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Information on EC 2.7.7.7 - DNA-directed DNA polymerase and Organism(s) Sulfolobus acidocaldarius and UniProt Accession Q4JB80
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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: Sulfolobus acidocaldarius
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
Saci_0554
deoxynucleate polymerase
-
-
-
-
deoxyribonucleate nucleotidyltransferase
-
-
-
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deoxyribonucleic acid duplicase
-
-
-
-
deoxyribonucleic acid polymerase
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-
-
-
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
-
-
-
-
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
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
DNA polymerase Dpo4 can replicate past a variety of DNA lesions. When replicating undamaged DNA, the enzyme is prone to make base pair substitutions
-
-
?
dATP + DNAn
?
-
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
?
-
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
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
-
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
-
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
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
-
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
-
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
-
-
?
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
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
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
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2',3'-dideoxyribosylthymine triphosphate
-
17% and 33% inhibition are observed with ddTTP/dTTP ratios of 1:1 and 5:1, respectively
additional information
no inhibition by 0.02 mg/ml aphidicolin. The enzyme is inhibited by dideoxy- and arabinosine-analogs and SH-blocking agents
-
additional information
-
the enzyme is resistant to 0.02 mg/ml aphidicolin
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
kinetic study of dNTP primer-extension opposite a benzo[a]pyrene-N2-dG-adduct with four DNA polymerases, including Sulfolobus solfataricus Dpo4 and Sulfolobus acidocaldarius Dbh. Vmax/Km is similar for correct dCTP insertion with Dpo4 and Dbh. Compared to Dpo4, Dbh misinsertion is slower for dATP (about 20fold), dGTP (about 110fold) and dTTP (about 6fold), due to decreases in Vmax. These findings provide support that Dbh is in the same Y-Family DNA polymerase class as eukaryotic DNA polymerase kappa and bacterial DNA polymerase IV, which accurately bypass N2-dG adducts
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 8
pH 5.5: about 70% of maximal activity, pH 8.0: about 20% of maximal activity, maximal activity in 50 mM potassium phosphate buffer
6.5 - 9
-
pH 6.5: about 70% of maximal activity, pH 9.0: about 70% of maximal activity
7 - 9.5
pH 7.0: about 70% of maximal activity, pH 9.5: about 70% of maximal activity, in 50 mM Tris-HCl buffer
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37 - 65
activity at 65°C (optimum) is 20fold higher than at 37°C. A rapid 10fold increase occurs at 70-80°C
55 - 80
-
55°C: about 45% of maximal activity, 80°C: about 45% of maximal activity, substrate activated calf-thymus DNA
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
100000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of mutant enzyme K242R/I243K/P244S are grown at room temperature by hanging-drop vapor diffusion, 2.4 A resolution crystal structure
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K242R/I243K/P244S
mutation of three linker amino acids, polymerase Dbh adopts the standard conformation of polymerase Dpo4. The interdomain linker also affects the single-base deletion frequency and the mispair extension efficiency of these polymerase
additional information
generaion of chimeras of Sulfolobus solfataricus DNA polymerase Dpo4 and Sulfolobus acidocaldarius DNA polymerase Dbh in which their little finger domains have been interchanged. Interestingly, by replacing the little finger domain of Dbh with that of Dpo4, the enzymatic properties of the chimeric enzyme are more Dpo4-like in that the enzyme is more processive, can bypass an abasic site and a thymine-thymine cyclobutane pyrimidine dimer, and predominantly makes base pair substitutions when replicating undamaged DNA. The converse is true for the Dpo4-LF-Dbh chimera, which is more Dbh-like in its processivity and ability to bypass DNA adducts and generate single-base deletion errors. The unique but variable little finger domain of Y-family polymerases plays a major role in determining the enzymatic and biological properties of each individual Y-family member
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, in the presence of 20% glycerol, no substantial loss of activity after several weeks
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Forterre, P.; Elie, C.; Sioud, M.; Hamal, A.
Studies on DNA polymerases and topoisomerases in archaebacteria
Can. J. Microbiol.
35
228-233
1989
Sulfolobus acidocaldarius, Thermoplasma acidophilum
deLucia, A.M.; Chaudhuri, S.; Potapova, O.; Grindley, N.D.; Joyce, C.M.
The properties of steric gate mutants reveal different constraints within the active sites of Y-family and A-family DNA polymerases
J. Biol. Chem.
281
27286-27291
2006
Sulfolobus acidocaldarius
Salhi, S.; Elie, C.; Jean-Jean, O.; Meunier-Rotival, M.; Forterre, P.; Rossignol, J.M.; de Recondo, A.M.
The DNA polymerase from the archaebacterium Sulfolobus acidocaldarius: a thermophilic and thermoresistant enzyme which can perform automated polymerase chain reaction
Biochem. Biophys. Res. Commun.
167
1341-1347
1990
Sulfolobus acidocaldarius
Sakofsky, C.J.; Foster, P.L.; Grogan, D.W.
Roles of the Y-family DNA polymerase Dbh in accurate replication of the Sulfolobus genome at high temperature
DNA Repair
11
391-400
2012
Sulfolobus acidocaldarius (Q4JB80), Sulfolobus acidocaldarius
Elie, C.; De Recondo, A.M.; Forterre, P.
Thermostable DNA polymerase from the archaebacterium Sulfolobus acidocaldarius. Purification, characterization and immunological properties
Eur. J. Biochem.
178
619-626
1989
Sulfolobus acidocaldarius, Sulfolobus acidocaldarius DSM 639
Salhi, S.; Elie, C.; Forterre, P.; de Recondo, A.M.; Rossignol, J.M.
DNA polymerase from Sulfolobus acidocaldarius. Replication at high temperature of long stretches of single-stranded DNA
J. Mol. Biol.
209
635-644
1989
Sulfolobus acidocaldarius
Klimczak, L.J.; Grummt, F.; Burger, K.J.
Purification and characterization of DNA polymerase from the archaebacterium Sulfolobus acidocaldarius
Nucleic Acids Res.
13
5269-5282
1985
Sulfolobus acidocaldarius (P95690), Sulfolobus acidocaldarius DSM 639 (P95690)
Bukhrashvili, I.S.; Chinchaladze, D.Z.; Lavrik, O.I.; Levina, A.S.; Nevinsky, G.A.; Prangishvili, D.A.
Comparison of initiating abilities of primers of different length in polymerization reactions catalyzed by DNA polymerases from thermoacidophilic archaebacteria
Biochim. Biophys. Acta
1008
102-107
1989
Sulfolobus acidocaldarius, Thermoplasma acidophilum
Chinchaladze, D.Z.; Prangishvili, D.A.; Scamrov, A.V.; Beabealashvili, R.S.; Dyatkina, N.B.; Krayevsky, A.A.
Nucleoside 5'-triphosphates modified at sugar residues as substrates for DNA polymerase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius
Biochim. Biophys. Acta
1008
113-115
1989
Sulfolobus acidocaldarius
Boudsocq, F.; Kokoska, R.J.; Plosky, B.S.; Vaisman, A.; Ling, H.; Kunkel, T.A.; Yang, W.; Woodgate, R.
Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication
J. Biol. Chem.
279
32932-32940
2004
Sulfolobus acidocaldarius (Q4JB80), Saccharolobus solfataricus (Q97W02), Saccharolobus solfataricus P2 (Q97W02), Sulfolobus acidocaldarius DSM 639 (Q4JB80)
Mukherjee, P.; Wilson, R.C.; Lahiri, I.; Pata, J.D.
Three residues of the interdomain linker determine the conformation and single-base deletion fidelity of Y-family translesion polymerases
J. Biol. Chem.
289
6323-6331
2014
Sulfolobus acidocaldarius (Q4JB80), Sulfolobus acidocaldarius DSM 639 (Q4JB80)
Sholder, G.; Loechler, E.L.
A method to accurately quantitate intensities of (32)P-DNA bands when multiple bands appear in a single lane of a gel is used to study dNTP insertion opposite a benzo[a]pyrene-dG adduct by Sulfolobus DNA polymerases Dpo4 and Dbh
DNA Repair
25
97-103
2014
Sulfolobus acidocaldarius, Saccharolobus solfataricus
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