1xdw - Revision history

OCA at 08:49, 14 February 2024

OCA — Wed, 14 Feb 2024 08:49:48 GMT

←Older revision		Revision as of 08:49, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1xdw' size='340' side='right'caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='1xdw' size='340' side='right'caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Acife Acife~~]. 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 [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XDW FirstGlance]. <br>	+	<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>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~hgh (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=905 ACIFE])~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.98Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [~~http~~://pdbe.org/1xdw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xdw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdw ProSAT]</span></td></tr>	+	<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>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 17:
	</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].		</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].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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:15634349<ref>PMID:15634349</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1xdw" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acife~~]]	+	[[Category: Acidaminococcus fermentans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bresser, J]]	+	[[Category: Bresser J]]
-	[[Category: Buckel, W]]	+	[[Category: Buckel W]]
-	[[Category: Macedo-Ribeiro, S]]	+	[[Category: Macedo-Ribeiro S]]
-	[[Category: Martins~~, B M~~]]	+	[[Category: Martins BM]]
-	[[Category: Messerschmidt, A]]	+	[[Category: Messerschmidt A]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Structural variant of the bab rossmann fold~~]]	+

OCA at 09:54, 6 January 2021

OCA — Wed, 06 Jan 2021 09:54:45 GMT

←Older revision		Revision as of 09:54, 6 January 2021
Line 1:		Line 1:

	==NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans==		==NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans==
-	<StructureSection load='1xdw' size='340' side='right' caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='1xdw' size='340' side='right'caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acife Acife]. 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 [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acife Acife]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1XDW FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 ACIFE])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 ACIFE])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://pdbe.org/1xdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdw ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://pdbe.org/1xdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdw ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Acife]]		[[Category: Acife]]
		+	[[Category: Large Structures]]
	[[Category: Bresser, J]]		[[Category: Bresser, J]]
	[[Category: Buckel, W]]		[[Category: Buckel, W]]

OCA at 07:15, 18 April 2018

OCA — Wed, 18 Apr 2018 07:15:46 GMT

←Older revision		Revision as of 07:15, 18 April 2018
Line 1:		Line 1:
		+
	==NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans==		==NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans==
	<StructureSection load='1xdw' size='340' side='right' caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='1xdw' size='340' side='right' caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acife Acife]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acife Acife]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDW FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 ACIFE])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 ACIFE])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://pdbe.org/1xdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://pdbe.org/1xdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xdw ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 10:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xd/1xdw_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 07:53, 9 February 2016

OCA — Tue, 09 Feb 2016 07:53:13 GMT

←Older revision		Revision as of 07:53, 9 February 2016
Line 14:		Line 14:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:09, 10 September 2015

OCA — Thu, 10 Sep 2015 20:09:18 GMT

←Older revision		Revision as of 20:09, 10 September 2015
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	<StructureSection load='1xdw' size='340' side='right' caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='1xdw' size='340' side='right' caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acife Acife]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDW FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 ~~Acidaminococcus fermentans~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 ACIFE])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://pdbe.org/1xdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1xdw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acidaminococcus fermentans~~]]	+	[[Category: Acife]]
	[[Category: Bresser, J]]		[[Category: Bresser, J]]
	[[Category: Buckel, W]]		[[Category: Buckel, W]]

OCA at 13:39, 6 January 2015

OCA — Tue, 06 Jan 2015 13:39:29 GMT

←Older revision		Revision as of 13:39, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 Acidaminococcus fermentans])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 Acidaminococcus fermentans])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Acidaminococcus fermentans]]		[[Category: Acidaminococcus fermentans]]
-	[[Category: Bresser, J.]]	+	[[Category: Bresser, J]]
-	[[Category: Buckel, W.]]	+	[[Category: Buckel, W]]
-	[[Category: Macedo-Ribeiro, S.]]	+	[[Category: Macedo-Ribeiro, S]]
-	[[Category: Martins, B M.]]	+	[[Category: Martins, B M]]
-	[[Category: Messerschmidt, A.]]	+	[[Category: Messerschmidt, A]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Structural variant of the bab rossmann fold]]		[[Category: Structural variant of the bab rossmann fold]]

OCA at 20:57, 29 September 2014

OCA — Mon, 29 Sep 2014 20:57:44 GMT

←Older revision		Revision as of 20:57, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1xdw.~~png\|left~~\|200px]]	+	==NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans==
		+	<StructureSection load='1xdw' size='340' side='right' caption='[[1xdw]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xdw]] is a 1 chain structure with sequence 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XDW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hgh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=905 Acidaminococcus fermentans])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xdw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xdw RCSB], [http://www.ebi.ac.uk/pdbsum/1xdw PDBsum]</span></td></tr>
		+	<table>
		+	== 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/xd/1xdw_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~{{STRUCTURE_1xdw\| PDB=1xdw \| SCENE= }}~~	+	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:15634349<ref>PMID:15634349</ref>

-	~~===NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15634349}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xdw]] is~~ a ~~1 chain structure with sequence 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].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015634349<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Acidaminococcus fermentans]]		[[Category: Acidaminococcus fermentans]]
	[[Category: Bresser, J.]]		[[Category: Bresser, J.]]

OCA: Protected "1xdw" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:55:21 GMT

Protected "1xdw" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:55, 5 January 2013

OCA at 11:55, 5 January 2013

OCA — Sat, 05 Jan 2013 11:55:19 GMT

←Older revision		Revision as of 11:55, 5 January 2013
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-	{{Seed}}
	[[Image:1xdw.png\|left\|200px]]		[[Image:1xdw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xdw", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1xdw\| PDB=1xdw \| SCENE= }}		{{STRUCTURE_1xdw\| PDB=1xdw \| SCENE= }}

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

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15634349}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15634349 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15634349}}		{{ABSTRACT_PUBMED_15634349}}

	==About this Structure==		==About this Structure==
-	~~1XDW~~ is a 1 chain structure of sequence 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].	+	[[1xdw]] is a 1 chain structure with sequence 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].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15634349~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015634349</ref><references group="xtra"/>
	[[Category: Acidaminococcus fermentans]]		[[Category: Acidaminococcus fermentans]]
	[[Category: Bresser, J.]]		[[Category: Bresser, J.]]
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	[[Category: Martins, B M.]]		[[Category: Martins, B M.]]
	[[Category: Messerschmidt, A.]]		[[Category: Messerschmidt, A.]]
		+	[[Category: Oxidoreductase]]
	[[Category: Structural variant of the bab rossmann fold]]		[[Category: Structural variant of the bab rossmann fold]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:07:50 2009''

OCA at 06:07, 17 February 2009

OCA — Tue, 17 Feb 2009 06:07:50 GMT

←Older revision		Revision as of 06:07, 17 February 2009
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	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XDW OCA].	+	1XDW is a 1 chain structure of sequence 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].

	==Reference==		==Reference==
-	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~~:~~//www.ncbi.nlm.nih.gov/pubmed/15634349 15634349~~]	+	<ref group="xtra">PMID:15634349</ref><references group="xtra"/>
		+	[[Category: Acidaminococcus fermentans]]
	[[Category: Bresser, J.]]		[[Category: Bresser, J.]]
	[[Category: Buckel, W.]]		[[Category: Buckel, W.]]
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	[[Category: Structural variant of the bab rossmann fold]]		[[Category: Structural variant of the bab rossmann fold]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 11~~:30:~~35 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:07:50 2009''