1VM6
Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
A | 0009085 | biological_process | lysine biosynthetic process |
A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
A | 0019877 | biological_process | diaminopimelate biosynthetic process |
A | 0050661 | molecular_function | NADP binding |
A | 0051287 | molecular_function | NAD binding |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
B | 0009085 | biological_process | lysine biosynthetic process |
B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
B | 0019877 | biological_process | diaminopimelate biosynthetic process |
B | 0050661 | molecular_function | NADP binding |
B | 0051287 | molecular_function | NAD binding |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
C | 0009085 | biological_process | lysine biosynthetic process |
C | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
C | 0019877 | biological_process | diaminopimelate biosynthetic process |
C | 0050661 | molecular_function | NADP binding |
C | 0051287 | molecular_function | NAD binding |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0008839 | molecular_function | 4-hydroxy-tetrahydrodipicolinate reductase |
D | 0009085 | biological_process | lysine biosynthetic process |
D | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0016726 | molecular_function | oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor |
D | 0019877 | biological_process | diaminopimelate biosynthetic process |
D | 0050661 | molecular_function | NADP binding |
D | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE ACT B 217 |
Chain | Residue |
B | SER183 |
B | ARG184 |
site_id | AC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE ACT B 218 |
Chain | Residue |
B | HOH342 |
B | HIS127 |
B | HIS128 |
B | LYS131 |
B | ACT222 |
B | NAD300 |
B | HOH315 |
B | HOH317 |
site_id | AC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE ACT C 217 |
Chain | Residue |
C | ASP43 |
C | GLY67 |
C | GLY200 |
site_id | AC4 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE ACT B 219 |
Chain | Residue |
B | GLU176 |
site_id | AC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE ACT A 217 |
Chain | Residue |
A | HIS127 |
A | HIS128 |
A | LYS131 |
A | ACT218 |
A | NAD300 |
A | HOH318 |
A | HOH326 |
A | HOH392 |
site_id | AC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE ACT B 220 |
Chain | Residue |
B | SER110 |
B | LYS114 |
B | ALA145 |
site_id | AC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE ACT B 221 |
Chain | Residue |
B | PHE98 |
B | ILE100 |
B | VAL186 |
B | GLY190 |
B | LYS193 |
C | HOH309 |
site_id | AC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE ACT C 218 |
Chain | Residue |
B | PHE108 |
B | LEU112 |
C | PHE108 |
C | GLU111 |
site_id | AC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE ACT D 217 |
Chain | Residue |
D | THR73 |
D | ASP133 |
D | NAD300 |
D | HOH321 |
D | HOH382 |
site_id | BC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE ACT A 218 |
Chain | Residue |
A | THR73 |
A | TYR96 |
A | LYS131 |
A | SER136 |
A | GLY137 |
A | THR138 |
A | ACT217 |
A | NAD300 |
site_id | BC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE ACT D 218 |
Chain | Residue |
D | THR73 |
D | TYR96 |
D | LYS131 |
D | SER136 |
D | GLY137 |
D | THR138 |
site_id | BC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE ACT B 222 |
Chain | Residue |
B | THR73 |
B | TYR96 |
B | LYS131 |
B | SER136 |
B | GLY137 |
B | THR138 |
B | ACT218 |
B | NAD300 |
site_id | BC4 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE NAD A 300 |
Chain | Residue |
A | GLY7 |
A | SER9 |
A | GLY10 |
A | ARG11 |
A | MET12 |
A | ASP32 |
A | VAL33 |
A | PHE48 |
A | SER49 |
A | SER50 |
A | ALA53 |
A | GLY71 |
A | THR73 |
A | ALA95 |
A | TYR96 |
A | ASN97 |
A | PHE98 |
A | LYS131 |
A | PHE187 |
A | ACT217 |
A | ACT218 |
A | HOH313 |
A | HOH314 |
A | HOH318 |
A | HOH326 |
site_id | BC5 |
Number of Residues | 31 |
Details | BINDING SITE FOR RESIDUE NAD B 300 |
Chain | Residue |
B | GLY71 |
B | THR73 |
B | ALA95 |
B | TYR96 |
B | ASN97 |
B | PHE98 |
B | LYS131 |
B | ASP133 |
B | PHE187 |
B | ACT218 |
B | ACT222 |
B | HOH307 |
B | HOH315 |
B | HOH316 |
B | HOH338 |
B | HOH342 |
B | HOH387 |
B | HOH435 |
B | HOH485 |
B | GLY7 |
B | SER9 |
B | GLY10 |
B | ARG11 |
B | MET12 |
B | ASP32 |
B | VAL33 |
B | PHE48 |
B | SER49 |
B | SER50 |
B | GLU52 |
B | ALA53 |
site_id | BC6 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE NAD C 300 |
Chain | Residue |
C | GLY7 |
C | SER9 |
C | GLY10 |
C | ARG11 |
C | MET12 |
C | ASP32 |
C | VAL33 |
C | PHE48 |
C | SER49 |
C | SER50 |
C | GLU52 |
C | ALA53 |
C | GLY71 |
C | THR72 |
C | THR73 |
C | ALA95 |
C | TYR96 |
C | ASN97 |
C | PHE98 |
C | PHE187 |
C | PG4302 |
C | HOH337 |
C | HOH342 |
C | HOH384 |
site_id | BC7 |
Number of Residues | 28 |
Details | BINDING SITE FOR RESIDUE NAD D 300 |
Chain | Residue |
D | GLY7 |
D | SER9 |
D | GLY10 |
D | ARG11 |
D | MET12 |
D | ASP32 |
D | VAL33 |
D | PHE48 |
D | SER49 |
D | SER50 |
D | ALA53 |
D | GLY71 |
D | THR72 |
D | THR73 |
D | ALA95 |
D | TYR96 |
D | ASN97 |
D | PHE98 |
D | LYS131 |
D | ASP133 |
D | PHE187 |
D | ACT217 |
D | HOH319 |
D | HOH325 |
D | HOH331 |
D | HOH367 |
D | HOH395 |
D | HOH431 |
site_id | BC8 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE EDO C 301 |
Chain | Residue |
B | HIS-1 |
B | HIS-2 |
B | MET1 |
B | ASP43 |
B | HOH355 |
B | HOH436 |
C | ARG84 |
C | SER87 |
C | GLY204 |
C | MET205 |
site_id | BC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PG4 C 302 |
Chain | Residue |
C | TYR96 |
C | PRO161 |
C | SER183 |
C | ARG184 |
C | NAD300 |
C | HOH326 |
site_id | CC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE PG4 B 301 |
Chain | Residue |
B | TYR8 |
B | GLN17 |
B | LYS30 |
B | GLU37 |
B | LEU39 |
site_id | CC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE PG4 B 302 |
Chain | Residue |
B | LEU75 |
B | LEU80 |
B | TYR96 |
B | HOH492 |
B | HOH493 |
site_id | CC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE PG4 B 303 |
Chain | Residue |
B | ARG107 |
B | PHE108 |
B | PHE213 |
Functional Information from PROSITE/UniProt
site_id | PS01298 |
Number of Residues | 18 |
Details | DAPB Dihydrodipicolinate reductase signature. EIvEtHhrfKkDapSGTA |
Chain | Residue | Details |
A | GLU122-ALA139 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 4 |
Details | ACT_SITE: Proton donor/acceptor => ECO:0000255|HAMAP-Rule:MF_00102 |
Chain | Residue | Details |
A | HIS127 | |
B | HIS127 | |
C | HIS127 | |
D | HIS127 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | ACT_SITE: Proton donor => ECO:0000305 |
Chain | Residue | Details |
A | LYS131 | |
B | LYS131 | |
C | LYS131 | |
D | LYS131 |
site_id | SWS_FT_FI3 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000269|PubMed:18250105, ECO:0007744|PDB:1VM6 |
Chain | Residue | Details |
B | SER9 | |
B | GLY71 | |
B | ALA95 | |
B | LYS131 | |
C | SER9 | |
C | GLY71 | |
C | ALA95 | |
C | LYS131 | |
D | SER9 | |
D | GLY71 | |
D | ALA95 | |
D | LYS131 | |
A | SER9 | |
A | GLY71 | |
A | ALA95 | |
A | LYS131 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00102 |
Chain | Residue | Details |
A | HIS128 | |
C | HIS128 | |
C | GLY137 | |
D | HIS128 | |
D | GLY137 | |
A | GLY137 | |
B | HIS128 | |
B | GLY137 |