2yim - Revision history

OCA at 10:53, 20 December 2023

2023-12-20T10:53:15Z

←Older revision		Revision as of 10:53, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='2yim' size='340' side='right'caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>		<StructureSection load='2yim' size='340' side='right'caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YIM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2~~-~~METHYLACETOACETYL+COA'>MC4</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.41Å</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]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [https://pdbe.org/2yim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [https://www.ebi.ac.uk/pdbsum/2yim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim 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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [https://pdbe.org/2yim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [https://www.ebi.ac.uk/pdbsum/2yim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim 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>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alpha-methylacyl-CoA racemase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Bhaumik, P]]	+	[[Category: Bhaumik P]]
-	[[Category: Conzelmann, E]]	+	[[Category: Conzelmann E]]
-	[[Category: Hiltunen~~, J K~~]]	+	[[Category: Hiltunen JK]]
-	[[Category: Juffer~~, A H~~]]	+	[[Category: Juffer AH]]
-	[[Category: Sharma, S]]	+	[[Category: Sharma S]]
-	[[Category: Venkatesan, R]]	+	[[Category: Venkatesan R]]
-	[[Category: Wierenga~~, R K]]~~	+	[[Category: Wierenga RK]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Methyl-coa racemase]]~~	+
-	~~[[Category: Molecular dynamic]]~~	+
-	~~[[Category: Oxyanion hole]]~~	+
-	~~[[Category: Qm/mm]]~~	+
-	~~[[Category: Transition state~~]]	+

OCA at 12:30, 27 April 2022

2022-04-27T12:30:44Z

←Older revision		Revision as of 12:30, 27 April 2022
Line 3:		Line 3:
	<StructureSection load='2yim' size='340' side='right'caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>		<StructureSection load='2yim' size='340' side='right'caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2YIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]]</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]]</div></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~~://proteopedia.org/fgij/fg.htm?mol=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [~~http~~://pdbe.org/2yim PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2yim PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim 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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [https://pdbe.org/2yim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [https://www.ebi.ac.uk/pdbsum/2yim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:52, 22 July 2020

2020-07-22T12:52:37Z

←Older revision		Revision as of 12:52, 22 July 2020
Line 1:		Line 1:

	==The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue==		==The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue==
-	<StructureSection load='2yim' size='340' side='right' caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>	+	<StructureSection load='2yim' size='340' side='right'caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2YIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2YIM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]]</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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [http://pdbe.org/2yim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [http://www.ebi.ac.uk/pdbsum/2yim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim 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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [http://pdbe.org/2yim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [http://www.ebi.ac.uk/pdbsum/2yim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
		+	[[Category: Large Structures]]
	[[Category: Myctu]]		[[Category: Myctu]]
	[[Category: Bhaumik, P]]		[[Category: Bhaumik, P]]

OCA at 22:44, 4 August 2016

2016-08-04T22:44:08Z

←Older revision		Revision as of 22:44, 4 August 2016
Line 1:		Line 1:
		+
	==The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue==		==The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue==
	<StructureSection load='2yim' size='340' side='right' caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>		<StructureSection load='2yim' size='340' side='right' caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yim]] 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=2YIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]]</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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [http://www.ebi.ac.uk/pdbsum/2yim 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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [http://pdbe.org/2yim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [http://www.ebi.ac.uk/pdbsum/2yim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yim ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 2yim" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
-	[[Category: ~~Mycobacterium tuberculosis~~]]	+	[[Category: Myctu]]
	[[Category: Bhaumik, P]]		[[Category: Bhaumik, P]]
	[[Category: Conzelmann, E]]		[[Category: Conzelmann, E]]

OCA at 22:36, 3 January 2015

2015-01-03T22:36:26Z

←Older revision		Revision as of 22:36, 3 January 2015
Line 2:		Line 2:
	<StructureSection load='2yim' size='340' side='right' caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>		<StructureSection load='2yim' size='340' side='right' caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yim]] 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=2YIM OCA]. <br>	+	<table><tr><td colspan='2'>[[2yim]] 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=2YIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YIM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~2.7~~.1.~~2 2~~.7.1.2] </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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [http://www.ebi.ac.uk/pdbsum/2yim 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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [http://www.ebi.ac.uk/pdbsum/2yim PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed QM/MM Calculations.,Sharma S, Bhaumik P, Schmitz W, Venkatesan R, Hiltunen JK, Conzelmann E, Juffer AH, Wierenga RK J Phys Chem B. 2012 Mar 22;116(11):3619-29. Epub 2012 Mar 7. PMID:22360758<ref>PMID:22360758</ref>		The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed QM/MM Calculations.,Sharma S, Bhaumik P, Schmitz W, Venkatesan R, Hiltunen JK, Conzelmann E, Juffer AH, Wierenga RK J Phys Chem B. 2012 Mar 22;116(11):3619-29. Epub 2012 Mar 7. PMID:22360758<ref>PMID:22360758</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 22:		Line 22:
	[[Category: Alpha-methylacyl-CoA racemase]]		[[Category: Alpha-methylacyl-CoA racemase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Bhaumik, P.]]	+	[[Category: Bhaumik, P]]
-	[[Category: Conzelmann, E.]]	+	[[Category: Conzelmann, E]]
-	[[Category: Hiltunen, J K.]]	+	[[Category: Hiltunen, J K]]
-	[[Category: Juffer, A H.]]	+	[[Category: Juffer, A H]]
-	[[Category: Sharma, S.]]	+	[[Category: Sharma, S]]
-	[[Category: Venkatesan, R.]]	+	[[Category: Venkatesan, R]]
-	[[Category: Wierenga, R K.]]	+	[[Category: Wierenga, R K]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Methyl-coa racemase]]		[[Category: Methyl-coa racemase]]

OCA at 07:42, 14 May 2014

2014-05-14T07:42:28Z

←Older revision		Revision as of 07:42, 14 May 2014
Line 1:		Line 1:
-	[[~~Image:~~2yim.~~png~~\|~~left~~\|~~200px~~]]	+	==The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue==
		+	<StructureSection load='2yim' size='340' side='right' caption='[[2yim]], [[Resolution\|resolution]] 1.41Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2yim]] 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=2YIM OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MC4:2-METHYLACETOACETYL+COA'>MC4</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1x74\|1x74]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2yim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yim RCSB], [http://www.ebi.ac.uk/pdbsum/2yim PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the active site of the bacterial alpha-methylacyl-CoA racemase of Mycobacterium tuberculosis (MCR), the chirality of the 2-methyl branched C2-atom is interconverted between (S) and (R) isomers. Protein crystallographic data and quantum mechanics/molecular mechanics (QM/MM) computational approaches show that this interconversion is achieved via a planar enolate intermediate. The crystal structure, at 1.4 A, visualizes the mode of binding of a reaction intermediate analogue, 2-methylacetoacetyl-CoA, in a well-defined planar enolate form. The computational studies confirm that in the conversion from (S) to (R), first a proton is abstracted by Ndelta1 (His126), and subsequently the planar enolate form is reprotonated by Odelta2 (Asp156). The calculations also show that the negatively charged thioester oxygen of the enolate intermediate is stabilized by an oxyanion hole formed by N (Asp127), as well as by the side chain atoms of the catalytic residues, Asp156 and His126, both being protonated simultaneously, at the intermediate stage of the catalytic cycle. The computational analysis also reveals that the conversion of the (S)- to (R)- chirality is achieved by a movement of 1.7 A of the chiral C2-carbon, with smaller shifts (approximately 1 A) of the carbon atom of the 2-methyl group, the C3-atom of the fatty acid tail, and the C1-carbon and O1-oxygen atoms of the thioester moiety.

-	<!--	+	The Enolization Chemistry of a Thioester-Dependent Racemase: The 1.4 A Crystal Structure of a Reaction Intermediate Complex Characterized by Detailed QM/MM Calculations.,Sharma S, Bhaumik P, Schmitz W, Venkatesan R, Hiltunen JK, Conzelmann E, Juffer AH, Wierenga RK J Phys Chem B. 2012 Mar 22;116(11):3619-29. Epub 2012 Mar 7. PMID:22360758<ref>PMID:22360758</ref>
-	The ~~line below this paragraph~~, ~~containing "STRUCTURE_2yim"~~, ~~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_2yim\| PDB=2yim \| SCENE= }}~~	+

-	~~===The enolisation chemistry of~~ a ~~thioester-dependent racemase: the 1.4 A crystal structure~~ of ~~a complex with a planar reaction intermediate analogue===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22360758}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22360758 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22360758}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2yim]] 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=2YIM OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022360758<~~/~~ref~~><~~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 at 05:13, 4 April 2012

2012-04-04T05:13:43Z

←Older revision		Revision as of 05:13, 4 April 2012
Line 1:		Line 1:
-	[[Image:2yim.~~jpg~~\|left\|200px]]	+	[[Image:2yim.png\|left\|200px]]

	<!--		<!--

OCA at 07:39, 28 March 2012

2012-03-28T07:39:40Z

←Older revision		Revision as of 07:39, 28 March 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:2yim.jpg\|left\|200px]]

-	The ~~entry 2yim~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2yim", 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_2yim\| PDB=2yim \| SCENE= }}

-	~~Authors~~: ~~Sharma, S~~.~~, Bhaumik, P., Venkatesan, R., Hiltunen, K.J., Conzelmann, E., Juffer,~~ A~~.H., Wierenga, R.K.~~	+	===The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue===

-	~~Description: The enolisation chemistry of a thioester~~-~~dependent racemase~~: the 1.4 ~~A crystal~~ structure ~~of a complex~~ with ~~a planar reaction intermediate analogue~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22360758}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22360758 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22360758}}
		+
		+	==About this Structure==
		+	[[2yim]] 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=2YIM OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022360758</ref><ref group="xtra">PMID:017320106</ref><references group="xtra"/>
		+	[[Category: Alpha-methylacyl-CoA racemase]]
		+	[[Category: Mycobacterium tuberculosis]]
		+	[[Category: Bhaumik, P.]]
		+	[[Category: Conzelmann, E.]]
		+	[[Category: Hiltunen, J K.]]
		+	[[Category: Juffer, A H.]]
		+	[[Category: Sharma, S.]]
		+	[[Category: Venkatesan, R.]]
		+	[[Category: Wierenga, R K.]]
		+	[[Category: Isomerase]]
		+	[[Category: Methyl-coa racemase]]
		+	[[Category: Molecular dynamic]]
		+	[[Category: Oxyanion hole]]
		+	[[Category: Qm/mm]]
		+	[[Category: Transition state]]

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

2011-05-25T04:55:25Z

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

←Older revision

Revision as of 04:55, 25 May 2011

OCA: New page: '''Unreleased structure''' The entry 2yim is ON HOLD until Paper Publication Authors: Sharma, S., Bhaumik, P., Venkatesan, R., Hiltunen, K.J., Conzelmann, E., Juffer, A.H., Wierenga, R....

2011-05-25T04:55:24Z

New page: '''Unreleased structure''' The entry 2yim is ON HOLD until Paper Publication Authors: Sharma, S., Bhaumik, P., Venkatesan, R., Hiltunen, K.J., Conzelmann, E., Juffer, A.H., Wierenga, R....

New page

'''Unreleased structure'''

The entry 2yim is ON HOLD until Paper Publication

Authors: Sharma, S., Bhaumik, P., Venkatesan, R., Hiltunen, K.J., Conzelmann, E., Juffer, A.H., Wierenga, R.K.

Description: The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue