4F56
The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0036054 | molecular_function | protein-malonyllysine demalonylase activity |
| A | 0036055 | molecular_function | protein-succinyllysine desuccinylase activity |
| A | 0070403 | molecular_function | NAD+ binding |
| B | 0036054 | molecular_function | protein-malonyllysine demalonylase activity |
| B | 0036055 | molecular_function | protein-succinyllysine desuccinylase activity |
| B | 0070403 | molecular_function | NAD+ binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 401 |
| Chain | Residue |
| A | CYS166 |
| A | CYS169 |
| A | CYS207 |
| A | CYS212 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 401 |
| Chain | Residue |
| B | CYS166 |
| B | CYS169 |
| B | CYS207 |
| B | CYS212 |
| site_id | AC3 |
| Number of Residues | 30 |
| Details | BINDING SITE FOR RESIDUE CGK C 101 |
| Chain | Residue |
| A | ALA59 |
| A | GLY60 |
| A | ALA63 |
| A | GLU64 |
| A | THR69 |
| A | PHE70 |
| A | ARG71 |
| A | TYR102 |
| A | ARG105 |
| A | GLN140 |
| A | ILE142 |
| A | HIS158 |
| A | VAL220 |
| A | PHE223 |
| A | GLY249 |
| A | THR250 |
| A | SER251 |
| A | VAL254 |
| A | ASN275 |
| A | THR276 |
| A | GLU277 |
| A | PRO292 |
| A | CYS293 |
| A | HOH511 |
| A | HOH697 |
| C | LYS9 |
| C | HOH201 |
| C | HOH202 |
| C | HOH203 |
| A | GLY58 |
| site_id | AC4 |
| Number of Residues | 32 |
| Details | BINDING SITE FOR RESIDUE CGK D 101 |
| Chain | Residue |
| B | GLY58 |
| B | ALA59 |
| B | GLY60 |
| B | ALA63 |
| B | GLU64 |
| B | THR69 |
| B | PHE70 |
| B | ARG71 |
| B | TYR102 |
| B | ARG105 |
| B | GLN140 |
| B | ILE142 |
| B | HIS158 |
| B | VAL220 |
| B | PHE223 |
| B | GLY249 |
| B | THR250 |
| B | SER251 |
| B | VAL254 |
| B | ASN275 |
| B | THR276 |
| B | GLU277 |
| B | PRO292 |
| B | CYS293 |
| B | HOH596 |
| B | HOH698 |
| D | LYS9 |
| D | HOH201 |
| D | HOH202 |
| D | HOH203 |
| D | HOH205 |
| D | HOH206 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU00236","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22076378","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29180469","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 54 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03160","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22076378","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22767592","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2006","submissionDatabase":"PDB data bank","title":"Crystal structure of human sirtuin homolog 5 in complex with NAD.","authoringGroup":["Structural genomics consortium (SGC)"]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03160","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphothreonine; by PKC","evidences":[{"source":"PubMed","id":"20228790","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Symmetric dimethylarginine; by PRMT5; alternate","evidences":[{"source":"UniProtKB","id":"P68433","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"11242053","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16457588","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5","evidences":[{"source":"PubMed","id":"10464286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11856369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12560483","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15681610","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16185088","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16457588","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphothreonine; by PKC and CHEK1","evidences":[{"source":"PubMed","id":"12560483","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18066052","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18243098","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22901803","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
