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.
Keywords:
Methylobacterium extorquens; biofuels; malate dehydrogenase; methylotrophs.
MeSH terms
-
Adenosine Diphosphate Ribose / chemistry*
-
Adenosine Diphosphate Ribose / metabolism
-
Amino Acid Sequence
-
Apoenzymes / chemistry
-
Apoenzymes / genetics
-
Apoenzymes / metabolism
-
Bacterial Proteins / chemistry*
-
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 / chemistry*
-
Malate Dehydrogenase / genetics
-
Malate Dehydrogenase / metabolism
-
Malates / chemistry*
-
Malates / metabolism
-
Methylobacterium extorquens / chemistry*
-
Methylobacterium extorquens / enzymology
-
Models, Molecular
-
NAD / chemistry*
-
NAD / metabolism
-
Oxaloacetic Acid / chemistry*
-
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
Substances
-
Apoenzymes
-
Bacterial Proteins
-
Malates
-
Protons
-
Recombinant Proteins
-
NAD
-
Adenosine Diphosphate Ribose
-
Oxaloacetic Acid
-
malic acid
-
Malate Dehydrogenase