DB code: M00020
| RLCP classification | 3.103.90020.1134 : Transfer | |
|---|---|---|
| CATH domain | 3.30.342.10 : DNA Polymerase; Chain A, domain 1 | |
| 3.30.420.10 : Nucleotidyltransferase; domain 5 | ||
| 3.90.-.- : | Catalytic domain | |
| 1.-.-.- : | Catalytic domain | |
| 1.20.-.- : | ||
| 3.-.-.- : | ||
| E.C. | 2.7.7.7 | |
| CSA | ||
| M-CSA | ||
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 3.30.420.10 : Nucleotidyltransferase; domain 5 | M00206 T00252 M00019 M00055 M00135 M00146 M00166 M00173 M00175 M00186 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| Q38087 |
DNA polymerase
|
EC
2.7.7.7
Gp43 |
NP_861746.1
(Protein)
NC_004928.1 (DNA/RNA sequence) |
PF00136
(DNA_pol_B)
PF03104 (DNA_pol_B_exo1) [Graphical View] |
| P04415 |
DNA polymerase
|
EC
2.7.7.7
Gp43 |
NP_049662.1
(Protein)
NC_000866.4 (DNA/RNA sequence) |
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 |
|---|---|---|---|---|---|
| Q38087 | DPOL_BPR69 | Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). | |||
| P04415 | DPOL_BPT4 | Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00230 | Purine metabolism | |
| MAP00240 | Pyrimidine metabolism |
| Compound table | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors | Substrates | Products | Intermediates | ||||||||
| KEGG-id | C02148 | C00677 | C00039 | C00013 | C00039 | ||||||
| E.C. | |||||||||||
| Compound | Divalent metal | Deoxynucleoside triphosphate | DNA(n) | Pyrophosphate | DNA(n+1) | ||||||
| Type | divalent metal (Ca2+, Mg2+) | nucleotide | nucleic acids | phosphate group/phosphate ion | nucleic acids | ||||||
| ChEBI |
29888 29888 |
||||||||||
| PubChem |
1023 21961011 1023 21961011 |
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| 1clqA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ig9A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ih7A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xC01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xD01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9yA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2C01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2D01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wajA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1noyA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1noyB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1nozA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1nozB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1clqA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ig9A02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ih7A02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xB02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xC02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xD02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9yA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2A02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2B02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2C02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2D02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafB02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wajA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1noyA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1noyB02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1nozA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1nozB02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1clqA03 |
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Analogue:_CA | Unbound | Unbound | Unbound | Unbound | |
| 1ig9A03 |
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Analogue:2x_CA | Bound:TTP | Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain P) | Unbound | Unbound | |
| 1ih7A03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xA03 |
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Analogue:2x_CA | Unbound | Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain I) | Unbound | Unbound | |
| 1q9xB03 |
|
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Analogue:2x_CA | Analogue:DGP_908 | Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain J) | Unbound | Unbound | |
| 1q9xC03 |
|
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Analogue:2x_CA | Analogue:DGP_908 | Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain K) | Unbound | Unbound | |
| 1q9xD03 |
|
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Analogue:2x_CA | Analogue:DGP_908 | Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain L) | Unbound | Unbound | |
| 1q9yA03 |
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Analogue:2x_CA | Bound:DCP | Analogue:G-C-G-G-A-C-T-G-C-T-T-A-C-DOC (chain P) | Unbound | Unbound | |
| 1rv2A03 |
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Unbound | Unbound | Unbound | Unbound | Bound:G-C-G-G-C-T-G-T-C-A-T-A-A-G-A (chain F) | |
| 1rv2B03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2C03 |
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Unbound | Unbound | Unbound | Unbound | Bound:G-C-G-G-C-T-G-T-C-A-T-A-A-G-A (chain J) | |
| 1rv2D03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafA03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafB03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wajA03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1clqA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ig9A04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ih7A04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xB04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xC04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xD04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9yA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2A04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2B04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2C04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2D04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafB04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wajA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1clqA05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ig9A05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ih7A05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xA05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xB05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xC05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xD05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9yA05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2A05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2B05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2C05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2D05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafA05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafB05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wajA05 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1clqA06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ig9A06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1ih7A06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xA06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xB06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xC06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9xD06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1q9yA06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2A06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2B06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2C06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1rv2D06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafA06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wafB06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1wajA06 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| literature [9] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1clqA01 |
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| 1ig9A01 |
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| 1ih7A01 |
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| 1q9xA01 |
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| 1q9xB01 |
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| 1q9xC01 |
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| 1q9xD01 |
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| 1q9yA01 |
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| 1rv2A01 |
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| 1rv2B01 |
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| 1rv2C01 |
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| 1rv2D01 |
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| 1wafA01 |
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| 1wafB01 |
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| 1wajA01 |
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| 1noyA01 |
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| 1noyB01 |
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| 1nozA01 |
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| 1nozB01 |
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| 1clqA02 |
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| 1ig9A02 |
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| 1ih7A02 |
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| 1q9xA02 |
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| 1q9xB02 |
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| 1q9xC02 |
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| 1q9xD02 |
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| 1q9yA02 |
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| 1rv2A02 |
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| 1rv2B02 |
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| 1rv2C02 |
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| 1rv2D02 |
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| 1wafA02 |
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| 1wafB02 |
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| 1wajA02 |
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| 1noyA02 |
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| 1noyB02 |
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| 1nozA02 |
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| 1nozB02 |
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| 1clqA03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1ig9A03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1ih7A03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1q9xA03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1q9xB03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1q9xC03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1q9xD03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1q9yA03 |
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ASP 414;LEU 415;ASP 626;SER 627(metal binding) | ||||
| 1rv2A03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1rv2B03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1rv2C03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1rv2D03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1wafA03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1wafB03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1wajA03 |
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ASP 411;LEU 412;ASP 623;SER 624(metal binding) | ||||
| 1clqA04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1ig9A04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1ih7A04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1q9xA04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1q9xB04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1q9xC04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1q9xD04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1q9yA04 |
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ARG 485;LYS 489;LYS 563;ASN 567 | ||||
| 1rv2A04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1rv2B04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1rv2C04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1rv2D04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1wafA04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1wafB04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1wajA04 |
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ARG 482;LYS 486;LYS 560;ASN 564 | ||||
| 1clqA05 |
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| 1ig9A05 |
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| 1ih7A05 |
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| 1q9xA05 |
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| 1q9xB05 |
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| 1q9xC05 |
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| 1q9xD05 |
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| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[4]
|
Fig.3, p.192 | 2 |
|
[9]
|
Fig.4, p.61 | |
|
[11]
|
p.8100 | |
|
[20]
|
p.661-665 | |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 1349852 |
| Journal | Cell |
| Year | 1992 |
| Volume | 69 |
| Pages | 425-37 |
| Authors | Kong XP, Onrust R, O'Donnell M, Kuriyan J |
| Title |
Three-dimensional structure of the beta subunit of E. |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 1314195 |
| Journal | FEBS Lett |
| Year | 1992 |
| Volume | 300 |
| Pages | 141-4 |
| Authors | Strick R, Knopf CW |
| Title | Improved band shift assay for the simultaneous analysis of protein-DNA interactions and enzymatic functions of DNA polymerases. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7903401 |
| Journal | J Mol Biol |
| Year | 1993 |
| Volume | 234 |
| Pages | 915-25 |
| Authors | Kuriyan J, O'Donnell M |
| Title | Sliding clamps of DNA polymerases. |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8594347 |
| Journal | Methods Enzymol |
| Year | 1995 |
| Volume | 262 |
| Pages | 189-202 |
| Authors | Eckstein F, Thomson JB |
| Title | Phosphate analogs for study of DNA polymerases. |
| Related PDB | |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-388. |
| Medline ID | 96292335 |
| PubMed ID | 8679562 |
| Journal | Biochemistry |
| Year | 1996 |
| Volume | 35 |
| Pages | 8110-9 |
| Authors | Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA |
| Title | Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. |
| Related PDB | 1noy 1noz |
| Related UniProtKB | P04415 |
| [6] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9265627 |
| Journal | Biochemistry |
| Year | 1997 |
| Volume | 36 |
| Pages | 10474-81 |
| Authors | Goodrich LD, Lin TC, Spicer EK, Jones C, Konigsberg WH |
| Title | Residues at the carboxy terminus of T4 DNA polymerase are important determinants for interaction with the polymerase accessory proteins. |
| Related PDB | |
| Related UniProtKB | |
| [7] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS). |
| Medline ID | 97358535 |
| PubMed ID | 9215631 |
| Journal | Cell |
| Year | 1997 |
| Volume | 89 |
| Pages | 1087-99 |
| Authors | Wang J, Sattar AK, Wang CC, Karam JD, Konigsberg WH, Steitz TA |
| Title | Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69. |
| Related PDB | 1waf 1waj |
| Related UniProtKB | Q38087 |
| [8] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9665721 |
| Journal | Biochemistry |
| Year | 1998 |
| Volume | 37 |
| Pages | 10156-63 |
| Authors | Otto MR, Bloom LB, Goodman MF, Beechem JM |
| Title | Stopped-flow fluorescence study of precatalytic primer strand base-unstacking transitions in the exonuclease cleft of bacteriophage T4 DNA polymerase. |
| Related PDB | |
| Related UniProtKB | |
| [9] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9519297 |
| Journal | Curr Opin Struct Biol |
| Year | 1998 |
| Volume | 8 |
| Pages | 54-63 |
| Authors | Brautigam CA, Steitz TA |
| Title | Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. |
| Related PDB | |
| Related UniProtKB | |
| [10] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10387009 |
| Journal | Biochemistry |
| Year | 1999 |
| Volume | 38 |
| Pages | 7696-709 |
| Authors | Alley SC, Shier VK, Abel-Santos E, Sexton DJ, Soumillion P, Benkovic SJ |
| Title | Sliding clamp of the bacteriophage T4 polymerase has open and closed subunit interfaces in solution. |
| Related PDB | |
| Related UniProtKB | |
| [11] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10387055 |
| Journal | Biochemistry |
| Year | 1999 |
| Volume | 38 |
| Pages | 8094-101 |
| Authors | Yang G, Lin T, Karam J, Konigsberg WH |
| Title | Steady-state kinetic characterization of RB69 DNA polymerase mutants that affect dNTP incorporation. |
| Related PDB | |
| Related UniProtKB | |
| [12] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF COMPLEX WITH GP45. |
| Medline ID | 20004392 |
| PubMed ID | 10535734 |
| Journal | Cell |
| Year | 1999 |
| Volume | 99 |
| Pages | 155-66 |
| Authors | Shamoo Y, Steitz TA |
| Title | Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. |
| Related PDB | 1clq 1b8h |
| Related UniProtKB | Q38087 |
| [13] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10616725 |
| Journal | Nucleosides Nucleotides |
| Year | 1999 |
| Volume | 18 |
| Pages | 2193-9 |
| Authors | Stattel JM, Wright GE |
| Title | Sensitivity of bacteriophage RB69 DNA polymerase to N2-(p-n-butylphenyl)-2'-deoxyguanosine nucleotides. |
| Related PDB | |
| Related UniProtKB | |
| [14] | |
| Resource | |
| Comments | |
| Medline ID | |
| 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 | |
| Related UniProtKB | |
| [15] | |
| Resource | |
| Comments | |
| 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 | |
| Related UniProtKB | |
| [16] | |
| Resource | |
| Comments | |
| 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 | |
| Related UniProtKB | |
| [17] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11401565 |
| Journal | Biochemistry |
| Year | 2001 |
| Volume | 40 |
| Pages | 7180-91 |
| Authors | Berdis AJ |
| Title | Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase. |
| Related PDB | |
| Related UniProtKB | |
| [18] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11504721 |
| Journal | J Biol Chem |
| Year | 2001 |
| Volume | 276 |
| Pages | 39340-9 |
| Authors | Alley SC, Trakselis MA, Mayer MU, Ishmael FT, Jones AD, Benkovic SJ |
| Title | Building a replisome solution structure by elucidation of protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme. |
| Related PDB | |
| Related UniProtKB | |
| [19] | |
| Resource | |
| Comments | |
| 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 | |
| Related UniProtKB | |
| [20] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11389835 |
| Journal | Cell |
| Year | 2001 |
| Volume | 105 |
| Pages | 657-67 |
| Authors | Franklin MC, Wang J, Steitz TA |
| Title | Structure of the replicating complex of a pol alpha family DNA polymerase. |
| Related PDB | 1ig9 1ih7 |
| Related UniProtKB | |
| [21] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12162740 |
| Journal | Biochemistry |
| Year | 2002 |
| Volume | 41 |
| Pages | 10256-61 |
| Authors | Yang G, Franklin M, Li J, Lin TC, Konigsberg W |
| Title | A conserved Tyr residue is required for sugar selectivity in a Pol alpha DNA polymerase. |
| Related PDB | |
| Related UniProtKB | |
| [22] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12087102 |
| Journal | J Biol Chem |
| Year | 2002 |
| Volume | 277 |
| Pages | 33041-8 |
| Authors | Petrov VM, Ng SS, Karam JD |
| Title | Protein determinants of RNA binding by DNA polymerase of the T4-related bacteriophage RB69. |
| Related PDB | |
| Related UniProtKB | |
| [23] | |
| 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 | |
| [24] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 15057283 |
| Journal | EMBO J |
| Year | 2004 |
| Volume | 23 |
| Pages | 1483-93 |
| Authors | Hogg M, Wallace SS, Doublie S |
| Title | Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site. |
| Related PDB | 1rv2 |
| Related UniProtKB | |
| [25] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 15057282 |
| Journal | EMBO J |
| Year | 2004 |
| Volume | 23 |
| Pages | 1494-505 |
| Authors | Freisinger E, Grollman AP, Miller H, Kisker C |
| Title | Lesion (in)tolerance reveals insights into DNA replication fidelity. |
| Related PDB | 1q9x 1q9y |
| Related UniProtKB | |
| Comments |
|---|
|
This enzyme belongs to the DNA polymerase type-B family.
In the CATH definition, On the third domain, According to the literature [9] & [11], (1) The metal ion A activates 3'-OH of DNA by lowering its pKa. (2) The activated 3'-O atom makes a nucleophilic attack on the alpha-phosphate group of dNTP, (3) The negative charges on the transferred group (alpha-phoshate) and the leaving group (beta-phosphate and gamma-phosphate) are stabilized by the metal ions and stabilizers on the fourth domain (Arg482, |
| Created | Updated |
|---|---|
| 2004-03-03 | 2009-02-26 |