4RUL
Crystal structure of full-length E.Coli topoisomerase I in complex with ssDNA
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003916 | molecular_function | DNA topoisomerase activity |
| A | 0003917 | molecular_function | DNA topoisomerase type I (single strand cut, ATP-independent) activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005694 | cellular_component | chromosome |
| A | 0005829 | cellular_component | cytosol |
| A | 0006265 | biological_process | DNA topological change |
| A | 0016853 | molecular_function | isomerase activity |
| A | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN A 1001 |
| Chain | Residue |
| A | CYS599 |
| A | CYS602 |
| A | CYS619 |
| A | CYS630 |
| A | THR632 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 1002 |
| Chain | Residue |
| A | CYS662 |
| A | CYS665 |
| A | CYS683 |
| A | CYS689 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 1003 |
| Chain | Residue |
| A | CYS711 |
| A | CYS714 |
| A | CYS731 |
| A | CYS736 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE ZN A 1004 |
| Chain | Residue |
| A | HIS566 |
| A | ASP570 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1005 |
| Chain | Residue |
| A | ARG169 |
| A | ARG173 |
| A | TYR177 |
| A | HOH1129 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1006 |
| Chain | Residue |
| A | ARG114 |
| A | ARG161 |
| A | ALA554 |
| A | HOH1118 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1007 |
| Chain | Residue |
| A | GLY300 |
| A | GLU479 |
| A | ARG515 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1008 |
| Chain | Residue |
| A | ARG515 |
| A | ARG516 |
| A | HOH1128 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1009 |
| Chain | Residue |
| A | TYR83 |
| A | TRP121 |
| A | ASN163 |
| A | GLN166 |
| A | TRP560 |
Functional Information from PROSITE/UniProt
| site_id | PS00396 |
| Number of Residues | 15 |
| Details | TOPO_IA_1 Topoisomerase (Topo) IA-type active site signature. QrLYEagy.........ITYmRTD |
| Chain | Residue | Details |
| A | GLN309-ASP323 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 31 |
| Details | ZN_FING: C4-type 1 |
| Chain | Residue | Details |
| A | CYS599-CYS630 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 27 |
| Details | ZN_FING: C4-type 2 |
| Chain | Residue | Details |
| A | CYS662-CYS689 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 25 |
| Details | ZN_FING: C4-type 3 |
| Chain | Residue | Details |
| A | CYS711-CYS736 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | ACT_SITE: O-(5'-phospho-DNA)-tyrosine intermediate => ECO:0000255|PROSITE-ProRule:PRU01383, ECO:0000269|PubMed:21482796, ECO:0000269|PubMed:8114910, ECO:0000269|PubMed:9497321 |
| Chain | Residue | Details |
| A | TYR319 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00952 |
| Chain | Residue | Details |
| A | GLU9 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000305 |
| Chain | Residue | Details |
| A | ASP111 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | SITE: Interaction with DNA |
| Chain | Residue | Details |
| A | HIS33 | |
| A | ARG168 | |
| A | ARG169 | |
| A | ASP172 | |
| A | TYR177 | |
| A | TRP184 | |
| A | ARG321 | |
| A | ARG507 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 7 |
| Details | M-CSA 366 |
| Chain | Residue | Details |
| A | GLU9 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, metal ligand, proton acceptor, proton donor, proton relay |
| A | ASP111 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, metal ligand, proton acceptor, proton donor, proton relay |
| A | ASP113 | metal ligand |
| A | GLU115 | metal ligand |
| A | TYR319 | activator, covalently attached, hydrogen bond acceptor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | ARG321 | electrostatic stabiliser |
| A | HIS365 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, increase acidity, proton acceptor, proton donor |
