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 | 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 | 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 | 0019674 | biological_process | NAD+ metabolic process |
| A | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0030060 | molecular_function | L-malate dehydrogenase (NAD+) activity |
| A | 0047995 | molecular_function | (2R)-hydroxyphenylpyruvate reductase [NAD(P)H] activity |
| A | 0051287 | molecular_function | NAD binding |
| B | 0003824 | molecular_function | catalytic activity |
| 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 | 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 | 0019674 | biological_process | NAD+ metabolic process |
| B | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0030060 | molecular_function | L-malate dehydrogenase (NAD+) activity |
| B | 0047995 | molecular_function | (2R)-hydroxyphenylpyruvate reductase [NAD(P)H] 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 | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"2775751","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 18 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10075524","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2775751","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10075524","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10075524","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"3606987","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P14152","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P40925","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P14152","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"UniProtKB","id":"P14152","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P40925","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P14152","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
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 | ALA162 | electrostatic stabiliser |
| A | GLN190 | proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 2 |
| Details | M-CSA 526 |
| Chain | Residue | Details |
| B | ALA162 | electrostatic stabiliser |
| B | GLN190 | proton acceptor, proton donor |
