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1xdw

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[[Image:1xdw.gif|left|200px]]<br /><applet load="1xdw" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1xdw, resolution 1.98&Aring;" />
 
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'''NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans'''<br />
 
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==Overview==
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==NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans==
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NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyses the reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate and belongs to the d-2-hydroxyacid NAD(+)-dependent dehydrogenase (d-2-hydroxyacid dehydrogenase) protein family. Its crystal structure was determined by phase combination to 1.98 A resolution. Structure-function relationships obtained by the comparison of HGDH with other members of the d-2-hydroxyacid dehydrogenase family give a chemically satisfying view of the substrate stereoselectivity and catalytic requirements for the hydride transfer reaction. A model for substrate recognition and turnover is discussed. The HGDH active site architecture is structurally optimized to recognize and bind the negatively charged substrate 2-oxoglutarate. The structural position of the side chain of Arg52, and its counterparts in other family members, strongly correlates with substrate specificity towards substitutions at the C3 atom (linear or branched substrates). Arg235 interacts with the substrate's alpha-carboxylate and carbonyl groups, having a dual role in both substrate binding and activation, and the gamma-carboxylate group can dock at an arginine cluster. The proton-relay system built up by Glu264 and His297 permits His297 to act as acid-base catalyst and the 4Re-hydrogen from NADH is transferred as hydride to the carbonyl group Si-face leading to the formation of the correct enantiomer (R)-2-hydroxyglutarate.
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<StructureSection load='1xdw' size='340' side='right'caption='[[1xdw]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidaminococcus_fermentans Acidaminococcus fermentans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XDW FirstGlance]. <br>
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1XDW is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Acidaminococcus_fermentans Acidaminococcus fermentans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDW OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [https://pdbe.org/1xdw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [https://www.ebi.ac.uk/pdbsum/1xdw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdw ProSAT]</span></td></tr>
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==Reference==
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</table>
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Structural basis for stereo-specific catalysis in NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase from Acidaminococcus fermentans., Martins BM, Macedo-Ribeiro S, Bresser J, Buckel W, Messerschmidt A, FEBS J. 2005 Jan;272(1):269-81. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15634349 15634349]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdw_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1xdw ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Acidaminococcus fermentans]]
[[Category: Acidaminococcus fermentans]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Bresser, J.]]
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[[Category: Bresser J]]
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[[Category: Buckel, W.]]
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[[Category: Buckel W]]
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[[Category: Macedo-Ribeiro, S.]]
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[[Category: Macedo-Ribeiro S]]
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[[Category: Martins, B M.]]
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[[Category: Martins BM]]
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[[Category: Messerschmidt, A.]]
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[[Category: Messerschmidt A]]
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[[Category: structural variant of the bab rossmann fold]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:53:45 2008''
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Current revision

NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans

PDB ID 1xdw

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