Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution

J Mol Biol. 1994 Mar 4;236(4):1123-40. doi: 10.1016/0022-2836(94)90016-7.


D-Glycerate dehydrogenase (GDH) catalyzes the NADH-linked reduction of hydroxypyruvate to D-glycerate. GDH is a member of a family of NAD-dependent dehydrogenases that is characterized by a specificity for the D-isomer of the hydroxyacid substrate. The crystal structure of the apoenzyme form of GDH from Hyphomicrobium methylovorum has been determined by the method of isomorphous replacement and refined at 2.4 A resolution using a restrained least-squares method. The crystallographic R-factor is 19.4% for all 24,553 measured reflections between 10.0 and 2.4 A resolution. The GDH molecule is a symmetrical dimer composed of subunits of molecular mass 38,000, and shares significant structural homology with another NAD-dependent enzyme, formate dehydrogenase. The GDH subunit consists of two structurally similar domains that are approximately related to each other by 2-fold symmetry. The domains are separated by a deep cleft that forms the putative NAD and substrate binding sites. One of the domains has been identified as the NAD-binding domain based on its close structural similarity to the NAD-binding domains of other NAD-dependent dehydrogenases. The topology of the second domain is different from that found in the various catalytic domains of other dehydrogenases. A model of a ternary complex of GDH has been built in which putative catalytic residues are identified based on sequence homology between the D-isomer specific dehydrogenases. A structural comparison between GDH and L-lactate dehydrogenase indicates a convergence of active site residues and geometries for these two enzymes. The reactions catalyzed are chemically equivalent but of opposing stereospecificity. A hypothesis is presented to explain how the two enzymes may exploit the same coenzyme stereochemistry and a similar spatial arrangement of catalytic residues to carry out reactions that proceed to opposite enantiomers.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Apoenzymes / chemistry
  • Apoenzymes / genetics
  • Bacteria / enzymology
  • Bacteria / genetics
  • Binding Sites / genetics
  • Carbohydrate Dehydrogenases / chemistry*
  • Carbohydrate Dehydrogenases / genetics
  • Crystallization
  • Crystallography, X-Ray
  • L-Lactate Dehydrogenase / chemistry
  • L-Lactate Dehydrogenase / genetics
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Molecular Weight
  • NAD / chemistry
  • Protein Conformation
  • Sequence Homology, Amino Acid
  • Stereoisomerism


  • Apoenzymes
  • NAD
  • Carbohydrate Dehydrogenases
  • L-Lactate Dehydrogenase
  • Glycerate dehydrogenase