3DU0
E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in 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 | 4 |
| Details | BINDING SITE FOR RESIDUE K A 293 |
| Chain | Residue |
| A | ALA152 |
| A | VAL154 |
| A | LYS155 |
| A | ILE157 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K A 294 |
| Chain | Residue |
| A | SER48 |
| A | ALA49 |
| A | LEU51 |
| A | GOL296 |
| A | HOH382 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL A 295 |
| Chain | Residue |
| A | SER48 |
| A | ALA49 |
| A | GLY78 |
| A | VAL103 |
| A | TYR106 |
| A | GOL296 |
| A | HOH327 |
| A | HOH333 |
| A | HOH382 |
| B | ASN80 |
| B | TYR107 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 296 |
| Chain | Residue |
| A | ALA49 |
| A | ASN80 |
| A | TYR106 |
| A | K294 |
| A | GOL295 |
| A | HOH383 |
| B | ASN80 |
| B | TYR106 |
| B | K294 |
| B | GOL295 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL A 297 |
| Chain | Residue |
| A | VAL135 |
| A | PRO136 |
| A | SER137 |
| A | ALA163 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL A 298 |
| Chain | Residue |
| A | GLY165 |
| A | ASN166 |
| A | LEU167 |
| A | HOH318 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K B 293 |
| Chain | Residue |
| B | ALA152 |
| B | VAL154 |
| B | LYS155 |
| B | ILE157 |
| B | HOH469 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE K B 294 |
| Chain | Residue |
| A | GOL296 |
| A | HOH383 |
| A | HOH384 |
| B | SER48 |
| B | ALA49 |
| B | LEU51 |
| B | HOH412 |
| site_id | AC9 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL B 295 |
| Chain | Residue |
| A | ASN80 |
| A | TYR107 |
| A | GOL296 |
| B | SER48 |
| B | ALA49 |
| B | GLY78 |
| B | VAL103 |
| B | TYR106 |
| B | HOH336 |
| B | HOH412 |
| B | HOH434 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL B 296 |
| Chain | Residue |
| B | ASN166 |
| B | LEU167 |
| B | HOH304 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL B 297 |
| Chain | Residue |
| B | PRO136 |
| B | SER137 |
| B | ALA163 |
Functional Information from PROSITE/UniProt
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 | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dhp |
| Chain | Residue | Details |
| A | ARG138 | |
| A | TYR133 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dhp |
| Chain | Residue | Details |
| B | ARG138 | |
| B | TYR133 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dhp |
| Chain | Residue | Details |
| A | THR44 | |
| A | THR45 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dhp |
| Chain | Residue | Details |
| B | THR44 | |
| B | THR45 |
| 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 | KPI161 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | ALA207 | 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 | KPI161 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| B | ALA207 | activator, increase electrophilicity, polar interaction, steric role |
