2gd2 - Revision history

OCA at 08:48, 25 October 2023

2023-10-25T08:48:46Z

←Older revision		Revision as of 08:48, 25 October 2023
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	<StructureSection load='2gd2' size='340' side='right'caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2gd2' size='340' side='right'caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CAA:ACETOACETYL~~-~~COENZYME+A'>CAA</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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]] 1.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1x74\|1x74]], [[2gce\|2gce]], [[2gci\|2gci]], [[2gd0\|2gd0]], [[2gd6\|2gd6]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CAB09031 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1773~~ "~~Bacillus tuberculosis~~" ~~(Zopf 1883) Klein 1884])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4]~~ </~~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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [https://pdbe.org/2gd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [https://www.ebi.ac.uk/pdbsum/2gd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gd2 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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [https://pdbe.org/2gd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [https://www.ebi.ac.uk/pdbsum/2gd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gd2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMACR_MYCTU AMACR_MYCTU] Catalyzes the epimerization of (2R)- and (2S)-methylacyl-coenzyme A (CoA) thioesters (PubMed:15632186, PubMed:19854148, PubMed:26348625). Accepts as substrates a wide range of alpha-methylacyl-CoAs, including (2R)-2-methylmyristoyl-CoA and (2S)-2-methylmyristoyl-CoA, (2R)-pristanoyl-CoA and (2S)-pristanoyl-CoA, and the cholesterol esters (25R)-3-oxo-cholest-4-en-26-oyl-CoA and (25S)-3-oxo-cholest-4-en-26-oyl-CoA (PubMed:15632186, PubMed:26348625). Can also catalyze the interconversion of the non-physiologic substrates (2R)-ibuprofenoyl-CoA and (2S)-ibuprofenoyl-CoA, which are potential competitive inhibitors of the enzyme (PubMed:19854148).<ref>PMID:15632186</ref> <ref>PMID:19854148</ref> <ref>PMID:26348625</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alpha-methylacyl-CoA racemase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bhaumik, P~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Wierenga, R K~~]]	+	[[Category: Bhaumik P]]
-	[[Category: ~~Alpha-methylacyl-coa racemase]]~~	+	[[Category: Wierenga RK]]
-	~~[[Category: Coa transferase]]~~	+
-	~~[[Category: Coenzyme some]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Proton transfer]]~~	+
-	~~[[Category: Racemase~~]]	+

OCA at 18:57, 10 March 2021

2021-03-10T18:57:08Z

←Older revision		Revision as of 18:57, 10 March 2021
Line 1:		Line 1:

	==The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety==		==The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety==
-	<StructureSection load='2gd2' size='340' side='right' caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='2gd2' size='340' side='right'caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]], [[2gce\|2gce]], [[2gci\|2gci]], [[2gd0\|2gd0]], [[2gd6\|2gd6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1x74\|1x74]], [[2gce\|2gce]], [[2gci\|2gci]], [[2gd0\|2gd0]], [[2gd6\|2gd6]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [~~http~~://pdbe.org/2gd2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2gd2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2gd2 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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [https://pdbe.org/2gd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [https://www.ebi.ac.uk/pdbsum/2gd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gd2 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/2gd2_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/2gd2_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>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
		+	[[Category: Large Structures]]
	[[Category: Bhaumik, P]]		[[Category: Bhaumik, P]]
	[[Category: Wierenga, R K]]		[[Category: Wierenga, R K]]

OCA at 07:51, 18 October 2017

2017-10-18T07:51:57Z

←Older revision		Revision as of 07:51, 18 October 2017
Line 1:		Line 1:
		+
	==The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety==		==The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety==
	<StructureSection load='2gd2' size='340' side='right' caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2gd2' size='340' side='right' caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [http://pdbe.org/2gd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2gd2 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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [http://pdbe.org/2gd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2gd2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gd2 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=2gd2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:25, 11 September 2015

2015-09-11T15:25:53Z

←Older revision		Revision as of 15:25, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2gd2' size='340' side='right' caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2gd2' size='340' side='right' caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]], [[2gce\|2gce]], [[2gci\|2gci]], [[2gd0\|2gd0]], [[2gd6\|2gd6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]], [[2gce\|2gce]], [[2gci\|2gci]], [[2gd0\|2gd0]], [[2gd6\|2gd6]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2gd2 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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [http://pdbe.org/2gd2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2gd2 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2gd2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Bhaumik, P]]		[[Category: Bhaumik, P]]
	[[Category: Wierenga, R K]]		[[Category: Wierenga, R K]]

OCA at 08:27, 16 January 2015

2015-01-16T08:27:27Z

←Older revision		Revision as of 08:27, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]], [[2gce\|2gce]], [[2gci\|2gci]], [[2gd0\|2gd0]], [[2gd6\|2gd6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]], [[2gce\|2gce]], [[2gci\|2gci]], [[2gd0\|2gd0]], [[2gd6\|2gd6]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </span></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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2gd2 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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2gd2 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 33:		Line 33:
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Bhaumik, P.]]	+	[[Category: Bhaumik, P]]
-	[[Category: Wierenga, R K.]]	+	[[Category: Wierenga, R K]]
	[[Category: Alpha-methylacyl-coa racemase]]		[[Category: Alpha-methylacyl-coa racemase]]
	[[Category: Coa transferase]]		[[Category: Coa transferase]]

OCA at 09:37, 30 September 2014

2014-09-30T09:37:48Z

←Older revision		Revision as of 09:37, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2gd2.~~png~~\|~~left~~\|200px]]	+	==The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety==
		+	<StructureSection load='2gd2' size='340' side='right' caption='[[2gd2]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2gd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GD2 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAA:ACETOACETYL-COENZYME+A'>CAA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]], [[2gce\|2gce]], [[2gci\|2gci]], [[2gd0\|2gd0]], [[2gd6\|2gd6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAB09031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-methylacyl-CoA_racemase Alpha-methylacyl-CoA racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.4 5.1.99.4] </span></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=2gd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gd2 RCSB], [http://www.ebi.ac.uk/pdbsum/2gd2 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/gd/2gd2_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 ==
		+	Alpha-methylacyl-CoA racemases are essential enzymes for branched-chain fatty acid metabolism. Their reaction mechanism and the structural basis of their wide substrate specificity are poorly understood. High-resolution crystal structures of Mycobacterium tuberculosis alpha-methylacyl-CoA racemase (MCR) complexed with substrate molecules show the active site geometry required for catalysis of the interconversion of (2S) and (2R)-methylacyl-CoA. The thioester oxygen atom and the 2-methyl group are in a cis-conformation with respect to each other. The thioester oxygen atom fits into an oxyanion hole and the 2-methyl group points into a hydrophobic pocket. The active site geometry agrees with a 1,1-proton transfer mechanism in which the acid/base-pair residues are His126 and Asp156. The structures of the complexes indicate that the acyl chains of the S-substrate and the R-substrate bind in an S-pocket and an R-pocket, respectively. A unique feature of MCR is a large number of methionine residues in the acyl binding region, located between the S-pocket and the R-pocket. It appears that the (S) to (R) interconversion of the 2-methylacyl chiral center is coupled to a movement of the acyl group over this hydrophobic, methionine-rich surface, when moving from its S-pocket to its R-pocket, whereas the 2-methyl moiety and the CoA group remain fixed in their respective pockets.

-	~~{{STRUCTURE_2gd2\| PDB=2gd2 \| SCENE= }}~~	+	The catalysis of the 1,1-proton transfer by alpha-methyl-acyl-CoA racemase is coupled to a movement of the fatty acyl moiety over a hydrophobic, methionine-rich surface.,Bhaumik P, Schmitz W, Hassinen A, Hiltunen JK, Conzelmann E, Wierenga RK J Mol Biol. 2007 Apr 6;367(4):1145-61. Epub 2007 Jan 27. PMID:17320106<ref>PMID:17320106</ref>

-	~~===The 1~~,~~1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves~~ a ~~smooth, methionine-rich surface for binding~~ the ~~fatty acyl moiety===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17320106}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2gd2]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017320106<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]

OCA: Protected "2gd2" [edit=sysop:move=sysop]

2013-01-07T14:32:16Z

Protected "2gd2" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:32, 7 January 2013

OCA at 14:32, 7 January 2013

2013-01-07T14:32:14Z

←Older revision		Revision as of 14:32, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2gd2.png\|left\|200px]]		[[Image:2gd2.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2gd2", 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_2gd2\| PDB=2gd2 \| SCENE= }}		{{STRUCTURE_2gd2\| PDB=2gd2 \| SCENE= }}

	===The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety===		===The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17320106}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17320106 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17320106}}		{{ABSTRACT_PUBMED_17320106}}

	==About this Structure==		==About this Structure==
-	~~2GD2~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA].	+	[[2gd2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17320106~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017320106</ref><references group="xtra"/>
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
Line 31:		Line 19:
	[[Category: Coa transferase]]		[[Category: Coa transferase]]
	[[Category: Coenzyme some]]		[[Category: Coenzyme some]]
		+	[[Category: Isomerase]]
	[[Category: Proton transfer]]		[[Category: Proton transfer]]
	[[Category: Racemase]]		[[Category: Racemase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:07:21 2009''

OCA at 00:07, 18 February 2009

2009-02-18T00:07:27Z

←Older revision		Revision as of 00:07, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2GD2 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA].	+	2GD2 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GD2 OCA].

	==Reference==		==Reference==
-	The catalysis of the 1,1-proton transfer by alpha-methyl-acyl-CoA racemase is coupled to a movement of the fatty acyl moiety over a hydrophobic, methionine-rich surface., Bhaumik P, Schmitz W, Hassinen A, Hiltunen JK, Conzelmann E, Wierenga RK, J Mol Biol. 2007 Apr 6;367(4):1145-61. Epub 2007 Jan 27. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17320106 17320106]~~	+	<ref group="xtra">PMID:17320106</ref><references group="xtra"/>
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Single protein]]
	[[Category: Bhaumik, P.]]		[[Category: Bhaumik, P.]]
	[[Category: Wierenga, R K.]]		[[Category: Wierenga, R K.]]
Line 35:		Line 34:
	[[Category: Racemase]]		[[Category: Racemase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 08~~:54:~~55 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:07:21 2009''

OCA at 05:54, 29 July 2008

2008-07-29T05:54:59Z

←Older revision		Revision as of 05:54, 29 July 2008
Line 1:		Line 1:
-	[[Image:2gd2.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2gd2.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2gd2\| PDB=2gd2 \| SCENE= }}		{{STRUCTURE_2gd2\| PDB=2gd2 \| SCENE= }}

-	~~'''~~The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety~~'''~~	+	===The 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety===


-	~~==Overview==~~	+	<!--
-	~~Alpha~~-~~methylacyl~~-CoA racemases are essential enzymes for branched-chain fatty acid metabolism. Their reaction mechanism and the structural basis of their wide substrate specificity are poorly understood. High-resolution crystal structures of Mycobacterium tuberculosis alpha-methylacyl-CoA racemase (MCR) complexed with substrate molecules show the active site geometry required for catalysis of the interconversion of (2S) and (2R)-methylacyl-CoA. The ~~thioester oxygen atom and~~ the ~~2-methyl group are in a cis-conformation with respect~~ to ~~each other. The thioester oxygen atom fits into an oxyanion hole and~~ the ~~2-methyl group points into a hydrophobic pocket. The active site geometry agrees with a 1,1-proton transfer mechanism in which the acid~~/~~base-pair residues are His126 and Asp156~~. ~~The structures of the complexes indicate that the acyl chains of the S-substrate and the R-substrate bind in an S-pocket and an R-pocket~~, ~~respectively. A unique feature of MCR~~ is ~~a large~~ number ~~of methionine residues in the acyl binding region, located between the S-pocket and the R-pocket~~. ~~It appears that the (S) to (R) interconversion of the 2~~-~~methylacyl chiral center is coupled to a movement of the acyl group over this hydrophobic, methionine~~-~~rich surface, when moving from its S-pocket to its R-pocket, whereas the 2-methyl moiety and the CoA group remain fixed in their respective pockets.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_17320106}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17320106 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17320106}}

	==About this Structure==		==About this Structure==
Line 30:		Line 34:
	[[Category: Proton transfer]]		[[Category: Proton transfer]]
	[[Category: Racemase]]		[[Category: Racemase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 04~~:58:02 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:54:55 2008''