4MDH

REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4mdha1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	Malate dehydrogenase	pig (Sus scrofa ) [TaxId: 9823 ],	SCOPe (2.08)
A	d4mdha2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	Malate dehydrogenase	pig (Sus scrofa ) [TaxId: 9823 ],	SCOPe (2.08)
B	d4mdhb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	Malate dehydrogenase	pig (Sus scrofa ) [TaxId: 9823 ],	SCOPe (2.08)
B	d4mdhb2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	Lactate & malate dehydrogenases, C-terminal domain	Malate dehydrogenase	pig (Sus scrofa ) [TaxId: 9823 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	LDH/MDH-like	8068856	4000045	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LDH/MDH/AglA-like	8068857	3000039	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8068857	3000039	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ldh_1_C_3	e4mdhA3	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_3	ECOD (1.6)
A	Ldh_1_N	e4mdhA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)
B	Ldh_1_C_3	e4mdhB3	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Ldh_1_C_3	ECOD (1.6)
B	Ldh_1_N	e4mdhB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Ldh_1_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02866	lactate/malate dehydrogenase, alpha/beta C-terminal domain (Ldh_1_C)	lactate/malate dehydrogenase, alpha/beta C-terminal domain	L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the in ...	L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes.	Domain
A, B	PF00056	lactate/malate dehydrogenase, NAD binding domain (Ldh_1_N)	lactate/malate dehydrogenase, NAD binding domain	L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the in ...	L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	CYTOPLASMIC MALATE DEHYDROGENASE	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors malate dehydrogenase activity catalytic activity L-malate dehydrogenase activity hydroxyphenylpyruvate reductase activity NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors malate dehydrogenase activity catalytic activity L-malate dehydrogenase activity hydroxyphenylpyruvate reductase activity NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy organic substance metabolic process oxoacid metabolic process malate metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy organic substance metabolic process oxoacid metabolic process malate metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process organic acid metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process nucleotide metabolic process NAD metabolic process NADH metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process phosphorus metabolic process pyridine nucleotide metabolic process oxaloacetate metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
A, B	IPR001252	Malate dehydrogenase, active site	Active Site
A, B	IPR001557	L-lactate/malate dehydrogenase	Family
A, B	IPR011274	Malate dehydrogenase, NAD-dependent, cytosolic	Family
A, B	IPR001236	Lactate/malate dehydrogenase, N-terminal	Domain
A, B	IPR010945	Malate dehydrogenase, type 2	Family
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR022383	Lactate/malate dehydrogenase, C-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	malate dehydrogenase (type 2) M-CSA #526	Malate dehydrogenase catalysis the readily reversible dehydrogenation of malate to oxaloacetate. As the activated cofactor/substrate complex has a net negative charge, a positive counter-charge is provided by conserved arginines in the active site. By this mechanism, malate dehydrogenase uses charge balancing to achieve fivefold orders of magnitude in discrimination between potential substrates.	Defined by 2 residues: ASP:A-159 [auth A-158]HIS:A-187 [auth A-186] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.1.37 (PDB Primary Data) Search M-CSA Motif + EC 1.1.1.37

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.