DB code: M00055
| RLCP classification | 3.103.90020.1141 : Transfer | |
|---|---|---|
| 1.15.10100.1172 : Hydrolysis | ||
| CATH domain | 3.40.50.1010 : Rossmann fold | |
| 1.10.150.20 : DNA polymerase; domain 1 | ||
| 3.30.420.10 : Nucleotidyltransferase; domain 5 | Catalytic domain | |
| 1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4 | ||
| 3.30.70.370 : Alpha-Beta Plaits | Catalytic domain | |
| 1.10.473.10 : | Catalytic domain | |
| E.C. | 3.1.11.3 3.1.11.1 2.7.7.7 | |
| CSA | ||
| M-CSA | ||
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 1.10.150.20 : DNA polymerase; domain 1 | M00104 M00173 M00175 M00208 D00158 |
| 1.10.473.10 : | M00175 |
| 1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4 | M00173 M00175 |
| 3.30.420.10 : Nucleotidyltransferase; domain 5 | M00206 T00252 M00019 M00020 M00135 M00146 M00166 M00173 M00175 M00186 |
| 3.30.70.370 : Alpha-Beta Plaits | M00104 M00173 M00175 |
| 3.40.50.1010 : Rossmann fold | M00175 D00158 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| P00582 |
DNA polymerase I
|
POL I
EC 2.7.7.7 |
NP_418300.1
(Protein)
NC_000913.2 (DNA/RNA sequence) YP_491586.1 (Protein) NC_007779.1 (DNA/RNA sequence) |
PF01367
(5_3_exonuc)
PF02739 (5_3_exonuc_N) PF00476 (DNA_pol_A) PF01612 (DNA_pol_A_exo1) [Graphical View] |
| KEGG enzyme name |
|---|
|
exodeoxyribonuclease (lambda-induced)
(EC 3.1.11.3 ) lambda exonuclease (EC 3.1.11.3 ) phage lambda-induced exonuclease (EC 3.1.11.3 ) Escherichia coli exonuclease IV (EC 3.1.11.3 ) E. coli exonuclease IV (EC 3.1.11.3 ) exodeoxyribonuclease IV (EC 3.1.11.3 ) exonuclease IV (EC 3.1.11.3 ) exodeoxyribonuclease I (EC 3.1.11.1 ) Escherichia coli exonuclease I (EC 3.1.11.1 ) E. coli exonuclease I (EC 3.1.11.1 ) exonuclease I (EC 3.1.11.1 ) DNA-directed DNA polymerase (EC 2.7.7.7 ) DNA polymerase I (EC 2.7.7.7 ) DNA polymerase II (EC 2.7.7.7 ) DNA polymerase III (EC 2.7.7.7 ) DNA polymerase alpha (EC 2.7.7.7 ) DNA polymerase beta (EC 2.7.7.7 ) DNA polymerase gamma (EC 2.7.7.7 ) DNA nucleotidyltransferase (DNA-directed) (EC 2.7.7.7 ) DNA nucleotidyltransferase (DNA-directed) (EC 2.7.7.7 ) deoxyribonucleate nucleotidyltransferase (EC 2.7.7.7 ) deoxynucleate polymerase (EC 2.7.7.7 ) deoxyribonucleic acid duplicase (EC 2.7.7.7 ) deoxyribonucleic acid polymerase (EC 2.7.7.7 ) deoxyribonucleic duplicase (EC 2.7.7.7 ) deoxyribonucleic polymerase (EC 2.7.7.7 ) deoxyribonucleic polymerase I (EC 2.7.7.7 ) DNA duplicase (EC 2.7.7.7 ) DNA nucleotidyltransferase (EC 2.7.7.7 ) DNA polymerase (EC 2.7.7.7 ) DNA replicase (EC 2.7.7.7 ) DNA-dependent DNA polymerase (EC 2.7.7.7 ) duplicase (EC 2.7.7.7 ) Klenow fragment (EC 2.7.7.7 ) sequenase (EC 2.7.7.7 ) Taq DNA polymerase (EC 2.7.7.7 ) Taq Pol I (EC 2.7.7.7 ) Tca DNA polymerase (EC 2.7.7.7 ) |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P00582 | DPO1_ECOLI | Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). | Single-chain monomer with multiple functions. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00230 | Purine metabolism | 2.7.7.7 |
| MAP00240 | Pyrimidine metabolism | 2.7.7.7 |
| Compound table | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors | Substrates | Products | Intermediates | ||||||||||||
| KEGG-id | C02148 | C00677 | C00039 | C00039 | C00001 | C00013 | C00039 | C00039 | C01150 | ||||||
| E.C. |
3.1.11.3
3.1.11.1 2.7.7.7 |
2.7.7.7
|
2.7.7.7
|
3.1.11.3
3.1.11.1 |
3.1.11.3
3.1.11.1 |
2.7.7.7
|
2.7.7.7
|
3.1.11.3
3.1.11.1 |
3.1.11.3
3.1.11.1 |
||||||
| Compound | Divalent metal | Deoxynucleoside triphosphate | DNA(n) | DNA(n+1) | H2O | Pyrophosphate | DNA(n+1) | DNA(n) | 5'-Phosphomononucleotides | ||||||
| Type | divalent metal (Ca2+, Mg2+) | nucleotide | nucleic acids | nucleic acids | H2O | phosphate group/phosphate ion | nucleic acids | nucleic acids | |||||||
| ChEBI |
15377 15377 |
29888 29888 |
|||||||||||||
| PubChem |
22247451 962 22247451 962 |
1023 21961011 1023 21961011 |
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| 1d8yA01 |
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Unbound | Unbound | Unbound | Bound:T-T-T-T (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 1d9dA01 |
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Bound:_ZN | Unbound | Unbound | Analogue:_DA-U31-C31 (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 1d9fA01 |
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Bound:_ZN | Unbound | Unbound | Analogue:_DT-U31-_DT (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 1kfsA01 |
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Bound:_MG,_ZN | Unbound | Unbound | Bound:A-C-G (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 1kfdA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1klnA01 |
|
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Bound:_ZN | Unbound | Unbound | Bound:G-C-C-T-C-G-C-G-G-C-G-G-C (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 1krpA01 |
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Bound:2x_ZN | Unbound | Unbound | Analogue:T-T-PST (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 1kspA01 |
|
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Unbound | Unbound | Unbound | Analogue:T-T-PST (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 1qslA01 |
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Analogue:_EU | Unbound | Unbound | Bound:A-C-G-C | Unbound | Unbound | Unbound | Unbound | ||
| 2kfnA01 |
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Bound:_MN,_ZN | Unbound | Unbound | Bound:T-A-US1-G (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 2kfzA01 |
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Bound:2x_ZN | Unbound | Unbound | Bound:T-A-US1-G (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 2kzmA01 |
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Bound:_MN,_ZN | Unbound | Unbound | Bound:C-G-C (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 2kzzA01 |
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Bound:2x_ZN | Unbound | Unbound | Bound:A-C-G (chain B) | Unbound | Unbound | Unbound | Unbound | ||
| 1d8yA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1d9dA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1d9fA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1kfsA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1kfdA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1klnA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1krpA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1kspA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1qslA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kfnA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kfzA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kzmA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kzzA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1d8yA03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1d9dA03 |
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Bound:_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1d9fA03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1kfsA03 |
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Bound:_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1kfdA03 |
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Unbound | Bound:CTP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1klnA03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1krpA03 |
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Bound:_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1kspA03 |
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Bound:_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1qslA03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kfnA03 |
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Bound:_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kfzA03 |
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Bound:_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kzmA03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kzzA03 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1d8yA04 |
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Unbound | Unbound | Unbound | Unbound | Analogue:SO4_38 | Unbound | Unbound | Unbound | ||
| 1d9dA04 |
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Unbound | Unbound | Unbound | Unbound | Analogue:SO4_38 | Unbound | Unbound | Unbound | ||
| 1d9fA04 |
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Unbound | Unbound | Unbound | Unbound | Analogue:SO4_38 | Unbound | Unbound | Unbound | ||
| 1kfsA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1kfdA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1klnA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1krpA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1kspA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1qslA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kfnA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kfzA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kzmA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2kzzA04 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| literature [12] & [16] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1d8yA01 |
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;TYR 497 | ; ;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | mutant D355A;E357A | ||
| 1d9dA01 |
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | |||
| 1d9fA01 |
|
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | |||
| 1kfsA01 |
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | mutant V324M | ||
| 1kfdA01 |
|
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | |||
| 1klnA01 |
|
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GLU 357;TYR 497 | ;GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | mutant D355A | ||
| 1krpA01 |
|
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | mutant V324M | ||
| 1kspA01 |
|
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | mutant V324M | ||
| 1qslA01 |
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | |||
| 2kfnA01 |
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | |||
| 2kfzA01 |
|
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | |||
| 2kzmA01 |
|
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | |||
| 2kzzA01 |
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GLU 357;TYR 497 | ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) | |||
| 1d8yA02 |
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| 1d9dA02 |
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| 1d9fA02 |
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| 1kfsA02 |
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| 1kfdA02 |
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| 1klnA02 |
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| 1krpA02 |
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| 1kspA02 |
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| 1qslA02 |
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| 2kfnA02 |
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| 2kfzA02 |
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| 2kzmA02 |
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| 2kzzA02 |
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| 1d8yA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1d9dA03 |
|
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1d9fA03 |
|
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1kfsA03 |
|
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1kfdA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1klnA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1krpA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1kspA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1qslA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 2kfnA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 2kfzA03 |
|
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 2kzmA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 2kzzA03 |
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ARG 682 | ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) | GLN 708 | ||
| 1d8yA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 1d9dA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 1d9fA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 1kfsA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 1kfdA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 1klnA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 1krpA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 1kspA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 1qslA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 2kfnA04 |
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 2kfzA04 |
|
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 2kzmA04 |
|
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| 2kzzA04 |
|
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HIS 734;ARG 754;LYS 758 | ILE 709 | |||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[5]
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||
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[6]
|
Fig.10, p.30-31 | 2 |
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[8]
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||
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[12]
|
Fig.4, Fig.5, p.34-36 | |
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[13]
|
Fig.3 | |
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[14]
|
p.2026 | |
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[16]
|
p.615-616 | |
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[20]
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||
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[22]
|
p.101-102 | |
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[23]
|
p.7521 | |
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[26]
|
p.372 | |
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[28]
|
p.306 | |
|
[30]
|
Fig.3 | |
|
[32]
|
Fig.1 | |
|
[33]
|
Fig.1 | |
|
[43]
|
||
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7013792 |
| Journal | Biochemistry |
| Year | 1981 |
| Volume | 20 |
| Pages | 1245-52 |
| Authors | Brody RS, Frey PA |
| Title | Unambiguous determination of the stereochemistry of nucleotidyl transfer catalyzed by DNA polymerase I from Escherichia coli. |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 6343618 |
| Journal | J Mol Biol |
| Year | 1983 |
| Volume | 166 |
| Pages | 453-6 |
| Authors | Brick P, Ollis D, Steitz TA |
| Title | Crystallization and 7 A resolution electron density map of the large fragment of Escherichia coli DNA polymerase I. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF KLENOW FRAGMENT. |
| Medline ID | 85137890 |
| PubMed ID | 3883192 |
| Journal | Nature |
| Year | 1985 |
| Volume | 313 |
| Pages | 762-6 |
| Authors | Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA |
| Title | Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. |
| Related PDB | |
| Related UniProtKB | P00582 |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3323527 |
| Journal | J Mol Biol |
| Year | 1987 |
| Volume | 198 |
| Pages | 123-7 |
| Authors | Clark JM, Joyce CM, Beardsley GP |
| Title | Novel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli. |
| Related PDB | |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 2832946 |
| Journal | Science |
| Year | 1988 |
| Volume | 240 |
| Pages | 199-201 |
| Authors | Derbyshire V, Freemont PS, Sanderson MR, Beese L, Friedman JM, Joyce CM, Steitz TA |
| Title | Genetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I. |
| Related PDB | |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT. |
| Medline ID | 91114709 |
| PubMed ID | 1989886 |
| Journal | EMBO J |
| Year | 1991 |
| Volume | 10 |
| Pages | 25-33 |
| Authors | Beese LS, Steitz TA |
| Title | Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. |
| Related PDB | |
| Related UniProtKB | P00582 |
| [7] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 1726742 |
| Journal | Nucleic Acids Symp Ser |
| Year | 1991 |
| Volume | (24) |
| Pages | 185-8 |
| Authors | Lavrik OI |
| Title | Oligonucleotides and their derivatives as tools for investigations of protein-nucleic acid interactions in template biocatalysis. |
| Related PDB | |
| Related UniProtKB | |
| [8] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 1569092 |
| Journal | J Biol Chem |
| Year | 1992 |
| Volume | 267 |
| Pages | 8417-28 |
| Authors | Polesky AH, Dahlberg ME, Benkovic SJ, Grindley ND, Joyce CM |
| Title | Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli. |
| Related PDB | |
| Related UniProtKB | |
| [9] | |
| Resource | |
| Comments | STRUCTURE BY NMR OF 728-777. |
| Medline ID | 93183012 |
| PubMed ID | 8442659 |
| Journal | Arch Biochem Biophys |
| Year | 1993 |
| Volume | 301 |
| Pages | 174-83 |
| Authors | Mullen GP, Vaughn JB Jr, Mildvan AS |
| Title |
Sequential proton NMR resonance assignments, |
| Related PDB | |
| Related UniProtKB | P00582 |
| [10] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (3.9 ANGSTROMS) OF KLENOW FRAGMENT. |
| Medline ID | 94083412 |
| PubMed ID | 8260491 |
| Journal | Biochemistry |
| Year | 1993 |
| Volume | 32 |
| Pages | 14095-101 |
| Authors | Beese LS, Friedman JM, Steitz TA |
| Title | Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate. |
| Related PDB | 1kfd |
| Related UniProtKB | P00582 |
| [11] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF KLENOW FRAGMENT. |
| Medline ID | 93227044 |
| PubMed ID | 8469987 |
| Journal | Science |
| Year | 1993 |
| Volume | 260 |
| Pages | 352-5 |
| Authors | Beese LS, Derbyshire V, Steitz TA |
| Title | Structure of DNA polymerase I Klenow fragment bound to duplex DNA. |
| Related PDB | 1kln |
| Related UniProtKB | P00582 |
| [12] | |
| Resource | |
| Comments | Review |
| Medline ID | |
| PubMed ID | |
| Journal | Curr Opin Struct Biol |
| Year | 1993 |
| Volume | 3 |
| Pages | 31-8 |
| Authors | Steitz TA |
| Title | DNA- and RNA-dependent DNA polymerases. |
| Related PDB | |
| Related UniProtKB | |
| [13] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7528445 |
| Journal | Science |
| Year | 1994 |
| Volume | 266 |
| Pages | 2022-5 |
| Authors | Steitz TA, Smerdon SJ, Jager J, Joyce CM |
| Title | A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. |
| Related PDB | |
| Related UniProtKB | |
| [14] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7801132 |
| Journal | Science |
| Year | 1994 |
| Volume | 266 |
| Pages | 2025-6 |
| Authors | Pelletier H |
| Title | Polymerase structures and mechanism. |
| Related PDB | |
| Related UniProtKB | |
| [15] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8594345 |
| Journal | Methods Enzymol |
| Year | 1995 |
| Volume | 262 |
| Pages | 147-71 |
| Authors | Mullen GP |
| Title | Solution structure of DNA polymerases and DNA polymerase-substrate complexes. |
| Related PDB | |
| Related UniProtKB | |
| [16] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS). |
| Medline ID | 95364959 |
| PubMed ID | 7637814 |
| Journal | Nature |
| Year | 1995 |
| Volume | 376 |
| Pages | 612-6 |
| Authors | Kim Y, Eom SH, Wang J, Lee DS, Suh SW, Steitz TA |
| Title | Crystal structure of Thermus aquaticus DNA polymerase. |
| Related PDB | 1taq |
| Related UniProtKB | P19821 |
| [17] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832. |
| Medline ID | 96016150 |
| PubMed ID | 7568114 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 1995 |
| Volume | 92 |
| Pages | 9264-8 |
| Authors | Korolev S, Nayal M, Barnes WM, Di Cera E, Waksman G |
| Title | Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability. |
| Related PDB | 1ktq |
| Related UniProtKB | P19821 |
| [18] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8679555 |
| Journal | Biochemistry |
| Year | 1996 |
| Volume | 35 |
| Pages | 7256-66 |
| Authors | Kaushik N, Pandey VN, Modak MJ |
| Title | Significance of the O-helix residues of Escherichia coli DNA polymerase I in DNA synthesis: dynamics of the dNTP binding pocket. |
| Related PDB | |
| Related UniProtKB | |
| [19] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS). |
| Medline ID | 96353982 |
| PubMed ID | 8717047 |
| Journal | Nature |
| Year | 1996 |
| Volume | 382 |
| Pages | 278-81 |
| Authors | Eom SH, Wang J, Steitz TA |
| Title | Structure of Taq ploymerase with DNA at the polymerase active site. |
| Related PDB | 1tau |
| Related UniProtKB | P19821 |
| [20] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9214499 |
| Journal | Nature |
| Year | 1997 |
| Volume | 388 |
| Pages | 33-4 |
| Authors | Artymiuk PJ, Poirrette AR, Rice DW, Willett P |
| Title | A polymerase I palm in adenylyl cyclase? |
| Related PDB | |
| Related UniProtKB | |
| [21] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9396823 |
| Journal | Nucleic Acids Res |
| Year | 1997 |
| Volume | 25 |
| Pages | 5110-8 |
| Authors | Moser MJ, Holley WR, Chatterjee A, Mian IS |
| Title | The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. |
| Related PDB | |
| Related UniProtKB | |
| [22] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 297-876 |
| Medline ID | 97169447 |
| PubMed ID | 9016716 |
| Journal | Structure |
| Year | 1997 |
| Volume | 5 |
| Pages | 95-108 |
| Authors | Kiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS |
| Title | Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution. |
| Related PDB | 1xwl |
| Related UniProtKB | P52026 |
| [23] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 295-832. |
| Medline ID | 99077817 |
| PubMed ID | 9857206 |
| Journal | EMBO J |
| Year | 1998 |
| Volume | 17 |
| Pages | 7514-25 |
| Authors | Li Y, Korolev S, Waksman G |
| Title | Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. |
| Related PDB | 2ktq 3ktq 4ktq |
| Related UniProtKB | P19821 |
| [24] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9523721 |
| Journal | Eur J Biochem |
| Year | 1998 |
| Volume | 252 |
| Pages | 124-32 |
| Authors | Amblar M, Lopez P |
| Title | Purification and properties of the 5'-3' exonuclease D190-->a mutant of DNA polymerase I from Streptococcus pneumoniae. |
| Related PDB | |
| Related UniProtKB | |
| [25] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9571040 |
| Journal | J Mol Biol |
| Year | 1998 |
| Volume | 278 |
| Pages | 147-65 |
| Authors | Astatke M, Grindley ND, Joyce CM |
| Title |
How E. |
| Related PDB | |
| Related UniProtKB | |
| [26] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF KLENOW FRAGMENT. |
| Medline ID | 98181033 |
| PubMed ID | 9514742 |
| Journal | J Mol Biol |
| Year | 1998 |
| Volume | 277 |
| Pages | 363-77 |
| Authors | Brautigam CA, Steitz TA |
| Title | Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. |
| Related PDB | 1kfs 1krp 1ksp |
| Related UniProtKB | P00582 |
| [27] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9584195 |
| Journal | Mol Cell Biol |
| Year | 1998 |
| Volume | 18 |
| Pages | 3552-62 |
| Authors | Mizuno T, Ito N, Yokoi M, Kobayashi A, Tamai K, Miyazawa H, Hanaoka F |
| Title | The second-largest subunit of the mouse DNA polymerase alpha-primase complex facilitates both production and nuclear translocation of the catalytic subunit of DNA polymerase alpha. |
| Related PDB | |
| Related UniProtKB | |
| [28] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 297-876 |
| Medline ID | 98101648 |
| PubMed ID | 9440698 |
| Journal | Nature |
| Year | 1998 |
| Volume | 391 |
| Pages | 304-7 |
| Authors | Kiefer JR, Mao C, Braman JC, Beese LS |
| Title | Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. |
| Related PDB | 2bdp 3bdp 4bdp |
| Related UniProtKB | P52026 |
| [29] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS). |
| Medline ID | 98445410 |
| PubMed ID | 9770525 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 1998 |
| Volume | 95 |
| Pages | 12562-7 |
| Authors | Murali R, Sharkey DJ, Daiss JL, Murthy HM |
| Title | Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme. |
| Related PDB | 1bgx |
| Related UniProtKB | P19821 |
| [30] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832. |
| Medline ID | 98266352 |
| PubMed ID | 9605316 |
| Journal | Protein Sci |
| Year | 1998 |
| Volume | 7 |
| Pages | 1116-23 |
| Authors | Li Y, Kong Y, Korolev S, Waksman G |
| Title | Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates. |
| Related PDB | 5ktq |
| Related UniProtKB | P19821 |
| [31] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS). |
| Medline ID | 20133099 |
| PubMed ID | 10666572 |
| Journal | Acta Crystallogr D Biol Crystallogr |
| Year | 1999 |
| Volume | 55 |
| Pages | 1971-7 |
| Authors | Urs UK, Murali R, Krishna Murthy HM |
| Title | Structure of taq DNA polymerase shows a new orientation for the structure-specific nuclease domain. |
| Related PDB | 1cmw |
| Related UniProtKB | P19821 |
| [32] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT. |
| Medline ID | 99105820 |
| PubMed ID | 9888810 |
| Journal | Biochemistry |
| Year | 1999 |
| Volume | 38 |
| Pages | 696-704 |
| Authors | Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
| Title | Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli. |
| Related PDB | 2kfn 2kfz 2kzm 2kzz |
| Related UniProtKB | P00582 |
| [33] | |
| Resource | |
| Comments | X-ray crystallography |
| Medline ID | |
| PubMed ID | 10631518 |
| Journal | Chem Biol |
| Year | 1999 |
| Volume | 6 |
| Pages | 901-8 |
| Authors | Brautigam CA, Aschheim K, Steitz TA |
| Title | Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment. |
| Related PDB | 1qsl |
| Related UniProtKB | |
| [34] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9915846 |
| Journal | J Biol Chem |
| Year | 1999 |
| Volume | 274 |
| Pages | 3067-75 |
| Authors | Minnick DT, Bebenek K, Osheroff WP, Turner RM Jr, Astatke M, Liu L, Kunkel TA, Joyce CM |
| Title | Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment). |
| Related PDB | |
| Related UniProtKB | |
| [35] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 293-831. |
| Medline ID | 99380545 |
| PubMed ID | 10449720 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 1999 |
| Volume | 96 |
| Pages | 9491-6 |
| Authors | Li Y, Mitaxov V, Waksman G |
| Title | Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. |
| Related PDB | 1qss 1qsy 1qtm |
| Related UniProtKB | P19821 |
| [36] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF KLENOW FRAGMENT. |
| Medline ID | 20056229 |
| PubMed ID | 10588690 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 1999 |
| Volume | 96 |
| Pages | 14240-5 |
| Authors | Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M |
| Title | Structural origins of the exonuclease resistance of a zwitterionic RNA. |
| Related PDB | 1d8y 1d9d 1d9f |
| Related UniProtKB | P00582 |
| [37] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10924147 |
| Journal | Biochemistry |
| Year | 2000 |
| Volume | 39 |
| Pages | 9508-13 |
| Authors | Kamiya H, Maki H, Kasai H |
| Title | Two DNA polymerases of Escherichia coli display distinct misinsertion specificities for 2-hydroxy-dATP during DNA synthesis. |
| Related PDB | |
| Related UniProtKB | |
| [38] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11004506 |
| Journal | Biochim Biophys Acta |
| Year | 2000 |
| Volume | 1492 |
| Pages | 341-52 |
| Authors | Izumi M, Yokoi M, Nishikawa NS, Miyazawa H, Sugino A, Yamagishi M, Yamaguchi M, Matsukage A, Yatagai F, Hanaoka F |
| Title |
Transcription of the catalytic 180-kDa subunit gene of mouse DNA polymerase alpha is controlled by E2F, |
| Related PDB | |
| Related UniProtKB | |
| [39] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10779513 |
| Journal | J Biol Chem |
| Year | 2000 |
| Volume | 275 |
| Pages | 19685-92 |
| Authors | Gangurde R, Kaushik N, Singh K, Modak MJ |
| Title |
A carboxylate triad is essential for the polymerase activity of Escherichia coli DNA polymerase I (Klenow fragment). |
| Related PDB | |
| Related UniProtKB | |
| [40] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10818095 |
| Journal | J Biol Chem |
| Year | 2000 |
| Volume | 275 |
| Pages | 23759-68 |
| Authors | Tuske S, Singh K, Kaushik N, Modak MJ |
| Title | The J-helix of Escherichia coli DNA polymerase I (Klenow fragment) regulates polymerase and 3'- 5'-exonuclease functions. |
| Related PDB | |
| Related UniProtKB | |
| [41] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11329298 |
| Journal | Biochemistry |
| Year | 2001 |
| Volume | 40 |
| Pages | 2282-90 |
| Authors | Alekseyev YO, Dzantiev L, Romano LJ |
| Title | Effects of benzo[a]pyrene DNA adducts on Escherichia coli DNA polymerase I (Klenow fragment) primer-template interactions: evidence for inhibition of the catalytically active ternary complex formation. |
| Related PDB | |
| Related UniProtKB | |
| [42] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11506573 |
| Journal | J Am Chem Soc |
| Year | 2001 |
| Volume | 123 |
| Pages | 8125-6 |
| Authors | Kuhn U, Warzeska S, Pritzkow H, Kramer R |
| Title | A bioinspired dicopper(II) catalyst for the transesterification of dimethyl phosphate. |
| Related PDB | |
| Related UniProtKB | |
| [43] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11278428 |
| Journal | J Biol Chem |
| Year | 2001 |
| Volume | 276 |
| Pages | 19172-81 |
| Authors | Amblar M, de Lacoba MG, Corrales MA, Lopez P |
| Title |
Biochemical analysis of point mutations in the 5'-3' exonuclease of DNA polymerase I of Streptococcus pneumoniae. |
| Related PDB | |
| Related UniProtKB | |
| [44] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11278911 |
| Journal | J Biol Chem |
| Year | 2001 |
| Volume | 276 |
| Pages | 18836-42 |
| Authors | Shinkai A, Patel PH, Loeb LA |
| Title | The conserved active site motif A of Escherichia coli DNA polymerase I is highly mutable. |
| Related PDB | |
| Related UniProtKB | |
| [45] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11346641 |
| Journal | J Biol Chem |
| Year | 2001 |
| Volume | 276 |
| Pages | 27562-7 |
| Authors | Tosaka A, Ogawa M, Yoshida S, Suzuki M |
| Title | O-helix mutant T664P of Thermus aquaticus DNA polymerase I: altered catalytic properties for incorporation of incorrect nucleotides but not correct nucleotides. |
| Related PDB | |
| Related UniProtKB | |
| [46] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11536367 |
| Journal | Mol Carcinog |
| Year | 2001 |
| Volume | 31 |
| Pages | 171-83 |
| Authors | Popanda O, Flohr C, Dai JC, Hunzicker A, Thielmann HW |
| Title | A mutation in subunit B of the DNA polymerase alpha-primase complex from Novikoff hepatoma cells concomitant with a conformational change and abnormal catalytic properties of the DNA polymerase alpha-primase complex. |
| Related PDB | |
| Related UniProtKB | |
| [47] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11677239 |
| Journal | J Biol Chem |
| Year | 2002 |
| Volume | 277 |
| Pages | 1653-61 |
| Authors | Arrigo CJ, Singh K, Modak MJ |
| Title | DNA polymerase I of Mycobacterium tuberculosis: functional role of a conserved aspartate in the hinge joining the M and N helices. |
| Related PDB | |
| Related UniProtKB | |
| [48] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12364611 |
| Journal | Nucleic Acids Res |
| Year | 2002 |
| Volume | 30 |
| Pages | 4314-20 |
| Authors | Yang SW, Astatke M, Potter J, Chatterjee DK |
| Title | Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides. |
| Related PDB | |
| Related UniProtKB | |
| [49] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12649320 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2003 |
| Volume | 100 |
| Pages | 3895-900 |
| Authors | Johnson SJ, Taylor JS, Beese LS |
| Title | Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. |
| Related PDB | 1l3s 1l3t 1l3u 1l3v 1l5u 1lv5 |
| Related UniProtKB | |
| Comments |
|---|
|
This enzyme is composed of the N-terminal 5'-3' exonuclease (E.C. The structure and mechanism of 5'-3' exonuclease have not been elucidated yet. According to the literature [6] & [12], (A) Transfer of phosphoryl group from NTP to DNA (This reaction is the same as that of M00175 in EzCatDB.): (A1) Divalent metal-1, (A2) The acceptor, (A3) Divalent metal-1 and metal-2 stabilize the transition state by interacting with the transferred group, (B) Hydrolysis of phosphoric ester of DNA: (B1) Divalent metal-A, (B2) The activated water makes a nucleophilic attack on the phosphoryl atom. (B3) Divalent metal-A and metal-B stabilize the transition state by interacting with the transferred group, |
| Created | Updated |
|---|---|
| 2004-03-03 | 2009-02-26 |