5X7M
Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0008836 | molecular_function | diaminopimelate decarboxylase activity |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| A | 0016830 | molecular_function | carbon-carbon lyase activity |
| A | 0016831 | molecular_function | carboxy-lyase activity |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0008836 | molecular_function | diaminopimelate decarboxylase activity |
| B | 0009085 | biological_process | lysine biosynthetic process |
| B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| B | 0016830 | molecular_function | carbon-carbon lyase activity |
| B | 0016831 | molecular_function | carboxy-lyase activity |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | binding site for residue PLP A 501 |
| Chain | Residue |
| A | LYS75 |
| A | TYR404 |
| A | HOH605 |
| B | CYS374 |
| A | HIS117 |
| A | ARG164 |
| A | HIS216 |
| A | GLY256 |
| A | GLY257 |
| A | GLU299 |
| A | GLY301 |
| A | ARG302 |
| site_id | AC2 |
| Number of Residues | 16 |
| Details | binding site for Di-peptide PLP B 501 and LYS B 75 |
| Chain | Residue |
| A | CYS374 |
| A | TYR412 |
| B | ALA73 |
| B | SER74 |
| B | ALA76 |
| B | PHE77 |
| B | ASP94 |
| B | GLU100 |
| B | HIS117 |
| B | HIS216 |
| B | GLY256 |
| B | GLY257 |
| B | GLU299 |
| B | GLY301 |
| B | ARG302 |
| B | TYR404 |
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. YAsKAFltktIArwVdeeG |
| Chain | Residue | Details |
| A | TYR72-GLY90 |
| site_id | PS00879 |
| Number of Residues | 17 |
| Details | ODR_DC_2_2 Orn/DAP/Arg decarboxylases family 2 signature 2. Selgva.LpELDLGGGYG |
| Chain | Residue | Details |
| A | SER243-GLY259 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton donor => ECO:0000255 |
| Chain | Residue | Details |
| A | CYS374 | |
| B | CYS374 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 14 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_02120 |
| Chain | Residue | Details |
| A | GLY257 | |
| B | ARG302 | |
| B | ARG343 | |
| B | TYR347 | |
| B | GLU375 | |
| B | TYR404 | |
| A | GLU299 | |
| A | ARG302 | |
| A | ARG343 | |
| A | TYR347 | |
| A | GLU375 | |
| A | TYR404 | |
| B | GLY257 | |
| B | GLU299 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000255|HAMAP-Rule:MF_02120 |
| Chain | Residue | Details |
| A | LYS75 | |
| B | LYS75 |
