Malate dehydrogenase

Crystal Structure of Malate Dehydrogenase 2x0i

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 Kreb's Cycle, which is critical to cellular respiration in cells [1]; however, the enzyme is also in many other metabolic pathways such as glyoxylate bypass, amino acid synthesis, glucogenesis, and oxidation/reduction balance . It is classified as an oxidoreductase[2]. Malate Dehydrogenase has been extensively studied due to its many isozymes . The enzyme exists in two places inside a cell: the 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 . 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 . During catalysis, the enzyme subunits are non-cooperative between active sites. The mitochondrial MDH is complexly, allosterically controlled by citrate, but no other known metabolic regulation mechanisms have been discovered. Further, the exact mechanism of regulation has yet to be discovered . Kinetically, the pH of optimization is 7.6 for oxaloacetate conversion and 9.6 for malate conversion. The reported K(m) value for malate conversion is 215 uM and the V(max) value is 87.8 uM/min .

<applet load='2x0i' size='400' frame='true' align='right' scene='Malate_dehydrogenase/Cv/1' / caption= 'Malate dehydrogenase monomer complex with NADH, sulfate and Na+ ion'>

StructureStructure

The secondary structure of a single subunit contains a wrapped by . Near the sodium bound end, 4 small anti-parallel beta sheets and 1 small alpha helix enable a turn in the residue chain. 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 for a NAD+ cofactor to attach near the beta sheeting. The structure most nearly resembles an alternating alpha/beta classification. As for the 3D structure, the enzyme forms a sort of for the substrate to bind.

MechanismMechanism

The mechanism of catalysis is dependent on . These residues are HIS 195 and ASP 168, which are both involved in hydrogen bonding, ASP 53 associated with , 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 into an up position 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. R102 and R109 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 .

Evolutionary DivergenceEvolutionary 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’s [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 Dehydrogenase3D Structures of Malate Dehydrogenase

Update June 2012

The holo-MDH contains NAD or its derivatives while the apo-MDH lacks it.

Holo-MDHHolo-MDH

2x0r – HmMDH (mutant)+NAD - Haloarcula marismortui
1o6z - HmMDH (mutant)+NADH
1hlp – HmMDH+NAD
1x0i – AfMDH+NADH – Archaeoglobus fulgidus
2x0j - AfMDH+etheno-NAD
1hlp – HmMDH+NAD
1x0i – AfMDH+NADH
2x0j - AfMDH+etheno-NAD
1ib6, 1ie3 – EcMDH (mutant)+NAD - Escherichia coli
1emd – EcMDH+NAD+citrate
3i0p – MDH+NAD – Entamoeba histolytica
3gvh – BmMDH+NAD – Brucella melitensis
3gvi - BmMDH+ADP
2hjr – MDH+adenosine diphosphoribose – Cryptosporidium parvum
2dfd – MDH+NAD – human type 2
1wze – TfMDH (mutant)+NAD – Thermus flavus
1wzi - TfMDH (mutant)+NDP
1bdm - TfMDH (mutant)+beta-6-hydroxy-1,4,5,6-tetrhydronicotinamide adenine dinucleotide
1bmd – TfMDH+NAD
1y7t – TtMDH+NADPH – Thermus thermophilus
2cvq - TtMDH+NADP
1v9n – MDH+NADPH – Pyrococcus horikoshii
1z2i – MDH+NAD – Agrobacterium tumefaciens
1uxg, 1uxh, 1uxi, 1uxj, 1uxk, 1ur5 – MDH (mutant)+NAD – Chloroflexus aurantiacus
1guz, 1guy, 1gv0 – CvMDH+NAD – Chlorobium vibrioforme
1civ – MDH+NADP – Flaveria bidentis
1b8u, 1b8v – AaMDH+NAD - Aquaspirillum arcticum
5mdh – SsMDH+NAD+alpha-ketomalonic acid – Sus scrofa
4mdh – SsMDH+NAD

apo-MDHapo-MDH

2j5r, 2j5k, 2j5q, 1d3a – HmMDH
2hlp – HmMDH (mutant)
3hhp, 2pwz – EcMDH
3fi9 – MDH – Porphyromonas gingivalis
3d5t - MDH – Burkholderia pseudomallei
2d4a – MDH – Aeropyrum pernix
1iz9 - TtMDH
1sev, 1smk – MDH – Citrullus lanatus
1gv1 – CvMDH
1b8p – AaMDH
7mdh – MDH – Sorgum bicolor
1mld – SsMDH
2cmd - EcMd+citrate
3nep – Md – Salinibacter ruber
3p7m – Md – Francisella tularensis
3tl2 – Md – Bacillus anthracis
4e0b – Md – Vibrio vulnificus

Additional ResourcesAdditional Resources

For additional information, see: Carbohydrate Metabolism