1KNW
Crystal structure of diaminopimelate decarboxylase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0008836 | molecular_function | diaminopimelate decarboxylase activity |
| A | 0009085 | biological_process | L-lysine biosynthetic process |
| A | 0009089 | biological_process | L-lysine biosynthetic process via diaminopimelate |
| A | 0016829 | molecular_function | lyase activity |
| A | 0016831 | molecular_function | carboxy-lyase activity |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE SO4 A 520 |
| Chain | Residue |
| A | MES510 |
| A | HOH704 |
| A | HOH784 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE LI A 530 |
| Chain | Residue |
| A | HIS151 |
| A | SER152 |
| A | LYS154 |
| A | ASN156 |
| A | HOH645 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE LI A 540 |
| Chain | Residue |
| A | SER384 |
| A | ARG389 |
| A | PRO390 |
| A | LEU391 |
| A | HOH590 |
| A | ASN303 |
| site_id | AC4 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE PLP A 554 |
| Chain | Residue |
| A | ALA52 |
| A | LYS54 |
| A | THR100 |
| A | HIS191 |
| A | GLY227 |
| A | GLU268 |
| A | GLY270 |
| A | ARG271 |
| A | CYS342 |
| A | TYR378 |
| A | MES510 |
| A | HOH595 |
| A | HOH602 |
| A | HOH614 |
| A | HOH629 |
| A | HOH631 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE MES A 510 |
| Chain | Residue |
| A | LYS54 |
| A | THR157 |
| A | HIS191 |
| A | TYR311 |
| A | GLU343 |
| A | SER344 |
| A | TYR378 |
| A | SO4520 |
| A | PLP554 |
| A | HOH609 |
| A | HOH614 |
| A | HOH704 |
| A | HOH864 |
Functional Information from PROSITE/UniProt
| site_id | PS00878 |
| Number of Residues | 19 |
| Details | ODR_DC_2_1 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. FAqKACsnihILrlMreqG |
| Chain | Residue | Details |
| A | PHE51-GLY69 |
| site_id | PS00879 |
| Number of Residues | 14 |
| Details | ODR_DC_2_2 Orn/DAP/Arg decarboxylases family 2 signature 2. Gqd....LqAISAGGGLS |
| Chain | Residue | Details |
| A | GLY216-SER229 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"HAMAP-Rule","id":"MF_02120","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 5 |
| Details | Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"Diaminopimelate decarboxylase uses a versatile active site for stereospecific decarboxylation.","authors":["Levdikov V.","Blagova L.","Bose N.","Momany C."]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"Diaminopimelate decarboxylase uses a versatile active site for stereospecific decarboxylation.","authors":["Levdikov V.","Blagova L.","Bose N.","Momany C."]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 3 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_02120","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"Diaminopimelate decarboxylase uses a versatile active site for stereospecific decarboxylation.","authors":["Levdikov V.","Blagova L.","Bose N.","Momany C."]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_02120","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"Diaminopimelate decarboxylase uses a versatile active site for stereospecific decarboxylation.","authors":["Levdikov V.","Blagova L.","Bose N.","Momany C."]}}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1bd0 |
| Chain | Residue | Details |
| A | LYS54 | |
| A | LYS163 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1bd0 |
| Chain | Residue | Details |
| A | LYS54 | |
| A | GLU268 | |
| A | HIS191 |
