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Information on EC 2.7.7.7 - DNA-directed DNA polymerase and Organism(s) Pyrococcus abyssi and UniProt Accession P0CL76
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2.7.7.7 DNA-directed DNA polymeraseIUBMB Comments
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.
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Word Map
- 2.7.7.7
- strand
-
single-stranded
-
fidelity
-
holoenzyme
- mismatch
- bacteriophage
- pcna
- fork
- polymerization
- aphidicolin
- duplex
-
proofreading
-
calf
- endonuclease
- thymus
-
clamp
-
misincorporation
- helicase
-
abasic
-
template-primer
- 5'-triphosphate
- dntps
-
stall
- thymine
-
error-free
- mispairs
-
anneal
-
sliding
-
uv-induced
-
incoming
-
exonucleolytic
- replisome
-
transversions
- deoxyribonucleoside
- xeroderma
- pigmentosum
- ssdna
-
deoxynucleotide
-
hypermutation
-
undamaged
-
okazaki
- dtmp
-
slippage
-
cyclobutane
- transcriptases
- dnab
-
watson-crick
-
high-fidelity
-
myeloblastosis
- aquaticus
- synthesis
- analysis
- drug development
- diagnostics
- biotechnology
- medicine
- molecular biology
The taxonomic range for the selected organisms is: Pyrococcus abyssi
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
dna polymerase alpha, dna polymerase beta, dna polymerase iii, pol beta, klenow fragment, dna polymerase delta, taq dna polymerase, pol delta, pol alpha, dna polymerase gamma, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
deoxynucleate polymerase
-
-
-
-
deoxyribonucleate nucleotidyltransferase
-
-
-
-
deoxyribonucleic acid duplicase
-
-
-
-
deoxyribonucleic acid polymerase
-
-
-
-
deoxyribonucleic duplicase
-
-
-
-
deoxyribonucleic polymerase
-
-
-
-
deoxyribonucleic polymerase I
-
-
-
-
DNA duplicase
-
-
-
-
DNA nucleotidyltransferase
-
-
-
-
DNA nucleotidyltransferase (DNA-directed)
-
-
-
-
DNA polmerase beta
-
-
-
-
DNA polymerase
DNA polymerase alpha
-
-
-
-
DNA polymerase gamma
-
-
-
-
DNA polymerase I
-
-
-
-
DNA polymerase II
DNA polymerase III
-
-
-
-
DNA replicase
-
-
-
-
DNA-dependent DNA polymerase
-
-
-
-
duplicase
-
-
-
-
Klenow fragment
-
-
-
-
nucleotidyltransferase, deoxyribonucleate
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-
-
-
Pol gamma
-
-
-
-
sequenase
-
-
-
-
Taq DNA polymerase
-
-
-
-
Taq Pol I
-
-
-
-
Tca DNA polymerase
-
-
-
-
DNA polymerase
-
-
-
-
DNA polymerase II
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleotidyl group transfer
-
-
-
-
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.
CAS REGISTRY NUMBER
COMMENTARY
9012-90-2
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
poly(dA)/oligo(dT)x + n dTTP
poly(dA)/oligo(dT)x+n + n diphosphate
preferred substrate
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
polB and polD preferentially insert dAMP opposite an apurinic/apyrimidinic site, albeit inefficiently
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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
-
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
-
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
-
-
?
additional information
?
-
-
DNA polymerase switching mechanism by which PabPol B displaces PabPol D from proliferating cell nuclear antigen on the DNA duplex
-
-
?
additional information
?
-
primer ssM13 DNA is the preferred substrate
-
-
?
additional information
?
-
primer ssM13 DNA is the preferred substrate
-
-
?
additional information
?
-
-
DNA polymerases PolB and PolD slip in vitro on a template that consists of single-stranded DNA (ssDNA) with a hairpin structure flanked by short direct repeats. Pyrococcus abyssi proliferating cell nuclear antigen increases replication fidelity of this template
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
PabPolD might play an important role in DNA replication likely together with PabpolB, suggesting that archaea require two DNA polymerases at the replication fork
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
-
varying magnesium concentration affects both slippage and overall DNA synthesisof DNA polymerase PolB and PolD. There is almost no synthesis by PolB, PolD or their exo-forms at low magnesium concentrations (0.10.5 mM). Synthesis is also inhibited at 1520 mM. Parental molecules are readily detectable together with heteroduplex molecules at low to medium magnesium concentrations (15 mM)
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
no inhibition by 0.1 mM aphidicolin
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 7.5
pH 6.5: about 65% of maximal activity, pH 9.2: about 20% of maximal activity, potassium phosphate buffer
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
the optimal temperature for polymerase activity could not be measured because activated DNA is not stable above 75°C
additional information
the optimal temperature for polymerase activity could not be measured because activated DNA is not stable above 75°C
additional information
the optimal temperature for polymerase activity could not be measured because activated DNA is not stable above 75°C
additional information
the optimal temperature for polymerase activity could not be measured because activated DNA is not stable above 75°C
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
139700
x * 68100 (polB) + x * 139700 (polc), calculated from sequence
140000
x * 90000 (polB) + x * 140000 (polC), SDS-PAGE
68100
x * 68100 (polB) + x * 139700 (polc), calculated from sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
x * 68100 (polB) + x * 139700 (polc), calculated from sequence
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
the (G)-PYF box is located in a hydrophobic region close to the active site. The (G)-PYF box mutants exhibit altered DNA binding properties. In addition, the thermal stability of all mutants is reduced compared to that of wild type, and this effect could be attributed to increased exposure of the hydrophobic region
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
the (G)-PYF box motif mediates intersubunit interactions, which may be crucial for the thermostability of the enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Palud, A.; Villani, G.; LHaridon, S.; Querellou, J.; Raffin, J.P.; Henneke, G.
Intrinsic properties of the two replicative DNA polymerases of Pyrococcus abyssi in replicating abasic sites: possible role in DNA damage tolerance?
Mol. Microbiol.
70
746-761
2008
Pyrococcus abyssi
Gueguen, Y.; Rolland, J.L.; Lecompte, O.; Azam, P.; Le Romancer, G.; Flament, D.; Raffin, J.P.; Dietrich, J.
Characterization of two DNA polymerases from the hyperthermophilic euryarchaeon Pyrococcus abyssi
Eur. J. Biochem.
268
5961-5969
2001
Pyrococcus abyssi (P0CL76), Pyrococcus abyssi (Q9V2F3 and Q9V2F4)
Dietrich, J.; Schmitt, P.; Zieger, M.; Preve, B.; Rolland, J.L.; Chaabihi, H.; Gueguen, Y.
PCR performance of the highly thermostable proof-reading B-type DNA polymerase from Pyrococcus abyssi
FEMS Microbiol. Lett.
217
89-94
2002
Pyrococcus abyssi, Pyrococcus abyssi Orsay
Henneke, G.; Flament, D.; Huebscher, U.; Querellou, J.; Raffin, J.P.
The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication
J. Mol. Biol.
350
53-64
2005
Pyrococcus abyssi
Rouillon, C.; Henneke, G.; Flament, D.; Querellou, J.; Raffin, J.P.
DNA polymerase switching on homotrimeric PCNA at the replication fork of the euryarchaea Pyrococcus abyssi
J. Mol. Biol.
369
343-355
2007
Pyrococcus abyssi, Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543
Castrec, B.; Laurent, S.; Henneke, G.; Flament, D.; Raffin, J.P.
The glycine-rich motif of Pyrococcus abyssi DNA polymerase D is critical for protein stability
J. Mol. Biol.
396
840-848
2010
Pyrococcus abyssi
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