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Information on EC 2.7.7.7 - DNA-directed DNA polymerase and Organism(s) Thermococcus kodakarensis and UniProt Accession P77933
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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: Thermococcus kodakarensis
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
-
-
-
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deoxyribonucleate nucleotidyltransferase
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-
-
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deoxyribonucleic acid duplicase
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-
-
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deoxyribonucleic acid polymerase
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-
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deoxyribonucleic duplicase
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-
-
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deoxyribonucleic polymerase
-
-
-
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deoxyribonucleic polymerase I
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-
-
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DNA duplicase
-
-
-
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DNA nucleotidyltransferase
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-
-
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DNA nucleotidyltransferase (DNA-directed)
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-
-
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DNA polmerase beta
-
-
-
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DNA polymerase
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-
-
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DNA polymerase alpha
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-
-
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DNA polymerase gamma
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-
-
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DNA polymerase I
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-
-
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DNA polymerase II
-
-
-
-
DNA polymerase III
-
-
-
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DNA replicase
-
-
-
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DNA-dependent DNA polymerase
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-
-
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duplicase
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-
-
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Klenow fragment
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-
-
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nucleotidyltransferase, deoxyribonucleate
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-
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Pol gamma
-
-
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sequenase
-
-
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Taq DNA polymerase
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-
-
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Taq Pol I
-
-
-
-
Tca DNA polymerase
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-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleotidyl group transfer
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-
-
-
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
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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
-
-
-
?
deoxynucleoside triphosphate + DNAn
diphosphate + DNAn+1
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
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
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-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts
-
-
?
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
-
-
-
?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
diphosphate + DNAn+1
-
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
75
73
-
optimal temperature for an equimolar dNTP pool is 72.5°C. The optimum temperature shifts to lower temperatures when the dNTP pool composition is biased
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop method. The Thumb domain of DNA polymerase shows an opened conformation. The fingers subdomain possesses many basic residues at the side of the polymerase active site. The residues are considered to be accessible to the incoming dNTP by electrostatic interaction. A beta-hairpin motif (residues 242-249) extends from the exonuclease domain as seen in the editing complex of the RB69 DNA polymerase from bacteriophage RB69. Many arginine residues are located at the forked-point (the junction of the template-binding and editing clefts) of KOD DNA polymerase, suggesting that the basic environment is suitable for partitioning of the primer and template DNA duplex and for stabilizing the partially melted DNA structure in the high-temperature environments
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
N210D
the mutant enzyme shows very weak 3'-5'-exonuclease activity compared to the wild-type enzyme (0.1%). No significant difference in DNA polymerase activity as compared with that of the wild-type enzyme. Mutation frequency in PCR becomes higher as 3'5' exonuclease activity decreases
Y311F
the mutant enzyme shows very weak 3'-5'-exonuclease activity compared to the wild-type enzyme (0.01%). No significant difference in DNA polymerase activity as compared with that of the wild-type enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
molecular biology
synthesis
-
the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved
molecular biology
long and accurate PCR can be achieved with a mixture of wild type DNA polymerase from Thermococcus kodakaraensis and its exonuclease deficient mutant enzyme N210D is utilized (at the ratio of 1:40)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Takagi, M.; Nishioka, M.; Kakihara, H.; Kitabayashi, M.; Inoue, H.; Kawakami, B.; Oka, M.; Imanaka, T.
Characterization of DNA polymerase from sp. strain KOD1 and its application to PCR
Appl. Environ. Microbiol.
63
4504-4510
1997
Thermococcus kodakarensis (P77933), Thermococcus kodakarensis
Griep, M.A.; Kotera, C.A.; Nelson, R.M.; Viljoen, H.J.
Kinetics of the DNA polymerase pyrococcus kodakaraensis
Chem. Eng. Sci.
61
3885-3892
2006
Thermococcus kodakarensis
-
Hashimoto, H.; Matsumoto, T.; Nishioka, M.; Yuasa, T.; Takeuchi, S.; Inoue, T.; Fujiwara, S.; Takagi, M.; Imanaka, T.; Kai, Y.
Crystallographic studies on a family B DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1
J. Biochem.
125
983-986
1999
Thermococcus kodakarensis
Hashimoto, H.; Nishioka, M.; Fujiwara, S.; Takagi, M.; Imanaka, T.; Inoue, T.; Kai, Y.
Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1
J. Mol. Biol.
306
469-477
2001
Thermococcus kodakarensis (P77933), Thermococcus kodakarensis
Nishioka, M.; Mizuguchi, H.; Fujiwara, S.; Komatsubara, S.; Kitabayashi, M.; Uemura, H.; Takagi, M.; Imanaka, T.
Long and accurate PCR with a mixture of KOD DNA polymerase and its exonuclease deficient mutant enzyme
J. Biotechnol.
88
141-149
2001
Thermococcus kodakarensis (P77933)
Cahova, H.; Panattoni, A.; Kielkowski, P.; Fanfrlik, J.; Hocek, M.
5-Substituted pyrimidine and 7-substituted 7-deazapurine dNTPs as substrates for DNA polymerases in competitive primer extension in the presence of natural dNTPs
ACS Chem. Biol.
11
3165-3171
2016
Geobacillus stearothermophilus, Thermococcus kodakarensis, Thermococcus litoralis (P30317), Pyrococcus woesei (P61876)
Yamashita, M.; Xu, J.; Morokuma, D.; Hirata, K.; Hino, M.; Mon, H.; Takahashi, M.; Hamdan, S.; Sakashita, K.; Iiyama, K.; Banno, Y.; Kusakabe, T.; Lee, J.
Characterization of recombinant Thermococcus kodakaraensis (KOD) DNA polymerases produced using silkworm-baculovirus expression vector system
Mol. Biotechnol.
59
221-233
2017
Thermococcus kodakarensis (P77933), Thermococcus kodakarensis, Thermococcus kodakarensis ATCC BAA-9180 (P77933)
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