3I7S
Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound in the active site.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0019877 | biological_process | diaminopimelate biosynthetic process |
| A | 0042802 | molecular_function | identical protein binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0008652 | biological_process | amino acid biosynthetic process |
| B | 0008840 | molecular_function | 4-hydroxy-tetrahydrodipicolinate synthase activity |
| B | 0009085 | biological_process | lysine biosynthetic process |
| B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0019877 | biological_process | diaminopimelate biosynthetic process |
| B | 0042802 | molecular_function | identical protein binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 293 |
| Chain | Residue |
| A | SER48 |
| B | TYR107 |
| A | ALA49 |
| A | GLY78 |
| A | VAL103 |
| A | TYR106 |
| A | GOL297 |
| A | HOH337 |
| A | HOH360 |
| B | ASN80 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL A 294 |
| Chain | Residue |
| A | LYS174 |
| A | GLU175 |
| A | VAL177 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE K A 295 |
| Chain | Residue |
| A | ALA152 |
| A | VAL154 |
| A | LYS155 |
| A | ILE157 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K A 296 |
| Chain | Residue |
| A | SER48 |
| A | ALA49 |
| A | LEU51 |
| A | GOL297 |
| A | HOH360 |
| A | HOH361 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE GOL A 297 |
| Chain | Residue |
| A | ALA49 |
| A | ASN80 |
| A | TYR106 |
| A | GOL293 |
| A | K296 |
| A | HOH301 |
| A | HOH321 |
| A | HOH331 |
| A | HOH360 |
| A | HOH361 |
| B | ASN80 |
| B | TYR106 |
| B | GOL293 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE PYR A 298 |
| Chain | Residue |
| A | ALA8 |
| A | GLY43 |
| A | THR44 |
| A | THR45 |
| A | LEU101 |
| A | TYR133 |
| A | HOH349 |
| A | HOH350 |
| A | HOH351 |
| A | HOH363 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PO4 A 299 |
| Chain | Residue |
| A | ARG21 |
| A | LYS25 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PO4 A 300 |
| Chain | Residue |
| A | ARG109 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 293 |
| Chain | Residue |
| A | ASN80 |
| A | TYR107 |
| A | GOL297 |
| B | SER48 |
| B | ALA49 |
| B | TYR106 |
| site_id | BC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 294 |
| Chain | Residue |
| B | ASP29 |
| B | VAL32 |
| B | ALA33 |
| B | ARG70 |
| B | HIS125 |
| B | K295 |
| B | GOL300 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE K B 295 |
| Chain | Residue |
| B | HIS125 |
| B | GOL294 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K B 296 |
| Chain | Residue |
| A | HOH301 |
| B | SER48 |
| B | ALA49 |
| B | LEU51 |
| B | HOH398 |
| site_id | BC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 297 |
| Chain | Residue |
| B | PRO110 |
| B | SER111 |
| B | GLN112 |
| B | CYS141 |
| B | ASP142 |
| B | LEU144 |
| B | GOL301 |
| B | HOH322 |
| site_id | BC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE K B 298 |
| Chain | Residue |
| B | GLU84 |
| site_id | BC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE K B 299 |
| Chain | Residue |
| B | ALA152 |
| B | VAL154 |
| B | LYS155 |
| B | ILE157 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 300 |
| Chain | Residue |
| B | LYS26 |
| B | ILE86 |
| B | HIS125 |
| B | GOL294 |
| site_id | BC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL B 301 |
| Chain | Residue |
| B | SER111 |
| B | GLN112 |
| B | GOL297 |
| site_id | BC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PYR B 302 |
| Chain | Residue |
| B | GLY43 |
| B | THR44 |
| B | THR45 |
| B | LEU101 |
| B | TYR133 |
| B | HOH379 |
| B | HOH383 |
| B | HOH385 |
| B | HOH403 |
| site_id | CC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PO4 B 303 |
| Chain | Residue |
| B | ARG109 |
Functional Information from PROSITE/UniProt
| site_id | PS00665 |
| Number of Residues | 18 |
| Details | DHDPS_1 Dihydrodipicolinate synthase signature 1. AIVsvGTTGESatlnhdE |
| Chain | Residue | Details |
| A | ALA38-GLU55 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor/acceptor"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Schiff-base intermediate with substrate"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20353808","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22552955","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Site: {"description":"Part of a proton relay during catalysis"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Site: {"description":"L-lysine inhibitor binding; via carbonyl oxygen"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | Site: {"description":"L-lysine inhibitor binding"} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 6 |
| Details | M-CSA 267 |
| Chain | Residue | Details |
| A | THR44 | hydrogen bond acceptor, hydrogen bond donor |
| A | TYR107 | hydrogen bond donor |
| A | TYR133 | activator, electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| A | ARG138 | electrostatic stabiliser |
| A | ARG161 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | ILE203 | activator, increase electrophilicity, polar interaction, steric role |
| site_id | MCSA2 |
| Number of Residues | 6 |
| Details | M-CSA 267 |
| Chain | Residue | Details |
| B | THR44 | hydrogen bond acceptor, hydrogen bond donor |
| B | TYR107 | hydrogen bond donor |
| B | TYR133 | activator, electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| B | ARG138 | electrostatic stabiliser |
| B | ARG161 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| B | ILE203 | activator, increase electrophilicity, polar interaction, steric role |
