PDBsum entry 1gdh

Oxidoreductase(choh (d)-NAD(p)+ (a))

PDB id: 1gdh

Contents

Protein chains

320 a.a. *

Ligands

SO4 ×2

Waters ×197

* Residue conservation analysis

PDB id:

1gdh

Name:

Oxidoreductase(choh (d)-NAD(p)+ (a))

Title:

Crystal structure of a NAD-dependent d-glycerate dehydrogenase at 2.4 angstroms resolution

Structure:

D-glycerate dehydrogenase. Chain: a, b. Engineered: yes

Source:

Hyphomicrobium methylovorum. Organism_taxid: 84

Biol. unit:

Dimer (from PQS)

Resolution:

2.40Å R-factor: 0.189

Authors:

J.D.Goldberg,T.Yoshida,P.Brick

Key ref:

J.D.Goldberg et al. (1994). Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution. J Mol Biol, 236, 1123-1140. PubMed id: 8120891 DOI: 10.1016/0022-2836(94)90016-7

Date:

22-Sep-93 Release date: 31-Jan-94

Protein chains

P36234  (DHGY_HYPME) -  Glycerate dehydrogenase from Hyphomicrobium methylovorum

Seq: 322 a.a.

Struc: 320 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.29 - glycerate dehydrogenase.
• Reaction: (R)-glycerate + NAD⁺ = 3-hydroxypyruvate + NADH + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/0022-2836(94)90016-7

J Mol Biol 236:1123-1140 (1994)

PubMed id: 8120891

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

J.D.Goldberg, T.Yoshida, P.Brick.

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.

Selected figure(s)

Figure 7.
Figure 7. .\ trrro iagram of the (:I)H holornzymr model intlic*ating the hypothetical juxtaposition of the SAD ~olrc~rtlr and protein srcontlar~ suc*turr rlemrnts.

Figure 9.
Figure 9. Stereo view showing the active ite of: a) D-glycerate ehydrogenase apoezyme: (b) D-glp?ratP ehydrogenase modelled ternary complex (only the nicotinamide ribose moiety of the coenzyme is shown): (c) I.-lactate ehydrogenase ternary complex with oxamate inhibitor (OXM). Co-ordinates are from dataset ILDM Protein Data Bak.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1994, 236, 1123-1140) copyright 1994.

Figures were selected by an automated process.