1XI1
Phi29 DNA polymerase ssDNA complex, monoclinic crystal form
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0001882 | molecular_function | nucleoside binding |
| A | 0003676 | molecular_function | nucleic acid binding |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| A | 0004518 | molecular_function | nuclease activity |
| A | 0004527 | molecular_function | exonuclease activity |
| A | 0006260 | biological_process | DNA replication |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016779 | molecular_function | nucleotidyltransferase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0034061 | molecular_function | DNA polymerase activity |
| A | 0039693 | biological_process | viral DNA genome replication |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0001882 | molecular_function | nucleoside binding |
| B | 0003676 | molecular_function | nucleic acid binding |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003887 | molecular_function | DNA-directed DNA polymerase activity |
| B | 0004518 | molecular_function | nuclease activity |
| B | 0004527 | molecular_function | exonuclease activity |
| B | 0006260 | biological_process | DNA replication |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016779 | molecular_function | nucleotidyltransferase activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0034061 | molecular_function | DNA polymerase activity |
| B | 0039693 | biological_process | viral DNA genome replication |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 576 |
| Chain | Residue |
| A | ASP145 |
| A | TYR148 |
| A | ASP169 |
| A | HOH633 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG B 576 |
| Chain | Residue |
| B | ASP145 |
| B | TYR148 |
| B | ASP169 |
Functional Information from PROSITE/UniProt
| site_id | PS00116 |
| Number of Residues | 9 |
| Details | DNA_POLYMERASE_B DNA polymerase family B signature. YCDTDSIHL |
| Chain | Residue | Details |
| A | TYR454-LEU462 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 74 |
| Details | Region: {"description":"Involved in DNA-binding, coordination between DNA synthesis and degradation and TP interaction","evidences":[{"source":"PubMed","id":"15777661","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8670845","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9931249","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 664 |
| Details | Region: {"description":"Initiation, polymerization and pyrophosphorolytic activities","evidences":[{"source":"PubMed","id":"8621470","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 44 |
| Details | Region: {"description":"TPR2","evidences":[{"source":"PubMed","id":"15845765","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 24 |
| Details | Region: {"description":"Involved in DNA-binding and TP interaction","evidences":[{"source":"PubMed","id":"14729920","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | Motif: {"description":"YCDTD","evidences":[{"source":"PubMed","id":"1850426","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"1XI1","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"8226957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19883660","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"2PYL","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"9784372","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 6 |
| Details | Site: {"description":"Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"2790959","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 4 |
| Details | Site: {"description":"Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site","evidences":[{"source":"PubMed","id":"8605889","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 6 |
| Details | Site: {"description":"Interaction with the primer terminal protein","evidences":[{"source":"PubMed","id":"11884636","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 6 |
| Details | Site: {"description":"Binds ssDNA; Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"9786901","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | Site: {"description":"Involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | Site: {"description":"Involved in the stabilization of the frayed 3' terminus at the exonuclease active site","evidences":[{"source":"PubMed","id":"19576228","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8226957","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | Site: {"description":"Probably involved in nucleotide binding selection","evidences":[{"source":"PubMed","id":"8537389","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI20 |
| Number of Residues | 4 |
| Details | Site: {"description":"Binds ssDNA; Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"8605889","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | Site: {"description":"Involved in the binding of DNA and dNTP","evidences":[{"source":"PubMed","id":"11917008","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI22 |
| Number of Residues | 4 |
| Details | Site: {"description":"Stabilization of the incoming nucleotide","evidences":[{"source":"PubMed","id":"14672657","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | Site: {"description":"Interacts with the phosphate groups of the incoming nucleotide","evidences":[{"source":"PubMed","id":"11917008","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | Site: {"description":"Probably involved in nucleotide binding selection","evidences":[{"source":"PubMed","id":"9199402","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | Site: {"description":"Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity","evidences":[{"source":"PubMed","id":"12805385","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI26 |
| Number of Residues | 4 |
| Details | Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI27 |
| Number of Residues | 4 |
| Details | Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"7962004","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI28 |
| Number of Residues | 4 |
| Details | Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"7852344","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI29 |
| Number of Residues | 2 |
| Details | Site: {"description":"Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities","evidences":[{"source":"PubMed","id":"24023769","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
