2QJJ
Crystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0008927 | molecular_function | mannonate dehydratase activity |
| 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 |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0008927 | molecular_function | mannonate dehydratase activity |
| 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 |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0008927 | molecular_function | mannonate dehydratase activity |
| 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 |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0008927 | molecular_function | mannonate dehydratase activity |
| 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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 1001 |
| Chain | Residue |
| A | ASP210 |
| A | GLU236 |
| A | GLU262 |
| A | HOH1219 |
| A | HOH1220 |
| A | HOH1221 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 1002 |
| Chain | Residue |
| B | HOH1217 |
| B | HOH1218 |
| B | HOH1219 |
| B | ASP210 |
| B | GLU236 |
| B | GLU262 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 1003 |
| Chain | Residue |
| C | ASP210 |
| C | GLU236 |
| C | GLU262 |
| C | HOH1212 |
| C | HOH1213 |
| C | HOH1214 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 1004 |
| Chain | Residue |
| D | ASP210 |
| D | GLU236 |
| D | GLU262 |
| D | HOH1211 |
| D | HOH1212 |
| D | HOH1213 |
Functional Information from PROSITE/UniProt
| site_id | PS00908 |
| Number of Residues | 26 |
| Details | MR_MLE_1 Mandelate racemase / muconate lactonizing enzyme family signature 1. AiAAVDmALwDIkAKmagmPLyqLLG |
| Chain | Residue | Details |
| A | ALA85-GLY110 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000305|PubMed:17944491 |
| Chain | Residue | Details |
| A | TYR159 | |
| A | HIS212 | |
| B | TYR159 | |
| B | HIS212 | |
| C | TYR159 | |
| C | HIS212 | |
| D | TYR159 | |
| D | HIS212 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 28 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ASN37 | |
| B | GLU262 | |
| B | ARG283 | |
| B | HIS312 | |
| B | ASP316 | |
| B | GLU339 | |
| C | ASN37 | |
| C | HIS122 | |
| C | GLU262 | |
| C | ARG283 | |
| C | HIS312 | |
| A | HIS122 | |
| C | ASP316 | |
| C | GLU339 | |
| D | ASN37 | |
| D | HIS122 | |
| D | GLU262 | |
| D | ARG283 | |
| D | HIS312 | |
| D | ASP316 | |
| D | GLU339 | |
| A | GLU262 | |
| A | ARG283 | |
| A | HIS312 | |
| A | ASP316 | |
| A | GLU339 | |
| B | ASN37 | |
| B | HIS122 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17944491 |
| Chain | Residue | Details |
| A | ASP210 | |
| A | GLU236 | |
| B | ASP210 | |
| B | GLU236 | |
| C | ASP210 | |
| C | GLU236 | |
| D | ASP210 | |
| D | GLU236 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | SITE: Important for activity and substrate specificity; Ala is observed in family members with high D-mannonate dehydratase activity that have no activity with D-gluconate |
| Chain | Residue | Details |
| A | ALA314 | |
| B | ALA314 | |
| C | ALA314 | |
| D | ALA314 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 9 |
| Details | M-CSA 960 |
| Chain | Residue | Details |
| A | ARG147 | modifies pKa |
| A | TYR159 | proton acceptor, proton donor |
| A | ASP210 | metal ligand |
| A | HIS212 | proton acceptor, proton donor |
| A | GLU236 | metal ligand |
| A | GLU262 | metal ligand |
| A | ARG283 | electrostatic stabiliser |
| A | GLU339 | electrostatic stabiliser |
| A | TRP402 | modifies pKa |
| site_id | MCSA2 |
| Number of Residues | 9 |
| Details | M-CSA 960 |
| Chain | Residue | Details |
| B | ARG147 | modifies pKa |
| B | TYR159 | proton acceptor, proton donor |
| B | ASP210 | metal ligand |
| B | HIS212 | proton acceptor, proton donor |
| B | GLU236 | metal ligand |
| B | GLU262 | metal ligand |
| B | ARG283 | electrostatic stabiliser |
| B | GLU339 | electrostatic stabiliser |
| B | TRP402 | modifies pKa |
| site_id | MCSA3 |
| Number of Residues | 9 |
| Details | M-CSA 960 |
| Chain | Residue | Details |
| C | ARG147 | modifies pKa |
| C | TYR159 | proton acceptor, proton donor |
| C | ASP210 | metal ligand |
| C | HIS212 | proton acceptor, proton donor |
| C | GLU236 | metal ligand |
| C | GLU262 | metal ligand |
| C | ARG283 | electrostatic stabiliser |
| C | GLU339 | electrostatic stabiliser |
| C | TRP402 | modifies pKa |
| site_id | MCSA4 |
| Number of Residues | 9 |
| Details | M-CSA 960 |
| Chain | Residue | Details |
| D | ARG147 | modifies pKa |
| D | TYR159 | proton acceptor, proton donor |
| D | ASP210 | metal ligand |
| D | HIS212 | proton acceptor, proton donor |
| D | GLU236 | metal ligand |
| D | GLU262 | metal ligand |
| D | ARG283 | electrostatic stabiliser |
| D | GLU339 | electrostatic stabiliser |
| D | TRP402 | modifies pKa |
