1YXD
Structure of E. coli dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine to 2.0 A
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| 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 | 0019877 | biological_process | diaminopimelate biosynthetic process |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0044281 | biological_process | small molecule metabolic process |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| 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 | 0019877 | biological_process | diaminopimelate biosynthetic process |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0044281 | biological_process | small molecule metabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE K A 1301 |
| Chain | Residue |
| A | ALA152 |
| A | VAL154 |
| A | LYS155 |
| A | ILE157 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CL A 1302 |
| Chain | Residue |
| A | HOH1349 |
| A | GLY43 |
| A | THR44 |
| A | LEU101 |
| A | LYS161 |
| A | HOH1345 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K B 2301 |
| Chain | Residue |
| B | ALA152 |
| B | VAL154 |
| B | LYS155 |
| B | ILE157 |
| B | HOH3498 |
| B | HOH3584 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL B 2302 |
| Chain | Residue |
| B | THR44 |
| B | LEU101 |
| B | LYS161 |
| B | HOH3342 |
| B | HOH3360 |
| site_id | AC5 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE LYS B 1300 |
| Chain | Residue |
| A | SER48 |
| A | ALA49 |
| A | LEU51 |
| A | HIS53 |
| A | HIS56 |
| A | TYR106 |
| A | HOH1436 |
| B | ASN80 |
| B | GLU84 |
| B | LYS2300 |
| B | HOH3302 |
| B | HOH3304 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE LYS B 2300 |
| Chain | Residue |
| A | ASN80 |
| A | GLU84 |
| B | SER48 |
| B | ALA49 |
| B | LEU51 |
| B | HIS56 |
| B | TYR106 |
| B | LYS1300 |
| B | HOH3375 |
| B | HOH3432 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE LYS B 3301 |
| Chain | Residue |
| A | HOH1482 |
| B | ALA33 |
| B | HOH3305 |
| B | HOH3308 |
Functional Information from PROSITE/UniProt
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton donor/acceptor |
| Chain | Residue | Details |
| A | TYR133 | |
| B | TYR133 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | ACT_SITE: Schiff-base intermediate with substrate |
| Chain | Residue | Details |
| A | LYS161 | |
| B | LYS161 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00418, ECO:0000269|PubMed:20353808, ECO:0000269|PubMed:22552955 |
| Chain | Residue | Details |
| A | THR45 | |
| A | ILE203 | |
| B | THR45 | |
| B | ILE203 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | SITE: Part of a proton relay during catalysis |
| Chain | Residue | Details |
| A | THR44 | |
| A | TYR107 | |
| B | THR44 | |
| B | TYR107 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | SITE: L-lysine inhibitor binding; via carbonyl oxygen |
| Chain | Residue | Details |
| A | ALA49 | |
| B | ALA49 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | SITE: L-lysine inhibitor binding |
| Chain | Residue | Details |
| A | ASN80 | |
| A | GLU84 | |
| A | TYR106 | |
| B | ASN80 | |
| B | GLU84 | |
| B | TYR106 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dhp |
| Chain | Residue | Details |
| A | ARG138 | |
| A | TYR133 | |
| A | LYS161 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dhp |
| Chain | Residue | Details |
| B | ARG138 | |
| B | TYR133 | |
| B | LYS161 |
| site_id | CSA3 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dhp |
| Chain | Residue | Details |
| A | THR44 | |
| A | LYS161 | |
| A | THR45 |
| site_id | CSA4 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dhp |
| Chain | Residue | Details |
| B | THR44 | |
| B | LYS161 | |
| 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 | LYS161 | 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 | LYS161 | 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 |
