1gdh: Difference between revisions
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|PDB= 1gdh |SIZE=350|CAPTION= <scene name='initialview01'>1gdh</scene>, resolution 2.4Å | |PDB= 1gdh |SIZE=350|CAPTION= <scene name='initialview01'>1gdh</scene>, resolution 2.4Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene> | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Glycerate_dehydrogenase Glycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.29 1.1.1.29] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerate_dehydrogenase Glycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.29 1.1.1.29] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gdh OCA], [http://www.ebi.ac.uk/pdbsum/1gdh PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1gdh RCSB]</span> | |||
}} | }} | ||
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[[Category: Goldberg, J D.]] | [[Category: Goldberg, J D.]] | ||
[[Category: Yoshida, T.]] | [[Category: Yoshida, T.]] | ||
[[Category: oxidoreductase(choh (d)-nad(p)+ (a))]] | [[Category: oxidoreductase(choh (d)-nad(p)+ (a))]] | ||
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Revision as of 20:41, 30 March 2008
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| , resolution 2.4Å | |||||||
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| Ligands: | |||||||
| Activity: | Glycerate dehydrogenase, with EC number 1.1.1.29 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION
OverviewOverview
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.
About this StructureAbout this Structure
1GDH is a Single protein structure of sequence from Hyphomicrobium methylovorum. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution., Goldberg JD, Yoshida T, Brick P, J Mol Biol. 1994 Mar 4;236(4):1123-40. PMID:8120891
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