DB code: M00173
| RLCP classification | 3.103.90020.1135 : Transfer | |
|---|---|---|
| CATH domain | 3.30.420.10 : Nucleotidyltransferase; domain 5 | |
| 1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4 | ||
| 3.30.70.370 : Alpha-Beta Plaits | Catalytic domain | |
| 1.10.150.20 : DNA polymerase; domain 1 | Catalytic domain | |
| E.C. | 2.7.7.7 | |
| CSA | ||
| M-CSA | ||
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 1.10.150.20 : DNA polymerase; domain 1 | M00055 M00104 M00175 M00208 D00158 |
| 1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4 | M00055 M00175 |
| 3.30.420.10 : Nucleotidyltransferase; domain 5 | M00206 T00252 M00019 M00020 M00055 M00135 M00146 M00166 M00175 M00186 |
| 3.30.70.370 : Alpha-Beta Plaits | M00055 M00104 M00175 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| P00581 |
DNA polymerase
|
EC
2.7.7.7
T7 DNA polymerase |
NP_041982.1
(Protein)
NC_001604.1 (DNA/RNA sequence) |
PF00476
(DNA_pol_A)
[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 |
|---|---|---|---|---|---|
| P00581 | DPOL_BPT7 | Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). | Composed of two subunits. One is encoded by the phage and the other is encoded by the host thioredoxin. |
| 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 |
|||||||||
| 1t7pA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1skrA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sksA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1skwA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl0A01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl0C01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl1A01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl2A01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1t8eA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tk0A01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tk5A01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tk8A01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tkdA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1x9mA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1x9sA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1x9wA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1t7pA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1skrA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sksA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1skwA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl0A02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl0C02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl1A02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl2A02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1t8eA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tk0A02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tk5A02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tk8A02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tkdA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1x9mA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1x9sA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1x9wA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1t7pA03 |
|
|
|
|
|
Bound:2x_MG | Unbound | Analogue:G-C-C-A-G-T-G-C-C-A-2DA (chain P) | Unbound | Unbound | |
| 1skrA03 |
|
|
|
|
|
Bound:2x_MG | Unbound | Analogue:G-C-C-A-G-T-G-C-C-A-2DA (chain P) | Unbound | Unbound | |
| 1sksA03 |
|
|
|
|
|
Unbound | Unbound | Analogue:G-G-C-C-A-G-T-G-C-C-2DT (chain P) | Unbound | Unbound | |
| 1skwA03 |
|
|
|
|
|
Unbound | Unbound | Analogue:C-A-G-T-G-C-C-2DT (chain P) | Unbound | Unbound | |
| 1sl0A03 |
|
|
|
|
|
Unbound | Unbound | Analogue:G-G-C-C-A-G-T-G-C-C-2DT (chain P) | Unbound | Unbound | |
| 1sl0C03 |
|
|
|
|
|
Unbound | Unbound | Analogue:G-G-C-C-A-G-T-G-C-C-2DT (chain Q) | Unbound | Unbound | |
| 1sl1A03 |
|
|
|
|
|
Unbound | Unbound | Analogue:C-A-G-T-G-C-C-T-2DA (chain P) | Unbound | Unbound | |
| 1sl2A03 |
|
|
|
|
|
Bound:2x_MG | Unbound | Analogue:C-A-G-T-G-C-C-T-2DA (chain P) | Unbound | Unbound | |
| 1t8eA03 |
|
|
|
|
|
Bound:2x_MG | Unbound | Analogue:C-G-A-A-A-A-C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-2DT (chain C) | Unbound | Unbound | |
| 1tk0A03 |
|
|
|
|
|
Bound:2x_MG | Unbound | Analogue:C-G-G-C-C-A-G-T-G-C-C-A-DDG (chain P) | Unbound | Unbound | |
| 1tk5A03 |
|
|
|
|
|
Unbound | Unbound | Analogue:G-C-C-A-G-T-G-C-C-A-DDG (chain P) | Unbound | Unbound | |
| 1tk8A03 |
|
|
|
|
|
Bound:2x_MG | Unbound | Analogue:A-C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-2DA (chain P) | Unbound | Unbound | |
| 1tkdA03 |
|
|
|
|
|
Bound:2x_MG | Unbound | Analogue:C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-DOC (chain C) | Unbound | Unbound | |
| 1x9mA03 |
|
|
|
|
|
Unbound | Unbound | Analogue:G-T-A-G-T-G-T-G-A-2DT (chain C) | Unbound | Unbound | |
| 1x9sA03 |
|
|
|
|
|
Unbound | Unbound | Analogue:G-G-T-A-G-T-G-T-G-A-2DT (chain P) | Unbound | Unbound | |
| 1x9wA03 |
|
|
|
|
|
Unbound | Unbound | Analogue:G-G-T-A-G-T-G-T-G-A-2DT (chain C) | Unbound | Unbound | |
| 1t7pA04 |
|
|
|
|
|
Unbound | Analogue:DG3 | Unbound | Unbound | Unbound | |
| 1skrA04 |
|
|
|
|
|
Unbound | Analogue:DAD | Unbound | Unbound | Unbound | |
| 1sksA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1skwA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl0A04 |
|
|
|
|
|
Unbound | Analogue:DAD | Unbound | Unbound | Unbound | |
| 1sl0C04 |
|
|
|
|
|
Unbound | Analogue:DAD | Unbound | Unbound | Unbound | |
| 1sl1A04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1sl2A04 |
|
|
|
|
|
Unbound | Analogue:DAD | Unbound | Unbound | Unbound | |
| 1t8eA04 |
|
|
|
|
|
Unbound | Analogue:DCT | Unbound | Unbound | Unbound | |
| 1tk0A04 |
|
|
|
|
|
Unbound | Analogue:DCT | Unbound | Unbound | Unbound | |
| 1tk5A04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1tk8A04 |
|
|
|
|
|
Unbound | Analogue:D3T | Unbound | Unbound | Unbound | |
| 1tkdA04 |
|
|
|
|
|
Unbound | Analogue:D3T | Unbound | Unbound | Unbound | |
| 1x9mA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1x9sA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1x9wA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | |
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| PDB;1kfn, 1krp, 1ksp, 2kfn, 2kfz, 2kzm, 2kzz & literature [25] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1t7pA01 |
|
|
|
|
|
|||||
| 1skrA01 |
|
|
|
|
|
|||||
| 1sksA01 |
|
|
|
|
|
|||||
| 1skwA01 |
|
|
|
|
|
|||||
| 1sl0A01 |
|
|
|
|
|
|||||
| 1sl0C01 |
|
|
|
|
|
|||||
| 1sl1A01 |
|
|
|
|
|
|||||
| 1sl2A01 |
|
|
|
|
|
|||||
| 1t8eA01 |
|
|
|
|
|
|||||
| 1tk0A01 |
|
|
|
|
|
|||||
| 1tk5A01 |
|
|
|
|
|
|||||
| 1tk8A01 |
|
|
|
|
|
|||||
| 1tkdA01 |
|
|
|
|
|
|||||
| 1x9mA01 |
|
|
|
|
|
|||||
| 1x9sA01 |
|
|
|
|
|
|||||
| 1x9wA01 |
|
|
|
|
|
|||||
| 1t7pA02 |
|
|
|
|
|
|||||
| 1skrA02 |
|
|
|
|
|
|||||
| 1sksA02 |
|
|
|
|
|
|||||
| 1skwA02 |
|
|
|
|
|
|||||
| 1sl0A02 |
|
|
|
|
|
|||||
| 1sl0C02 |
|
|
|
|
|
|||||
| 1sl1A02 |
|
|
|
|
|
|||||
| 1sl2A02 |
|
|
|
|
|
|||||
| 1t8eA02 |
|
|
|
|
|
|||||
| 1tk0A02 |
|
|
|
|
|
|||||
| 1tk5A02 |
|
|
|
|
|
|||||
| 1tk8A02 |
|
|
|
|
|
|||||
| 1tkdA02 |
|
|
|
|
|
|||||
| 1x9mA02 |
|
|
|
|
|
|||||
| 1x9sA02 |
|
|
|
|
|
|||||
| 1x9wA02 |
|
|
|
|
|
|||||
| 1t7pA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1skrA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1sksA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1skwA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1sl0A03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1sl0C03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1sl1A03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1sl2A03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1t8eA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1tk0A03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1tk5A03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1tk8A03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1tkdA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1x9mA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1x9sA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1x9wA03 |
|
|
|
|
|
ASP 475;ALA 476;ASP 654(Two Mg2+ binding) | ||||
| 1t7pA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1skrA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1sksA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1skwA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1sl0A04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1sl0C04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1sl1A04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1sl2A04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1t8eA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1tk0A04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1tk5A04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1tk8A04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1tkdA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1x9mA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1x9sA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| 1x9wA04 |
|
|
|
|
|
HIS 506;ARG 518;LYS 522;TYR 526 | GLY 478 | |||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[1]
|
p.254-256 | |
|
[2]
|
Fig.4, p.61 | |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) |
| Medline ID | 98101638 |
| PubMed ID | 9440688 |
| Journal | Nature |
| Year | 1998 |
| Volume | 391 |
| Pages | 251-8 |
| Authors | Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T |
| Title | Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. |
| Related PDB | 1t7p |
| Related UniProtKB | P00581 |
| [2] | |
| 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 | |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 15235589 |
| Journal | Nat Struct Mol Biol |
| Year | 2004 |
| Volume | 11 |
| Pages | 784-90 |
| Authors | Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T |
| Title | Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7. |
| Related PDB | 1skr 1sks 1skw 1sl0 1sl1 1sl2 |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 15297882 |
| Journal | EMBO J |
| Year | 2004 |
| Volume | 23 |
| Pages | 3452-61 |
| Authors | Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T |
| Title | Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. |
| Related PDB | 1t8e 1tk0 1tk5 1tk8 1tkd |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 15528277 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2004 |
| Volume | 101 |
| Pages | 16186-91 |
| Authors | Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T |
| Title | Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis. |
| Related PDB | 1x9m 1x9s 1x9w |
| Related UniProtKB | |
| Comments |
|---|
|
This enzyme belongs to the DNA polymerase type-A family.
Although this enzyme belongs to the DNA polymerase type-A family, According to the literature [1] & [2], (1) The metal ion A (bound to Asp475 & Asp654) 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 (Gly478, |
| Created | Updated |
|---|---|
| 2004-03-03 | 2009-02-26 |