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

González, Javier M.; Marti-Arbona, Ricardo; Chen, Julian C.; Broom-Peltz, Brian; Unkefer, Clifford Jay

doi:10.1107/S2053230X18011809

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

Journal Article · Wed Sep 19 00:00:00 EDT 2018 · Acta Crystallographica. Section F, Structural Biology Communications

DOI:https://doi.org/10.1107/S2053230X18011809· OSTI ID:1477666

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Universidad Nacional de Santiago del Estero (Argentina); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

In this paper, three high-resolution X-ray crystal structures of malate dehydrogenase (MDH; EC 1.1.1.37) from the methylotrophMethylobacterium extorquensAM1 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. Finally, 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.

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Research Organization:: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1477666

Report Number(s):: LA-UR-18-24857; ACSFEN

Journal Information:: Acta Crystallographica. Section F, Structural Biology Communications, Vol. 74, Issue 10; ISSN 2053-230X

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 5 works

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