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Acta Crystallogr F Struct Biol Commun ; 74(Pt 10): 610-616, 2018 Oct 01.
Article in English | MEDLINE | ID: mdl-30279311

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 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.


Subject(s)
Adenosine Diphosphate Ribose/chemistry , Bacterial Proteins/chemistry , Malate Dehydrogenase/chemistry , Malates/chemistry , Methylobacterium extorquens/chemistry , NAD/chemistry , Oxaloacetic Acid/chemistry , Adenosine Diphosphate Ribose/metabolism , Amino Acid Sequence , Apoenzymes/chemistry , Apoenzymes/genetics , Apoenzymes/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalytic Domain , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Hydrogen Bonding , Kinetics , Malate Dehydrogenase/genetics , Malate Dehydrogenase/metabolism , Malates/metabolism , Methylobacterium extorquens/enzymology , Models, Molecular , NAD/metabolism , Oxaloacetic Acid/metabolism , Protein Binding , Protein Conformation, alpha-Helical , Protein Interaction Domains and Motifs , Protein Multimerization , Protons , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity
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