3FSY
Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) in complex with succinyl-CoA from Mycobacterium tuberculosis
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000287 | molecular_function | magnesium ion binding |
A | 0005737 | cellular_component | cytoplasm |
A | 0005886 | cellular_component | plasma membrane |
A | 0008666 | molecular_function | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity |
A | 0009085 | biological_process | lysine biosynthetic process |
A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
A | 0009274 | cellular_component | peptidoglycan-based cell wall |
A | 0016746 | molecular_function | acyltransferase activity |
A | 0019877 | biological_process | diaminopimelate biosynthetic process |
A | 0031402 | molecular_function | sodium ion binding |
A | 0046872 | molecular_function | metal ion binding |
A | 0120226 | molecular_function | succinyl-CoA binding |
B | 0000287 | molecular_function | magnesium ion binding |
B | 0005737 | cellular_component | cytoplasm |
B | 0005886 | cellular_component | plasma membrane |
B | 0008666 | molecular_function | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity |
B | 0009085 | biological_process | lysine biosynthetic process |
B | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
B | 0009274 | cellular_component | peptidoglycan-based cell wall |
B | 0016746 | molecular_function | acyltransferase activity |
B | 0019877 | biological_process | diaminopimelate biosynthetic process |
B | 0031402 | molecular_function | sodium ion binding |
B | 0046872 | molecular_function | metal ion binding |
B | 0120226 | molecular_function | succinyl-CoA binding |
C | 0000287 | molecular_function | magnesium ion binding |
C | 0005737 | cellular_component | cytoplasm |
C | 0005886 | cellular_component | plasma membrane |
C | 0008666 | molecular_function | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity |
C | 0009085 | biological_process | lysine biosynthetic process |
C | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
C | 0009274 | cellular_component | peptidoglycan-based cell wall |
C | 0016746 | molecular_function | acyltransferase activity |
C | 0019877 | biological_process | diaminopimelate biosynthetic process |
C | 0031402 | molecular_function | sodium ion binding |
C | 0046872 | molecular_function | metal ion binding |
C | 0120226 | molecular_function | succinyl-CoA binding |
D | 0000287 | molecular_function | magnesium ion binding |
D | 0005737 | cellular_component | cytoplasm |
D | 0005886 | cellular_component | plasma membrane |
D | 0008666 | molecular_function | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity |
D | 0009085 | biological_process | lysine biosynthetic process |
D | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
D | 0009274 | cellular_component | peptidoglycan-based cell wall |
D | 0016746 | molecular_function | acyltransferase activity |
D | 0019877 | biological_process | diaminopimelate biosynthetic process |
D | 0031402 | molecular_function | sodium ion binding |
D | 0046872 | molecular_function | metal ion binding |
D | 0120226 | molecular_function | succinyl-CoA binding |
E | 0000287 | molecular_function | magnesium ion binding |
E | 0005737 | cellular_component | cytoplasm |
E | 0005886 | cellular_component | plasma membrane |
E | 0008666 | molecular_function | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity |
E | 0009085 | biological_process | lysine biosynthetic process |
E | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
E | 0009274 | cellular_component | peptidoglycan-based cell wall |
E | 0016746 | molecular_function | acyltransferase activity |
E | 0019877 | biological_process | diaminopimelate biosynthetic process |
E | 0031402 | molecular_function | sodium ion binding |
E | 0046872 | molecular_function | metal ion binding |
E | 0120226 | molecular_function | succinyl-CoA binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE SCA A 331 |
Chain | Residue |
A | GLU257 |
D | PRO271 |
D | GLY305 |
D | HOH580 |
A | ARG290 |
A | ARG291 |
A | ASN292 |
A | SER293 |
A | LEU301 |
B | GLY265 |
B | ARG267 |
B | LYS277 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MPD A 340 |
Chain | Residue |
A | HIS94 |
A | ARG95 |
A | VAL156 |
A | PRO157 |
A | THR158 |
site_id | AC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SCA B 331 |
Chain | Residue |
B | GLU257 |
B | ARG290 |
B | ARG291 |
B | ASN292 |
B | SER293 |
B | GLY305 |
C | GLY265 |
C | ARG267 |
site_id | AC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE ACY B 332 |
Chain | Residue |
B | ARG201 |
B | SER203 |
B | SER219 |
B | ILE220 |
B | GLY222 |
B | HOH493 |
B | HOH503 |
site_id | AC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MPD B 340 |
Chain | Residue |
B | HIS94 |
B | ARG95 |
B | PRO157 |
B | THR158 |
B | HOH542 |
C | GLU128 |
site_id | AC6 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE SCA A 332 |
Chain | Residue |
A | ARG201 |
A | SER203 |
A | SER219 |
A | MET221 |
A | THR263 |
A | GLY265 |
A | LYS277 |
A | HOH493 |
A | HOH503 |
A | HOH545 |
A | HOH557 |
A | HOH570 |
A | HOH571 |
A | HOH586 |
C | GLU199 |
C | GLY216 |
C | GLY241 |
C | ALA242 |
C | VAL255 |
C | GLU257 |
C | ALA258 |
C | ARG290 |
C | ARG291 |
C | ASN292 |
C | SER293 |
C | HOH515 |
site_id | AC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE ACY C 331 |
Chain | Residue |
C | ARG201 |
C | SER203 |
C | SER219 |
C | ILE220 |
C | GLY222 |
C | HOH493 |
C | HOH503 |
site_id | AC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE ACY D 331 |
Chain | Residue |
D | ARG201 |
D | SER203 |
D | GLY216 |
D | SER219 |
D | ILE220 |
D | GLY222 |
site_id | AC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MPD D 340 |
Chain | Residue |
D | HIS94 |
D | ARG95 |
D | VAL156 |
D | PRO157 |
D | THR158 |
D | HOH557 |
site_id | BC1 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE SCA E 331 |
Chain | Residue |
E | SER293 |
E | HOH414 |
E | HOH418 |
E | HOH420 |
E | GLU199 |
E | ARG201 |
E | SER203 |
E | GLY216 |
E | SER219 |
E | MET221 |
E | GLY241 |
E | ALA242 |
E | GLU257 |
E | ALA258 |
E | THR263 |
E | GLY265 |
E | LYS277 |
E | ARG290 |
E | ARG291 |
E | ASN292 |
site_id | BC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE MG A 333 |
Chain | Residue |
A | ASP166 |
A | NA337 |
A | HOH401 |
B | ASP166 |
B | HOH401 |
C | ASP166 |
C | HOH401 |
site_id | BC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 334 |
Chain | Residue |
A | GLU183 |
A | HOH547 |
B | GLU183 |
B | HOH512 |
C | GLU183 |
site_id | BC4 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE MG D 332 |
Chain | Residue |
D | ASP166 |
D | ASP166 |
D | ASP166 |
D | NA334 |
D | NA334 |
D | NA334 |
D | HOH401 |
D | HOH401 |
D | HOH401 |
site_id | BC5 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE MG D 333 |
Chain | Residue |
D | GLU183 |
D | GLU183 |
D | GLU183 |
D | HOH552 |
D | HOH552 |
D | HOH552 |
D | HOH572 |
D | HOH572 |
D | HOH572 |
site_id | BC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG E 332 |
Chain | Residue |
E | ASP166 |
E | ASP166 |
E | ASP166 |
E | HOH401 |
E | HOH401 |
E | HOH401 |
site_id | BC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG E 333 |
Chain | Residue |
E | GLU183 |
E | GLU183 |
E | GLU183 |
site_id | BC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG E 334 |
Chain | Residue |
D | HOH536 |
D | HOH536 |
D | HOH536 |
E | HOH417 |
E | HOH417 |
E | HOH417 |
site_id | BC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG A 335 |
Chain | Residue |
A | HOH580 |
A | HOH581 |
A | HOH582 |
A | HOH583 |
site_id | CC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG B 333 |
Chain | Residue |
B | HOH560 |
B | HOH561 |
B | HOH562 |
B | HOH563 |
B | HOH564 |
B | HOH565 |
site_id | CC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 336 |
Chain | Residue |
A | HOH575 |
A | HOH576 |
A | HOH577 |
A | HOH578 |
D | HOH579 |
site_id | CC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE NA A 337 |
Chain | Residue |
A | ASP164 |
A | ASP166 |
A | MG333 |
B | ASP164 |
B | ASP166 |
C | ASP164 |
C | ASP166 |
site_id | CC4 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE NA D 334 |
Chain | Residue |
D | ASP164 |
D | ASP164 |
D | ASP164 |
D | ASP166 |
D | ASP166 |
D | ASP166 |
D | MG332 |
D | MG332 |
D | MG332 |
site_id | CC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE NA E 335 |
Chain | Residue |
E | ASP164 |
E | ASP164 |
E | ASP164 |
E | ASP166 |
E | ASP166 |
E | ASP166 |
site_id | CC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE NA B 334 |
Chain | Residue |
B | ASP210 |
B | HOH571 |
B | HOH571 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 5 |
Details | ACT_SITE: Acyl-anhydride intermediate => ECO:0000305|PubMed:19394346 |
Chain | Residue | Details |
A | GLU199 | |
B | GLU199 | |
C | GLU199 | |
D | GLU199 | |
E | GLU199 |
site_id | SWS_FT_FI2 |
Number of Residues | 50 |
Details | BINDING: BINDING => ECO:0000269|PubMed:19394346 |
Chain | Residue | Details |
A | ASP166 | |
A | ALA242 | |
A | GLU257 | |
A | GLY265 | |
A | LYS277 | |
A | ARG290 | |
B | ASP166 | |
B | GLU183 | |
B | ARG201 | |
B | GLY216 | |
B | SER219 | |
B | ALA242 | |
B | GLU257 | |
B | GLY265 | |
B | LYS277 | |
B | ARG290 | |
C | ASP166 | |
C | GLU183 | |
C | ARG201 | |
C | GLY216 | |
C | SER219 | |
C | ALA242 | |
C | GLU257 | |
C | GLY265 | |
C | LYS277 | |
C | ARG290 | |
D | ASP166 | |
D | GLU183 | |
D | ARG201 | |
D | GLY216 | |
D | SER219 | |
D | ALA242 | |
D | GLU257 | |
D | GLY265 | |
D | LYS277 | |
D | ARG290 | |
E | ASP166 | |
E | GLU183 | |
E | ARG201 | |
E | GLY216 | |
E | SER219 | |
E | ALA242 | |
E | GLU257 | |
E | GLY265 | |
E | LYS277 | |
E | ARG290 | |
A | GLU183 | |
A | ARG201 | |
A | GLY216 | |
A | SER219 |