5X7N
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 | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0008836 | molecular_function | diaminopimelate decarboxylase activity |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0009089 | biological_process | 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 |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0008652 | biological_process | amino acid biosynthetic process |
| B | 0008836 | molecular_function | diaminopimelate decarboxylase activity |
| B | 0009085 | biological_process | lysine biosynthetic process |
| B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| B | 0016829 | molecular_function | 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 | 6 |
| Details | binding site for residue GOL A 501 |
| Chain | Residue |
| A | PHE77 |
| A | LEU78 |
| A | ALA407 |
| A | HOH655 |
| A | HOH694 |
| B | ARG411 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 502 |
| Chain | Residue |
| A | SER194 |
| A | HOH629 |
| B | ASP320 |
| A | LYS166 |
| A | PHE188 |
| A | SER189 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 503 |
| Chain | Residue |
| A | GLY316 |
| A | SER392 |
| A | HOH607 |
| B | ASN120 |
| B | LYS121 |
| B | GLN143 |
| site_id | AC4 |
| Number of Residues | 16 |
| Details | binding site for residue PLP A 504 |
| Chain | Residue |
| A | LYS75 |
| A | HIS117 |
| A | HIS216 |
| A | GLY256 |
| A | GLY257 |
| A | GLU299 |
| A | GLY301 |
| A | ARG302 |
| A | TYR404 |
| A | LYS505 |
| A | HOH608 |
| A | HOH631 |
| A | HOH642 |
| A | HOH714 |
| A | HOH836 |
| B | CYS374 |
| site_id | AC5 |
| Number of Residues | 12 |
| Details | binding site for residue LYS A 505 |
| Chain | Residue |
| A | LYS75 |
| A | ARG302 |
| A | ARG343 |
| A | TYR347 |
| A | TYR404 |
| A | MET408 |
| A | PLP504 |
| A | HOH605 |
| A | HOH631 |
| A | HOH731 |
| B | CYS374 |
| B | GLU375 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 501 |
| Chain | Residue |
| A | ARG411 |
| B | PHE77 |
| B | LEU78 |
| B | ALA407 |
| B | ARG417 |
| B | HOH631 |
| B | HOH678 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 502 |
| Chain | Residue |
| A | ASP320 |
| B | LYS166 |
| B | PHE188 |
| B | SER189 |
| B | SER194 |
| B | HOH607 |
| B | HOH817 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 503 |
| Chain | Residue |
| A | ALA178 |
| A | THR179 |
| A | ARG233 |
| B | ASP223 |
| B | GLU225 |
| B | HOH754 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 504 |
| Chain | Residue |
| A | ASN120 |
| A | LYS121 |
| A | GLN143 |
| A | HOH656 |
| B | THR317 |
| B | SER392 |
| B | HOH650 |
| B | HOH793 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 505 |
| Chain | Residue |
| B | ALA111 |
| B | SER112 |
| B | HOH601 |
| B | HOH672 |
| site_id | AD2 |
| Number of Residues | 10 |
| Details | binding site for residue LYS B 507 |
| Chain | Residue |
| A | CYS374 |
| A | GLU375 |
| B | LYS75 |
| B | ARG302 |
| B | ARG343 |
| B | TYR347 |
| B | TYR404 |
| B | MET408 |
| B | PLP506 |
| B | HOH857 |
| site_id | AD3 |
| Number of Residues | 22 |
| Details | binding site for Di-peptide PLP B 506 and LYS B 75 |
| Chain | Residue |
| B | GLY257 |
| B | GLU299 |
| B | GLY301 |
| B | ARG302 |
| B | TYR404 |
| B | LYS507 |
| B | HOH617 |
| B | HOH666 |
| B | HOH739 |
| B | HOH787 |
| B | HOH828 |
| A | CYS374 |
| A | TYR412 |
| A | ASN413 |
| B | ALA73 |
| B | SER74 |
| B | ALA76 |
| B | PHE77 |
| B | GLU100 |
| B | ARG164 |
| B | HIS216 |
| B | GLY256 |
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 | Active site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 18 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_02120","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"HAMAP-Rule","id":"MF_02120","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
