DB code: M00019

RLCP classification 3.103.90020.1131 : Transfer
CATH domain 3.30.-.- :
3.30.420.10 : Nucleotidyltransferase; domain 5
3.30.70.270 : Alpha-Beta Plaits Catalytic domain
1.10.287.280 : Helix Hairpins Catalytic domain
3.90.710.10 :
E.C. 2.7.7.7
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.287.280 : Helix Hairpins M00104
3.30.420.10 : Nucleotidyltransferase; domain 5 M00206 T00252 M00020 M00055 M00135 M00146 M00166 M00173 M00175 M00186
3.30.70.270 : Alpha-Beta Plaits M00206 M00135 M00146 M00166 M00209

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P56689 DNA polymerase
EC 2.7.7.7
TO POL
PF00136 (DNA_pol_B)
PF03104 (DNA_pol_B_exo1)
[Graphical View]
Q56366 DNA polymerase
EC 2.7.7.7
PF00136 (DNA_pol_B)
PF03104 (DNA_pol_B_exo1)
[Graphical View]
Q7SIG7 DNA polymerase
EC 2.7.7.7
D Tok Pol
PF00136 (DNA_pol_B)
PF03104 (DNA_pol_B_exo1)
[Graphical View]

KEGG enzyme name
DNA-directed DNA polymerase
DNA polymerase I
DNA polymerase II
DNA polymerase III
DNA polymerase alpha
DNA polymerase beta
DNA polymerase gamma
DNA nucleotidyltransferase (DNA-directed)
DNA nucleotidyltransferase (DNA-directed)
deoxyribonucleate nucleotidyltransferase
deoxynucleate polymerase
deoxyribonucleic acid duplicase
deoxyribonucleic acid polymerase
deoxyribonucleic duplicase
deoxyribonucleic polymerase
deoxyribonucleic polymerase I
DNA duplicase
DNA nucleotidyltransferase
DNA polymerase
DNA replicase
DNA-dependent DNA polymerase
duplicase
Klenow fragment
sequenase
Taq DNA polymerase
Taq Pol I
Tca DNA polymerase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P56689 DPOL_THEGO Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Q56366 DPOL_THES9 Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Q7SIG7 DPOL_DESST Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Binds 2 magnesium ions.

KEGG Pathways
Map code Pathways E.C.
MAP00240 Pyrimidine metabolism
MAP00230 Purine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00677 C00039 C00013 C00039
E.C.
Compound Magnesium Deoxynucleoside triphosphate DNA(n) Pyrophosphate DNA(n+1)
Type divalent metal (Ca2+, Mg2+) nucleotide nucleic acids phosphate group/phosphate ion nucleic acids
ChEBI 18420
29888
PubChem 888
1023
21961011
1tgoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qhtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qqcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1d5aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gcxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tgoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qhtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qqcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Unbound Unbound
1d5aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Unbound Unbound
1gcxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tgoA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qhtA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qqcA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1d5aA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gcxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tgoA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qhtA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qqcA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1d5aA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gcxA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1tgoA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qhtA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qqcA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1d5aA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1gcxA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [12] & [17]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1tgoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qhtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qqcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1d5aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gcxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tgoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qhtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qqcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1d5aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gcxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tgoA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 404;ASP 542(Magnesium binding)
1qhtA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 404;ASP 542(Magnesium binding)
1qqcA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 404;ASP 542(Magnesium binding)
1d5aA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 404;ASP 542(Magnesium binding)
1gcxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 404;ASP 542(Magnesium binding)
1tgoA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 460;LYS 464;LYS 487;ASN 491
1qhtA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 460;LYS 464;LYS 487;ASN 491
1qqcA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 460;LYS 464;LYS 487;ASN 491
1d5aA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 460;LYS 464;LYS 487;ASN 491
1gcxA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 460;LYS 464;LYS 487;ASN 491
1tgoA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qhtA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qqcA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1d5aA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gcxA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[12]
p.453-456
[17]
p.471-473

References
[1]
Resource
Comments
Medline ID
PubMed ID 9757117
Journal Acta Crystallogr D Biol Crystallogr
Year 1998
Volume 54
Pages 994-5
Authors Zhou M, Mao C, Rodriguez AC, Kiefer JR, Kucera RB, Beese LS
Title Crystallization and preliminary diffraction analysis of a hyperthermostable DNA polymerase from a Thermococcus archaeon.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9685491
Journal Nucleic Acids Res
Year 1998
Volume 26
Pages 3746-52
Authors Aravind L, Koonin EV
Title Phosphoesterase domains associated with DNA polymerases of diverse origins.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 10430556
Journal Genetics
Year 1999
Volume 152
Pages 1249-67
Authors Cann IK, Ishino Y
Title Archaeal DNA replication: identifying the pieces to solve a puzzle.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 10348896
Journal J Biochem (Tokyo)
Year 1999
Volume 125
Pages 983-6
Authors Hashimoto H, Matsumoto T, Nishioka M, Yuasa T, Takeuchi S, Inoue T, Fujiwara S, Takagi M, Imanaka T, Kai Y
Title Crystallographic studies on a family B DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10075991
Journal Nucleic Acids Res
Year 1999
Volume 27
Pages 1609-18
Authors Aravind L, Koonin EV
Title DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID 99199230
PubMed ID 10097083
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 3600-5
Authors Hopfner KP, Eichinger A, Engh RA, Laue F, Ankenbauer W, Huber R, Angerer B
Title Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.
Related PDB 1tgo
Related UniProtKB P56689
[7]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10545321
Journal Structure Fold Des
Year 1999
Volume 7
Pages 1189-99
Authors Zhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J
Title Crystal structure of an archaebacterial DNA polymerase.
Related PDB 1d5a 1qqc
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11027519
Journal Biochem Biophys Res Commun
Year 2000
Volume 276
Pages 600-6
Authors Henneke G, Raffin JP, Ferrari E, Jonsson ZO, Dietrich J, Hubscher U
Title The PCNA from Thermococcus fumicolans functionally interacts with DNA polymerase delta.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10997874
Journal DNA Res
Year 2000
Volume 7
Pages 243-51
Authors Iwai T, Kurosawa N, Itoh YH, Kimura N, Horiuchi T
Title Sequence analysis of three family B DNA polymerases from the thermoacidophilic crenarchaeon Sulfurisphaera ohwakuensis.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10827184
Journal J Biol Chem
Year 2000
Volume 275
Pages 24693-700
Authors Ma WP, Kaiser MW, Lyamicheva N, Schaefer JJ, Allawi HT, Takova T, Neri BP, Lyamichev VI
Title RNA template-dependent 5' nuclease activity of Thermus aquaticus and Thermus thermophilus DNA polymerases.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11071805
Journal J Mol Biol
Year 2000
Volume 304
Pages 1-9
Authors de Vega M, Lazaro JM, Salas M
Title Phage phi 29 DNA polymerase residues involved in the proper stabilisation of the primer-terminus at the 3'-5' exonuclease active site.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10860752
Journal J Mol Biol
Year 2000
Volume 299
Pages 447-62
Authors Rodriguez AC, Park HW, Mao C, Beese LS
Title Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.
Related PDB 1qht
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11024170
Journal Nucleic Acids Res
Year 2000
Volume 28
Pages 3910-7
Authors Bohlke K, Pisani FM, Vorgias CE, Frey B, Sobek H, Rossi M, Antranikian G
Title PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11058140
Journal Nucleic Acids Res
Year 2000
Volume 28
Pages 4391-6
Authors Saves I, Eleaume H, Dietrich J, Masson JM
Title The thy pol-2 intein of Thermococcus hydrothermalis is an isoschizomer of PI-TliI and PI-TfuII endonucleases.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11584001
Journal J Biol Chem
Year 2001
Volume 276
Pages 45484-90
Authors Liu L, Komori K, Ishino S, Bocquier AA, Cann IK, Kohda D, Ishino Y
Title The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11319225
Journal J Biol Chem
Year 2001
Volume 276
Pages 27376-83
Authors Shen Y, Musti K, Hiramoto M, Kikuchi H, Kawarabayashi Y, Matsui I
Title Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11178906
Journal J Mol Biol
Year 2001
Volume 306
Pages 469-77
Authors Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y
Title Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.
Related PDB 1gcx
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11443345
Journal J Mol Evol
Year 2001
Volume 52
Pages 419-25
Authors Takemura M
Title Poxviruses and the origin of the eukaryotic nucleus.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11959500
Journal Curr Opin Struct Biol
Year 2002
Volume 12
Pages 217-24
Authors Jeruzalmi D, O'Donnell M, Kuriyan J
Title Clamp loaders and sliding clamps.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12445650
Journal FEMS Microbiol Lett
Year 2002
Volume 217
Pages 89-94
Authors Dietrich J, Schmitt P, Zieger M, Preve B, Rolland JL, Chaabihi H, Gueguen Y
Title PCR performance of the highly thermostable proof-reading B-type DNA polymerase from Pyrococcus abyssi.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12415300
Journal Nat Rev Mol Cell Biol
Year 2002
Volume 3
Pages 826-35
Authors Davey MJ, Jeruzalmi D, Kuriyan J, O'Donnell M
Title Motors and switches: AAA+ machines within the replisome.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12415291
Journal Nat Struct Biol
Year 2002
Volume 9
Pages 922-7
Authors Fogg MJ, Pearl LH, Connolly BA
Title Structural basis for uracil recognition by archaeal family B DNA polymerases.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 11788711
Journal Nucleic Acids Res
Year 2002
Volume 30
Pages 482-96
Authors Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV
Title A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the DNA polymerase type-B family.
Although the structure of the C-terminal domain is slightly different from counterparts of bacteriophage, this enzyme shares similar catalytic domains and catalytic residues with the counterparts (M00020 in EzCatDB).
Thus, the catalytic mechanism of DNA polymerase must be similar to that of the counterpart (M00020 in EzCatDB).

Created Updated
2004-03-16 2018-04-23