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

Abstract

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 -helix to a 3 10 -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.

Protein Conformational Space at the Edge of Allostery: Turning a Nonallosteric Malate Dehydrogenase into an “Allosterized” Enzyme Using Evolution-Guided Punctual Mutations

“…In numerous crystal structures of LDHs and MalDHs, the active site loop that carries the substrate discriminating amino acid at position 102 has been described in two different conformations ( Iwata et al 1994 ; Auerbach et al 1998 ; Winter et al 2003 ; Coquelle et al 2007 ; Arai et al 2010 ; González et al 2018 ). These correspond to either open or closed conformations, as observed in the Apo or Holo structures, respectively.…”