2OQ4
Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000703 | molecular_function | oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity |
| A | 0003676 | molecular_function | nucleic acid binding |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003684 | molecular_function | damaged DNA binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0003906 | molecular_function | DNA-(apurinic or apyrimidinic site) endonuclease activity |
| A | 0006281 | biological_process | DNA repair |
| A | 0006284 | biological_process | base-excision repair |
| A | 0006974 | biological_process | DNA damage response |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| A | 0016799 | molecular_function | hydrolase activity, hydrolyzing N-glycosyl compounds |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019104 | molecular_function | DNA N-glycosylase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0140078 | molecular_function | class I DNA-(apurinic or apyrimidinic site) endonuclease activity |
| B | 0000703 | molecular_function | oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity |
| B | 0003676 | molecular_function | nucleic acid binding |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003684 | molecular_function | damaged DNA binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0003906 | molecular_function | DNA-(apurinic or apyrimidinic site) endonuclease activity |
| B | 0006281 | biological_process | DNA repair |
| B | 0006284 | biological_process | base-excision repair |
| B | 0006974 | biological_process | DNA damage response |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| B | 0016799 | molecular_function | hydrolase activity, hydrolyzing N-glycosyl compounds |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019104 | molecular_function | DNA N-glycosylase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0140078 | molecular_function | class I DNA-(apurinic or apyrimidinic site) endonuclease activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PED D 427 |
| Chain | Residue |
| A | PRO1 |
| A | GLN2 |
| A | LEU70 |
| A | ASN168 |
| A | PHE230 |
| A | PRO253 |
| D | DA426 |
| D | DG428 |
| D | HOH1053 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PED F 427 |
| Chain | Residue |
| B | PRO1 |
| B | GLN2 |
| B | ASN168 |
| B | ARG252 |
| F | DA426 |
| F | DG428 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 501 |
| Chain | Residue |
| A | CYS237 |
| A | CYS240 |
| A | CYS257 |
| A | CYS260 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 501 |
| Chain | Residue |
| B | CYS237 |
| B | CYS240 |
| B | CYS257 |
| B | CYS260 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 601 |
| Chain | Residue |
| A | PRO1 |
| A | GLU5 |
| A | ARG212 |
| D | HOH1053 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 602 |
| Chain | Residue |
| B | GLU81 |
| B | GLU82 |
| B | PRO83 |
| B | HOH1085 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 B 603 |
| Chain | Residue |
| B | ARG8 |
| B | ASN12 |
Functional Information from PROSITE/UniProt
| site_id | PS01242 |
| Number of Residues | 25 |
| Details | ZF_FPG_1 Zinc finger FPG-type signature. Cer..CGsiIekttlss....RPfyWCpgCQ |
| Chain | Residue | Details |
| A | CYS237-GLN261 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 34 |
| Details | Zinc finger: {"description":"FPG-type"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Schiff-base intermediate with DNA"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor; for beta-elimination activity","evidences":[{"evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor; for delta-elimination activity","evidences":[{"evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"11847126","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1k82 |
| Chain | Residue | Details |
| A | GLN2 | |
| A | LYS52 | |
| A | PRO1 | |
| A | ARG252 |
| site_id | CSA2 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1k82 |
| Chain | Residue | Details |
| B | GLN2 | |
| B | LYS52 | |
| B | PRO1 | |
| B | ARG252 |
