Malate dehydrogenase (type 1)

 

Malonate dehydrogenase (MDHase) catalyses the reversible oxidation of malonate to oxaloacetate, a reaction dependent upon the oxidation/reduction of NAD cofactor. The enzyme functions as an important component in the citric acid cycle in the prokaryotic cytoplasm and the malate/aspartate shuttle in eukaryotic cytoplasm.

 

Reference Protein and Structure

Sequence
P61889 UniProt (1.1.1.37) IPR023958 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1emd - CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF ESCHERICHIA COLI MALATE DEHYDROGENASE, CITRATE AND NAD AT 1.9 ANGSTROMS RESOLUTION (1.9 Å) PDBe PDBsum 1emd
Catalytic CATH Domains
3.90.110.10 CATHdb (see all for 1emd)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.37)

NAD(1-)
CHEBI:57540ChEBI
+
(S)-malate(2-)
CHEBI:15589ChEBI
→
oxaloacetate(2-)
CHEBI:16452ChEBI
+
hydron
CHEBI:15378ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
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 catalyses the interconversion of malonate and oxaloacetate with the oxidation and reduction of the NAD cofactor. A histidine-aspartate pair form a proton relay system in the active site, which allows the histidine to act as both a general acid and general base to the substrate. In the direction of reduction, a water molecule acts as the proton donor while in the direction of oxidation the 2-hydroxy group of the substrate acts as the donor.

Catalytic Residues Roles

UniProt PDB* (1emd)
His177 His177A The residue acts as a general base towards the 2-hydroyl group of the oxaloacetate in the direction of oxidation, and as a general acid in the direction of reduction. It is involved in a proton relay mechanism with Asp 150. proton acceptor, proton donor
Asp150 Asp150A The residue acts to relay a proton from a water molecule to the His 195 residue in reduction of oxaloacetate to malate. modifies pKa
*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 reactant used, overall product formed, inferred reaction step, native state of enzyme regenerated

References

  1. 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.
  2. Zaitseva J et al. (2009), Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 866-869. Structure of Escherichia coli malate dehydrogenase at 1.45 A resolution. DOI:10.1107/S1744309109032217. PMID:19724119.
  3. Bell JK et al. (2001), J Biol Chem, 276, 31156-31162. Structural analyses of a malate dehydrogenase with a variable active site. DOI:10.1074/jbc.M100902200. PMID:11389141.
  4. 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.
  5. Hall MD et al. (1993), J Mol Biol, 232, 213-222. Crystal Structure of a Ternary Complex of Escherichia coli Malate Dehydrogenase Citrate and NAD at 1·9 Å Resolution. DOI:10.1006/jmbi.1993.1377. PMID:8331658.
  6. Hall MD et al. (1992), J Mol Biol, 226, 867-882. Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution. PMID:1507230.
  7. 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. His177, activated by Asp150, abstracts a proton from the hydroxyl group, with concomitant elimination of a hydride to the NAD(P) cofactor.

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Catalytic Residues Roles

Residue Roles
Asp150A modifies pKa
His177A proton acceptor

Chemical Components

proton transfer, hydride transfer, overall reactant used, overall product formed

Step 2. Inferred step in which water abstracts a proton from the catalytic histidine.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp150A modifies pKa
His177A proton donor

Chemical Components

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

Step 1. His177, activated by Asp150, abstracts a proton from the hydroxyl group, with concomitant elimination of a hydride to the NAD(P) cofactor.

Step 2. Inferred step in which water abstracts a proton from the catalytic histidine.

Products.

Contributors

James W. Murray, Craig Porter, Gemma L. Holliday