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 | 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 | 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 | 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 |