3I7S
Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound in the active site.
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 | 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 | 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 | ARG161 | |
B | ARG161 |
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 | 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 |