mn2+
P74918
PI-TfuI utilizes either Mg2+ or Mn2+, PI-TfuII only utilizes Mg2+
Mn2+
-
DNA polymerase lambda is not able to perform de novo DNA synthesis in the absence of a metal ion activator. Synthesis of de novo DNA is much stronger with Mn2+ than with Mg2+
Mn2+
-
synthesizes DNA processively in the presence of Mn2+ and Mg2+
Mn2+
Q29Y55
optimal Mn2+ concentration is 0.5 mM
Mn2+
-
DNA polymerase iota exhibits the greatest activity in the presence of low levels of Mn2+ (0.05-0.25 mM). Mn2+ increases the catalytic activity of DNA polymerase iota by about 30000-60000fold through a strong decrease in the Km value for nucleotide incorporation. Whereas DNA polymerase iota preferentially misinserts G opposite T by a factor of about 1.4-2.5fold over the correct base A in the presence of 0.25 and 5 mM Mg2+, respectively, the correct insertion of A is actually favored 2fold over the misincorporation of guanine in the presence of 0.075 mM Mn2+. Low levels of Mn2+ also dramatically increase the ability of DNA polymerase iota to traverse a variety of DNA lesions in vitro. The cation utilized by DNA polymerase iota in vivo may be Mn2+
Mn2+
-
incorporation of the NNTPs is observed only in the presence of its optimal activator, Mn2+; poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
Mn2+
-
the polymerase activity of PolX is strongly stimulated by Mn2+
Mn2+
-
pol iota displays its highest activity in the presence of MnCl2 at low concentrations of 0.05-0.1mM, its activity also peaks at low Mg2+, but is considerably higher in the presence of Mn2+
Mn2+
B6E9X1
polI activity is absolutely dependent on the presence of divalent cations Mg2+ and Mn2+, Mn2+ cannot be replaced with Mg2+ completely
Mn2+
-
supports chemistry, but leads to markedly decreased fidelity by accelerating the rate of incorporation of mismatches, routinely used to generate random mutations during PCR. Mn2+ accommodates square planar, tetrahedral, and octahedral coordination
Mn2+
-
activates
Mn2+
Q6DRD3
activates, Mn2+ shows a 8.6fold higher catalytic efficiency than Mg2+
Mn2+
Q7LYT8
divalent cation required. Maximum activity is observed with 6 mM MgCl2, whereas about 50% activity is obtained with MnCl2 at its optimal concentration of 6 mM
Mn2+
Q07635
DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+; DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+; DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+; DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+
Na+
-
0.2 M, stimulates phage T5-induced enzyme
Na+
-
50 mM stimulates DNA polymerase beta 2fold
Na+
-
pols beta, iota and zeta exhibit maximal activity under conditions of moderate NaCl concentrations of 20-60 mM
NaCl
B6E9X1
required, optimal at 100 mM
NaCl
Q6DRD3
activates best at 50 mM
NaCl
-
optimal concentration: 0-75 mM
NaCl
Q7LYT8
optimum salt concentration is either 50 mM KCl or 75 mM NaCl
NH4+
-
0.2 M, stimulates phage T5-induced enzyme
NH4Cl
B6E9X1
required, optimal at 80 mM
Zn2+
-
pol I contains one Zn2+ per molecule
Zn2+
-
10-13% of the activity with Mg2+, optimal concentration: 0.3-0.5 mM
Zn2+
-
increases enzymatic activity, no absolute dependence on zinc
Zn2+
-
required, Zn2+ is bound to the CysA motif in yeast B family DNA polymerases
Mn2+
Q54324
in a MnCl2-soaked crystal, a Mn2+ is bound to one of the oxygens of the Asp111 side chain
additional information
-
the PolX catalytic domain exhibits no polymerase activity with 5 mM Zn2+, Ni2+, Ca2+ or Co2+, or without a metal ion
additional information
B6E9X1
polI activity requires the presence of monovalent ions, above 100 mM, monovalent salts become inhibitory for the activity
additional information
-
Ca2+ supports nucleotide binding but not catalysis
additional information
-
DNA binding, dNTP binding and catalytic activity of mutant enzyme in the presence of two metal ions, Mg2+ and Mn2+, overview. Amino acid residues D378 and D531 are mainly responsible for the binding of metal chelated substrate dNTP
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
(2E)-2-(3-nitro-4-[[6-(trifluoromethyl)pyridin-3-yl]sulfanyl]benzylidene)-5-thioxo-1,3-thiazolidin-4-one
-
-
(2E)-2-(4-chloro-3-ethylbenzylidene)-5-thioxo-1,3-thiazolidin-4-one
-
-
(2E)-2-(pentafluorobenzylidene)-5-thioxodihydrothiophen-3(2H)-one
-
-
(2E)-2-[4-(2-hydroxyethyl)-3-nitrobenzylidene]-5-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-(4-chloro-3-nitrobenzylidene)-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[3-bromo-4-[(4-fluorobenzyl)oxy]benzylidene]-1,3-thiazolidine-2,4-dione
-
-
(5Z)-5-[3-bromo-4-[(4-fluorophenyl)sulfanyl]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[3-nitro-4-(pyridin-3-ylsulfanyl)benzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-(4-methylphenoxy)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-(cyclohexylsulfanyl)-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-bromophenyl)sulfanyl]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-chlorophenyl)sulfanyl]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-fluorobenzyl)oxy]-3-nitrobenzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-fluorobenzyl)oxy]benzylidene]-2-thioxo-1,3-thiazolidin-4-one
-
-
(5Z)-5-[4-[(4-methylphenyl)sulfanyl]-3-nitrobenzylidene]-3-(prop-2-en-1-yl)-2-thioxo-1,3-thiazolidin-4-one
-
-
(9-adenylmethylcarbonyl)-4-aminobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
(biphenylcarbonyl)-4-oxobutyl triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A; inhibits wild-type enzyme and mutant enzyme Y505A
(E)-enedione
-
-
(NH4)2SO4
-
optimal concentration of 20 mM, inhibition below and above 20 mM
1,10-phenanthroline
-
-
1,2,3,4-tetrahydro-5-methoxynaphthalene-1,4-diol
-
i.e. nodulisporol. Strong inhibition of pol lambda, but does not influence the activities of mammalian pols alpha to kappa, and shows no effect on the activities of plant pols alpha and beta, prokaryotic pols, and other DNA metabolic enzymes such as calf terminal deoxynucleotidyl transferase, human immunodeficiency virus type-1 (HIV-1) reverse transcriptase, human telomerase, T7 RNA polymerase, and bovine deoxyribonuclease I
1,3-bis[2-chloroethyl]-2-nitrosourea
-
-
1-deoxyrubralactone
-
potent inhibitor of isozymes pol kappa, pol lambda, pol iota, and pol eta, but does not inhibit DNA polymerase isozymes pol delta, pol epsilon, and pol gamma
1-deoxyrubralactone
-
potent inhibitor
10-epi pyragonicin
-
-
16-oxoaphidicholin
-
-
19-epi jimenezin
-
-
2',3'-dideoxy-ATP
-
poor inhibitor
2',3'-dideoxyribosylthymine triphosphate
-
17% and 33% inhibition are observed with ddTTP/dTTP ratios of 1:1 and 5:1, respectively
2',3'-dideoxythymidine 5'-triphosphate
Ruellia sp.
-
-
2',3'-dideoxythymidine 5'-triphosphate
-
-
2',3'-dideoxythymidine 5'-triphosphate
-
-
2',3'-dideoxythymidine 5'-triphosphate
-
-
2-(4-azidophenacyl)thio-2'-deoxyadenosine 5'-triphosphate
-
template-competitive DNA polymerase inhibitor
-
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha at 100fold lower concentration than DNA polymerase delta
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
polymerase delta and epsilon
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
phage T4 enzyme inhibited with lower sensitivity than other members of the B family DNA polymerases
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
inhibition of DNA polymerase alpha
2-(p-n-Butylanilino)-2'-deoxyadenosine 5'-triphosphate
-
-
2-butylanilino-dATP
-
potent and highly selective inhibitor
2-methoxy-4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 2,4-dichlorobenzoate
-
-
2-methoxy-4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl 3-bromobenzoate
-
-
2-thiomethyl-6-phenyl-4-(4'-hydroxybutyl)-1,2,4,-triazole (5,1-C)(1,2,4)triazine-7-one triphosphate
-
fully competitive with respect to the nucleotide substrate dTTP; fully competitive with respect to the nucleotide substrate dTTP, inhibits wild-type enzyme and mutant enzyme Y505A
3'-azido-2',3'-dideoxythymidine 5'-phosphate
-
50% inhibition at 0.22 mM
3'-azido-2',3'-dideoxythymidine triphosphate
-
-
3,4-dihydro-4-hydroxy-8-methoxynaphthalen-1(2H)-one
-
i.e. nodulisporone. Strong inhibition of pol lambda, but does not influence the activities of mammalian pols alpha to kappa, and shows no effect on the activities of plant pols alpha and beta, prokaryotic pols, and other DNA metabolic enzymes such as calf terminal deoxynucleotidyl transferase, human immunodeficiency virus type-1 (HIV-1) reverse transcriptase, human telomerase, T7 RNA polymerase, and bovine deoxyribonuclease I
3,5-dimethyl-8-methoxy-3,4-dihydroisocoumarin
-
-
3-(2'-deoxy-beta-D-erythro-pentofuranosyl) pyrimido[1,2-alpha]purin-10(3H)-one
-
i.e. M1dG. When paired opposite cytosine in duplex DNA at physiological pH,M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG. To improve the understanding of the basis for M1dG-induced mutagenesis, the mechanism of translesion DNA synthesis opposite M1dG by the model Y-family polymerase Dpo4 is studied at a molecular level using kinetic and structural approaches. Steady-state and transient-state kinetic results both indicate that Dpo4 catalysis is inhibited by M1dG (260-2900-fold), with dATP being the favored insertion event for both sequences tested
-
3-epiaphidicholine
-
-
-
35dd(G) DNA
-
competitive inhibition
-
4-chloromercuribenzoic acid
-
-
4-chloromercuribenzoic acid
-
-
4-chlorophenyl 2,4-dinitrophenyl sulfide
-
-
4-hydroxy-5-methyl-3-tetradecyl-dihydrofuran-2(3H)-one
-
-
4-hydroxymercuribenzoate
-
95% inhibition at 0.4 mM