Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase

Three high‐resolution X‐ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotroph Methylobacterium extorquens AM1 are presented. By comparing the structures of apo MDH, a binary complex of MDH and NAD+, and a ternary complex of MDH and oxaloacetate with ADP‐ribose occupying the pyridine nucleotide‐binding site, conformational changes associated with the formation of the catalytic complex were characterized. While the substrate‐binding site is accessible in the enzyme resting state or NAD+‐bound forms, the substrate‐bound form exhibits a closed conformation. This conformational change involves the transition of an α‐helix to a 310‐helix, which causes the adjacent loop to close the active site following coenzyme and substrate binding. In the ternary complex, His284 forms a hydrogen bond to the C2 carbonyl of oxaloacetate, placing it in a position to donate a proton in the formation of (2S)‐malate. Crystal structures of apo malate dehydrogenase (MDH) from Methylobacterium extorquens, MDH bound to NAD+, and MDH with oxaloacetate and ADP‐ribose revealed conformational changes, closing the active site upon coenzyme and substrate binding. In the ternary complex, His284 is in position to donate a proton in the formation of (2S)‐malate.