3TWA
Crystal structure of gluconate dehydratase (TARGET EFI-501679) from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 complexed with magnesium and glycerol
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0009063 | biological_process | amino acid catabolic process |
| A | 0016052 | biological_process | carbohydrate catabolic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0047929 | molecular_function | gluconate dehydratase activity |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0009063 | biological_process | amino acid catabolic process |
| B | 0016052 | biological_process | carbohydrate catabolic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0047929 | molecular_function | gluconate dehydratase activity |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0009063 | biological_process | amino acid catabolic process |
| C | 0016052 | biological_process | carbohydrate catabolic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0047929 | molecular_function | gluconate dehydratase activity |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0009063 | biological_process | amino acid catabolic process |
| D | 0016052 | biological_process | carbohydrate catabolic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0047929 | molecular_function | gluconate dehydratase activity |
| E | 0000287 | molecular_function | magnesium ion binding |
| E | 0009063 | biological_process | amino acid catabolic process |
| E | 0016052 | biological_process | carbohydrate catabolic process |
| E | 0016829 | molecular_function | lyase activity |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0047929 | molecular_function | gluconate dehydratase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 420 |
| Chain | Residue |
| A | ASP225 |
| A | GLU251 |
| A | GLU277 |
| A | HOH424 |
| A | HOH518 |
| A | HOH708 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 421 |
| Chain | Residue |
| A | GLU277 |
| A | HIS327 |
| A | PRO329 |
| A | ASP331 |
| A | HOH492 |
| B | TYR82 |
| B | TRP83 |
| A | GLN45 |
| A | TYR160 |
| A | HIS227 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 422 |
| Chain | Residue |
| A | GLY330 |
| A | ILE332 |
| A | PRO334 |
| A | VAL337 |
| A | THR356 |
| A | PRO357 |
| A | MET358 |
| A | LEU362 |
| A | HOH482 |
| A | HOH536 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL A 423 |
| Chain | Residue |
| A | GLY86 |
| A | ILE88 |
| B | PRO87 |
| B | ILE88 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 420 |
| Chain | Residue |
| B | ASP225 |
| B | GLU251 |
| B | GLU277 |
| B | HOH423 |
| B | HOH517 |
| B | HOH622 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL B 421 |
| Chain | Residue |
| A | TYR82 |
| A | TRP83 |
| B | GLN45 |
| B | TYR160 |
| B | HIS227 |
| B | GLU277 |
| B | HIS327 |
| B | PRO329 |
| B | ASP331 |
| B | HOH538 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL B 422 |
| Chain | Residue |
| B | GLY330 |
| B | ILE332 |
| B | PRO334 |
| B | VAL337 |
| B | THR356 |
| B | PRO357 |
| B | MET358 |
| B | LEU362 |
| B | HOH490 |
| B | HOH509 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 420 |
| Chain | Residue |
| C | ASP225 |
| C | GLU251 |
| C | GLU277 |
| C | HOH431 |
| C | HOH520 |
| C | HOH675 |
| site_id | AC9 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL C 421 |
| Chain | Residue |
| C | GLN45 |
| C | TYR160 |
| C | HIS227 |
| C | GLU277 |
| C | HIS327 |
| C | PRO329 |
| C | ASP331 |
| C | HOH566 |
| D | TYR82 |
| D | TRP83 |
| site_id | BC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL C 422 |
| Chain | Residue |
| C | GLY330 |
| C | ILE332 |
| C | PRO334 |
| C | VAL337 |
| C | THR356 |
| C | PRO357 |
| C | LEU362 |
| C | HOH505 |
| C | HOH536 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL C 423 |
| Chain | Residue |
| C | GLY86 |
| C | PRO87 |
| C | ILE88 |
| D | PRO87 |
| D | ILE88 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 420 |
| Chain | Residue |
| D | ASP225 |
| D | GLU251 |
| D | GLU277 |
| D | HOH528 |
| D | HOH580 |
| D | HOH618 |
| site_id | BC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL D 421 |
| Chain | Residue |
| D | PRO329 |
| D | ASP331 |
| D | HOH497 |
| C | TYR82 |
| C | TRP83 |
| D | GLN45 |
| D | TYR160 |
| D | HIS227 |
| D | GLU277 |
| D | HIS327 |
| site_id | BC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL D 422 |
| Chain | Residue |
| D | ILE332 |
| D | PRO334 |
| D | VAL337 |
| D | THR356 |
| D | PRO357 |
| D | MET358 |
| D | LEU362 |
| D | HOH501 |
| D | HOH504 |
| site_id | BC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL E 420 |
| Chain | Residue |
| E | GLN45 |
| E | TRP83 |
| E | TYR160 |
| E | HIS227 |
| E | HIS327 |
| E | PRO329 |
| E | ASP331 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG E 421 |
| Chain | Residue |
| E | ASP225 |
| E | GLU251 |
| E | GLU277 |
| E | HOH422 |
| E | HOH761 |
| E | HOH889 |
Functional Information from PROSITE/UniProt
| site_id | PS00908 |
| Number of Residues | 26 |
| Details | MR_MLE_1 Mandelate racemase / muconate lactonizing enzyme family signature 1. AlSGVDmALwDIkGKlagmPVydLLG |
| Chain | Residue | Details |
| A | ALA92-GLY117 |
| site_id | PS00909 |
| Number of Residues | 32 |
| Details | MR_MLE_2 Mandelate racemase / muconate lactonizing enzyme family signature 2. FihDvHervtpvtAinlaktLeqyqlfyLEDP |
| Chain | Residue | Details |
| A | PHE222-PRO253 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 10 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000250 |
| Chain | Residue | Details |
| A | TYR160 | |
| A | HIS227 | |
| B | TYR160 | |
| B | HIS227 | |
| C | TYR160 | |
| C | HIS227 | |
| D | TYR160 | |
| D | HIS227 | |
| E | TYR160 | |
| E | HIS227 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 30 |
| Details | BINDING: |
| Chain | Residue | Details |
| C | HIS327 | |
| C | ASP331 | |
| C | GLU354 | |
| D | GLN45 | |
| D | GLU277 | |
| D | ARG298 | |
| D | HIS327 | |
| D | ASP331 | |
| D | GLU354 | |
| E | GLN45 | |
| E | GLU277 | |
| E | ARG298 | |
| E | HIS327 | |
| E | ASP331 | |
| E | GLU354 | |
| A | GLN45 | |
| A | GLU277 | |
| A | ARG298 | |
| A | HIS327 | |
| A | ASP331 | |
| A | GLU354 | |
| B | GLN45 | |
| B | GLU277 | |
| B | ARG298 | |
| B | HIS327 | |
| B | ASP331 | |
| B | GLU354 | |
| C | GLN45 | |
| C | GLU277 | |
| C | ARG298 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 5 |
| Details | BINDING: BINDING => ECO:0000250 |
| Chain | Residue | Details |
| A | HIS129 | |
| B | HIS129 | |
| C | HIS129 | |
| D | HIS129 | |
| E | HIS129 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 10 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:24697546 |
| Chain | Residue | Details |
| C | GLU251 | |
| D | ASP225 | |
| D | GLU251 | |
| E | ASP225 | |
| E | GLU251 | |
| B | GLU251 | |
| C | ASP225 | |
| A | ASP225 | |
| A | GLU251 | |
| B | ASP225 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 5 |
| Details | SITE: Important for activity and substrate specificity; Pro is observed in family members with low D-mannonate dehydratase activity => ECO:0000250 |
| Chain | Residue | Details |
| A | PRO329 | |
| B | PRO329 | |
| C | PRO329 | |
| D | PRO329 | |
| E | PRO329 |
