Malate dehydrogenase (type 2)

 

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.

 

Reference Protein and Structure

Sequence
P11708 UniProt (1.1.1.37) IPR011274 (Sequence Homologues) (PDB Homologues)
Biological species
Sus scrofa (pig) Uniprot
PDB
4mdh - REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION (2.5 Å) PDBe PDBsum 4mdh
Catalytic CATH Domains
3.90.110.10 CATHdb (see all for 4mdh)
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Enzyme Reaction (EC:1.1.1.37)

(S)-malate(2-)
CHEBI:15589ChEBI
+
NAD(1-)
CHEBI:57540ChEBI
→
oxaloacetate(2-)
CHEBI:16452ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: L-malate dehydrogenase, L-malate-NAD(+) oxidoreductase, MDH, NAD-L-malate dehydrogenase, NAD-dependent malate dehydrogenase, NAD-dependent malic dehydrogenase, NAD-linked malate dehydrogenase, NAD-malate dehydrogenase, NAD-malic dehydrogenase, NAD-specific malate dehydrogenase, Malate (NAD) dehydrogenase, Malic acid dehydrogenase, Malic dehydrogenase,

Enzyme Mechanism

Introduction

The enzyme uses a catalytic Asp-His dyad. The C2 position of malate is situated above the C4 position of the nicotinamide moiety of NAD+. His186 is in position to abstract a proton from the hydroxyl group attached to C2 which then forms a carbonyl group with the transfer of a hydride to NAD+. Thus oxaloacetate and NADH are formed and may leave the active site. Asp158 hydrogen bonds to His186 stabilising the protonated imidazole ring.

Catalytic Residues Roles

UniProt PDB* (4mdh)
His187 His186(187)A Abstracts a proton from the hydroxyl group at C2. proton acceptor, proton donor
Asp159 Asp158(159)A Electrostatic stabilisation of the charge formed on His186 during the dehydrogenation. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, hydride transfer, overall product formed, overall reactant used, aromatic bimolecular nucleophilic addition, inferred reaction step, native state of enzyme regenerated

References

  1. Birktoft JJ et al. (1989), Biochemistry, 28, 6065-6081. Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-.ANG. resolution. DOI:10.1021/bi00440a051. PMID:2775751.
  2. Chapman AD et al. (1999), J Mol Biol, 285, 703-712. Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, α-Ketomalonate and TetrahydoNAD. DOI:10.1006/jmbi.1998.2357. PMID:10075524.
  3. Lemaire M et al. (1996), Eur J Biochem, 236, 947-952. The Catalytic Site of Chloroplastic NADP-Dependent Malate Dehydrogenase Contains A His/Asp Pair. DOI:10.1111/j.1432-1033.1996.00947.x. PMID:8665917.
  4. Goward CR et al. (1994), Protein Sci, 3, 1883-1888. Malate dehydrogenase: A model for structure, evolution, and catalysis. DOI:10.1002/pro.5560031027. PMID:7849603.
  5. Birktoft JJ et al. (1983), J Biol Chem, 258, 472-482. The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase. DOI:10.2210/pdb2mdh/pdb. PMID:6848515.

Step 1. His186 abstracts a proton from the hydroxyl group of L-malate. A hydride is transferred from L-malate to NAD+ in an aromatic bimolecular nucleophilic addition reaction, forming NADH and the product.

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Catalytic Residues Roles

Residue Roles
Asp158(159)A electrostatic stabiliser
His186(187)A proton acceptor

Chemical Components

proton transfer, hydride transfer, overall product formed, overall reactant used, ingold: aromatic bimolecular nucleophilic addition

Step 2. In an inferred reaction step His186 is deprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His186(187)A proton donor

Chemical Components

proton transfer, inferred reaction step, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. His186 abstracts a proton from the hydroxyl group of L-malate. A hydride is transferred from L-malate to NAD+ in an aromatic bimolecular nucleophilic addition reaction, forming NADH and the product.

Step 2. In an inferred reaction step His186 is deprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Gemma L. Holliday, Amelia Brasnett