Malate dehydrogenase

Function

Malate Dehydrogenase (MDH; PDB entry 2x0i) is most known for its role in the metabolic pathway of the tricarboxylic acid cycle, also know as the Krebs cycle (after Sir Hans Krebs), which is critical to cellular respiration in cells [1]; however, the enzyme is also involved on many other metabolic pathways such as glyoxylate bypass, amino acid synthesis, gluconeogenesis, and oxidation/reduction balance ^[1]. It is classified as an oxidoreductase[2]. Malate dehydrogenase has been extensively studied due to its many isozymes ^[2]. The enzyme exists in two subcellular locations: mitochondria and cytoplasm. In the mitochondria, the enzyme catalyzes the reaction of malate to oxaloacetate; however, in the cytoplasm, the enzyme catalyzes oxaloacetate to malate to allow transport ^[3]. This conversion is an essential catalytic step in each different metabolic mechanism. The enzyme malate dehydrogenase is composed of either a dimer or tetramer depending on the location of the enzyme and the organism it is located in ^[4]. During catalysis, the enzyme subunits are non-cooperative between active sites. The mitochondrial MDH suffers a complex allosteric control by citrate, but no other known metabolic regulation mechanisms have been discovered. Further, the exact mechanism of regulation has yet to be discovered ^[5]. The optimal pH is 7.6 for oxaloacetate conversion and 9.6 for malate conversion. The reported K_m value for malate conversion is 215 µM and the V_max value is 87.8 µM/min ^[6]. For halophilic MDH details, see Halophilic malate dehydrogenase. See also:

• Krebs cycle carbons
• Krebs cycle importance
• Krebs cycle overview
• Citric Acid Cycle
• Krebs cycle step 8
• Glyoxylate cycle

Structure

The secondary structure of a single subunit contains a 9 beta sheet parallel backbone wrapped by 9 large alpha helices. Near the sodium bound end, 4 small anti-parallel beta sheets and 1 small alpha helix enable a turn in the residue chain (small turn). Opposite the sodium bound ligand, 6 alpha helices point towards a common point, three on each side of the beta sheet backbone. The alpha helices form a small groove for a NAD⁺ cofactor to attach near the beta sheets. The structure most nearly resembles an alternating alpha/beta classification. As for the 3D structure, the enzyme forms a sort of crevice for the substrate to bind.

Mechanism

The mechanism of catalysis is dependent on several invariant residues. These residues are His195 and Asp168, which are both involved in hydrogen bonding, Asp53 associated with NAD+ binding, and a triad of arginine residues at 102, 109, and 171. During the conversion of malate to oxaloacetate, a key conformational change occurs on the binding of substrate in which a “loop” flips to block the active site from the solvent. When this occurs, the other residues in the active site are brought closer to the substrate to enable the conversion. Arg102 and Arg109 are involved in this loop flip and thus invariant. After the loop flip, the malate complex is stabilized via hydrogen bonding before accepting a proton transfer from NADH to form oxaloacetate ^[7].

Evolutionary Divergence

The evolutionary past of MDH shows a divergence to form lactate dehydrogenase (LDH) which functions in a very similar way to MDH. Although there is a very low sequence conservation among MDH and LDH [3] the structure of the enzyme has remained relatively conserved. The key difference between the two is in the substrate: LDH catalyzes pyruvate to lactate.

3D Structures of Malate Dehydrogenase

Malate Dehydrogenase 3D structures