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. |
|---|---|---|
| MAP00230 | Purine metabolism | |
| MAP00240 | Pyrimidine 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 18420 |
29888 29888 |
|||||||||
| PubChem |
888 888 |
1023 21961011 1023 21961011 |
|||||||||
| 1tgoA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qhtA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qqcA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1d5aA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1gcxA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tgoA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qhtA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qqcA02 |
|
|
|
|
|
Bound:2x_MG | Unbound | Unbound | Unbound | Unbound | |
| 1d5aA02 |
|
|
|
|
|
Bound:2x_MG | Unbound | Unbound | Unbound | Unbound | |
| 1gcxA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tgoA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qhtA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qqcA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1d5aA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1gcxA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tgoA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qhtA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qqcA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1d5aA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1gcxA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tgoA05 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qhtA05 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1qqcA05 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1d5aA05 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1gcxA05 |
|
|
|
|
|
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 |
|
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|||||
| 1qhtA01 |
|
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|
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| 1qqcA01 |
|
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|
|||||
| 1d5aA01 |
|
|
|
|
|
|||||
| 1gcxA01 |
|
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|
|
|||||
| 1tgoA02 |
|
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|
|||||
| 1qhtA02 |
|
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| 1qqcA02 |
|
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|
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| 1d5aA02 |
|
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|
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| 1gcxA02 |
|
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|
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| 1tgoA03 |
|
|
|
|
|
ASP 404;ASP 542(Magnesium binding) | ||||
| 1qhtA03 |
|
|
|
|
|
ASP 404;ASP 542(Magnesium binding) | ||||
| 1qqcA03 |
|
|
|
|
|
ASP 404;ASP 542(Magnesium binding) | ||||
| 1d5aA03 |
|
|
|
|
|
ASP 404;ASP 542(Magnesium binding) | ||||
| 1gcxA03 |
|
|
|
|
|
ASP 404;ASP 542(Magnesium binding) | ||||
| 1tgoA04 |
|
|
|
|
|
ARG 460;LYS 464;LYS 487;ASN 491 | ||||
| 1qhtA04 |
|
|
|
|
|
ARG 460;LYS 464;LYS 487;ASN 491 | ||||
| 1qqcA04 |
|
|
|
|
|
ARG 460;LYS 464;LYS 487;ASN 491 | ||||
| 1d5aA04 |
|
|
|
|
|
ARG 460;LYS 464;LYS 487;ASN 491 | ||||
| 1gcxA04 |
|
|
|
|
|
ARG 460;LYS 464;LYS 487;ASN 491 | ||||
| 1tgoA05 |
|
|
|
|
|
|||||
| 1qhtA05 |
|
|
|
|
|
|||||
| 1qqcA05 |
|
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|||||
| 1d5aA05 |
|
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|
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|||||
| 1gcxA05 |
|
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|
|
|
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| 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, |
| 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. |
| 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, Thus, |
| Created | Updated |
|---|---|
| 2004-03-16 | 2009-02-26 |