1GDH

CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION

Summary for 1GDH

• Entry DOI: 10.2210/pdb1gdh/pdb
• Descriptor: D-GLYCERATE DEHYDROGENASE, SULFATE ION (3 entities in total)
• Functional Keywords: oxidoreductase(choh (d)-nad(p)+ (a))
• Biological source: Hyphomicrobium methylovorum
• Total number of polymer chains: 2
• Total formula weight: 70060.94

Authors

Goldberg, J.D.,Yoshida, T.,Brick, P. (deposition date: 1993-09-22, release date: 1994-01-31, Last modification date: 2024-02-07)

Primary citation

Goldberg, J.D.,Yoshida, T.,Brick, P.
Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution.
J.Mol.Biol., 236:1123-1140, 1994

PubMed Abstract: 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.

PubMed: 8120891
DOI: 10.1016/0022-2836(94)90016-7

Experimental method

X-RAY DIFFRACTION (2.4 Å)