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| [[Image:1gdh.gif|left|200px]]<br /><applet load="1gdh" size="450" color="white" frame="true" align="right" spinBox="true"
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| caption="1gdh, resolution 2.4Å" />
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| '''CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION'''<br />
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| ==Overview== | | ==CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION== |
| 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.
| | <StructureSection load='1gdh' size='340' side='right'caption='[[1gdh]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1gdh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hyphomicrobium_methylovorum Hyphomicrobium methylovorum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GDH FirstGlance]. <br> |
| 1GDH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hyphomicrobium_methylovorum Hyphomicrobium methylovorum] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GDH OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> |
| | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| ==Reference== | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gdh OCA], [https://pdbe.org/1gdh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gdh RCSB], [https://www.ebi.ac.uk/pdbsum/1gdh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gdh ProSAT]</span></td></tr> |
| 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8120891 8120891]
| | </table> |
| [[Category: Glycerate dehydrogenase]]
| | == Function == |
| | [https://www.uniprot.org/uniprot/DHGY_HYPME DHGY_HYPME] Active on hydroxypyruvate and glyoxylate. |
| | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> |
| | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/1gdh_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> |
| | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gdh ConSurf]. |
| | <div style="clear:both"></div> |
| | __TOC__ |
| | </StructureSection> |
| [[Category: Hyphomicrobium methylovorum]] | | [[Category: Hyphomicrobium methylovorum]] |
| [[Category: Single protein]] | | [[Category: Large Structures]] |
| [[Category: Brick, P.]] | | [[Category: Brick P]] |
| [[Category: Goldberg, J.D.]] | | [[Category: Goldberg JD]] |
| [[Category: Yoshida, T.]] | | [[Category: Yoshida T]] |
| [[Category: SO4]]
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| [[Category: oxidoreductase(choh (d)-nad(p)+ (a))]]
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| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:57:54 2007''
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