4MDH
REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION
Replaces: 2MDHReplaces: 1MDHFunctional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006099 | biological_process | tricarboxylic acid cycle |
| A | 0006107 | biological_process | oxaloacetate metabolic process |
| A | 0006108 | biological_process | malate metabolic process |
| A | 0006734 | biological_process | NADH metabolic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016615 | molecular_function | malate dehydrogenase activity |
| A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| A | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0030060 | molecular_function | L-malate dehydrogenase (NAD+) activity |
| A | 0047995 | molecular_function | hydroxyphenylpyruvate reductase activity |
| A | 0051287 | molecular_function | NAD binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006099 | biological_process | tricarboxylic acid cycle |
| B | 0006107 | biological_process | oxaloacetate metabolic process |
| B | 0006108 | biological_process | malate metabolic process |
| B | 0006734 | biological_process | NADH metabolic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016615 | molecular_function | malate dehydrogenase activity |
| B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| B | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0030060 | molecular_function | L-malate dehydrogenase (NAD+) activity |
| B | 0047995 | molecular_function | hydroxyphenylpyruvate reductase activity |
| B | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 A 334 |
| Chain | Residue |
| A | ASN130 |
| A | LEU157 |
| A | ARG161 |
| A | HIS186 |
| A | GLY230 |
| A | SER241 |
| A | NAD335 |
| A | HOH445 |
| A | HOH540 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 B 334 |
| Chain | Residue |
| B | ASN130 |
| B | HIS186 |
| B | NAD335 |
| B | HOH469 |
| site_id | AC3 |
| Number of Residues | 28 |
| Details | BINDING SITE FOR RESIDUE NAD A 335 |
| Chain | Residue |
| A | GLY10 |
| A | ALA12 |
| A | GLY13 |
| A | GLN14 |
| A | ILE15 |
| A | ASP41 |
| A | ILE42 |
| A | VAL86 |
| A | GLY87 |
| A | SER88 |
| A | MET89 |
| A | PRO90 |
| A | VAL128 |
| A | GLY129 |
| A | ASN130 |
| A | LEU154 |
| A | HIS186 |
| A | SER241 |
| A | ALA245 |
| A | SO4334 |
| A | HOH362 |
| A | HOH366 |
| A | HOH370 |
| A | HOH396 |
| A | HOH424 |
| A | HOH541 |
| A | HOH552 |
| B | GLY301 |
| site_id | AC4 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE NAD B 335 |
| Chain | Residue |
| B | GLY10 |
| B | ALA12 |
| B | GLY13 |
| B | GLN14 |
| B | ILE15 |
| B | ASP41 |
| B | ILE42 |
| B | MET45 |
| B | VAL86 |
| B | SER88 |
| B | VAL128 |
| B | GLY129 |
| B | ASN130 |
| B | LEU154 |
| B | LEU157 |
| B | HIS186 |
| B | SER240 |
| B | SO4334 |
| B | HOH358 |
| B | HOH475 |
| B | HOH476 |
| B | HOH511 |
| B | HOH543 |
| B | HOH544 |
| B | HOH560 |
Functional Information from PROSITE/UniProt
| site_id | PS00068 |
| Number of Residues | 13 |
| Details | MDH Malate dehydrogenase active site signature. LTRLDhnRAkaqI |
| Chain | Residue | Details |
| A | LEU154-ILE166 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000305|PubMed:2775751 |
| Chain | Residue | Details |
| A | SER187 | |
| B | SER187 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10075524, ECO:0000269|PubMed:2775751 |
| Chain | Residue | Details |
| A | ALA11 | |
| A | ILE42 | |
| A | GLY129 | |
| B | ALA11 | |
| B | ILE42 | |
| B | GLY129 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:10075524 |
| Chain | Residue | Details |
| A | ARG92 | |
| A | LYS98 | |
| A | PRO131 | |
| A | ALA162 | |
| B | ARG92 | |
| B | LYS98 | |
| B | PRO131 | |
| B | ALA162 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10075524 |
| Chain | Residue | Details |
| A | VAL105 | |
| A | GLY112 | |
| B | VAL105 | |
| B | GLY112 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylserine => ECO:0000269|PubMed:3606987 |
| Chain | Residue | Details |
| A | GLU2 | |
| B | GLU2 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P14152 |
| Chain | Residue | Details |
| A | CYS110 | |
| A | ASP214 | |
| A | GLU318 | |
| B | CYS110 | |
| B | ASP214 | |
| B | GLU318 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P40925 |
| Chain | Residue | Details |
| A | TYR118 | |
| A | LYS121 | |
| B | TYR118 | |
| B | LYS121 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P14152 |
| Chain | Residue | Details |
| A | TRP217 | |
| A | ARG309 | |
| B | TRP217 | |
| B | ARG309 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:P14152 |
| Chain | Residue | Details |
| A | GLY230 | |
| B | GLY230 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P40925 |
| Chain | Residue | Details |
| A | SER241 | |
| A | ALA333 | |
| B | SER241 | |
| B | ALA333 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P14152 |
| Chain | Residue | Details |
| A | ILE298 | |
| B | ILE298 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O88989 |
| Chain | Residue | Details |
| A | SER332 | |
| B | SER332 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | a catalytic site defined by CSA, PubMed 2775751 |
| Chain | Residue | Details |
| A | HIS186 | |
| A | ASP158 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | a catalytic site defined by CSA, PubMed 2775751 |
| Chain | Residue | Details |
| B | HIS186 | |
| B | ASP158 |
| site_id | MCSA1 |
| Number of Residues | 2 |
| Details | M-CSA 526 |
| Chain | Residue | Details |
| A | HIS159 | electrostatic stabiliser |
| A | SER187 | proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 2 |
| Details | M-CSA 526 |
| Chain | Residue | Details |
| B | HIS159 | electrostatic stabiliser |
| B | SER187 | proton acceptor, proton donor |
