3qli - Revision history

OCA at 10:48, 21 February 2024

OCA — Wed, 21 Feb 2024 10:48:27 GMT

←Older revision		Revision as of 10:48, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3qli' size='340' side='right'caption='[[3qli]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3qli' size='340' side='right'caption='[[3qli]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus~~ pestis~~" (lehmann and neumann 1896) migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QLI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QLI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[3qlk\|3qlk]], [[3qll\|3qll]], [[3s8d\|3s8d]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">aCH1, y2385, YPO1926, YP_1668 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])~~</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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [https://pdbe.org/3qli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [https://www.ebi.ac.uk/pdbsum/3qli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qli 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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [https://pdbe.org/3qli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [https://www.ebi.ac.uk/pdbsum/3qli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qli ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9ZC36_YERPE Q9ZC36_YERPE]
-	Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 A X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway.	+
-		+
-	Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis.,Torres R, Swift RV, Chim N, Wheatley N, Lan B, Atwood BR, Pujol C, Sankaran B, Bliska JB, Amaro RE, Goulding CW PLoS One. 2011;6(9):~~e25084. Epub 2011 Sep 26. PMID:21966419<ref>PMID:21966419<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3qli" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Goulding, C W~~]]	+	[[Category: Yersinia pestis]]
-	[[Category: ~~Torres, R~~]]	+	[[Category: Goulding CW]]
-	[[Category: ~~4-hydroxybutryrate coenzyme a transferase]]~~	+	[[Category: Torres R]]
-	~~[[Category: Coenzyme a transferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:13, 8 June 2022

OCA — Wed, 08 Jun 2022 06:13:50 GMT

←Older revision		Revision as of 06:13, 8 June 2022
Line 1:		Line 1:

	==Crystal Structure of RipA from Yersinia pestis==		==Crystal Structure of RipA from Yersinia pestis==
-	<StructureSection load='3qli' size='340' side='right' caption='[[3qli]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3qli' size='340' side='right'caption='[[3qli]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QLI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QLI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qlk\|3qlk]], [[3qll\|3qll]], [[3s8d\|3s8d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3qlk\|3qlk]], [[3qll\|3qll]], [[3s8d\|3s8d]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aCH1, y2385, YPO1926, YP_1668 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aCH1, y2385, YPO1926, YP_1668 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [~~http~~://pdbe.org/3qli PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qli PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qli 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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [https://pdbe.org/3qli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [https://www.ebi.ac.uk/pdbsum/3qli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qli ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Goulding, C W]]		[[Category: Goulding, C W]]
	[[Category: Torres, R]]		[[Category: Torres, R]]

OCA at 03:44, 5 August 2016

OCA — Fri, 05 Aug 2016 03:44:34 GMT

←Older revision		Revision as of 03:44, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of RipA from Yersinia pestis==		==Crystal Structure of RipA from Yersinia pestis==
	<StructureSection load='3qli' size='340' side='right' caption='[[3qli]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3qli' size='340' side='right' caption='[[3qli]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Yersinia_pestis Yersinia~~ pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QLI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QLI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qlk\|3qlk]], [[3qll\|3qll]], [[3s8d\|3s8d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qlk\|3qlk]], [[3qll\|3qll]], [[3s8d\|3s8d]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aCH1, y2385, YPO1926, YP_1668 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 ~~Yersinia~~ pestis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aCH1, y2385, YPO1926, YP_1668 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [http://www.ebi.ac.uk/pdbsum/3qli 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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [http://pdbe.org/3qli PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [http://www.ebi.ac.uk/pdbsum/3qli PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qli 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 3qli" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Yersinia pestis]]
	[[Category: Goulding, C W]]		[[Category: Goulding, C W]]
	[[Category: Torres, R]]		[[Category: Torres, R]]

OCA at 22:14, 3 January 2015

OCA — Sat, 03 Jan 2015 22:14:49 GMT

←Older revision		Revision as of 22:14, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QLI FirstGlance]. <br>		<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QLI FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qlk\|3qlk]], [[3qll\|3qll]], [[3s8d\|3s8d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qlk\|3qlk]], [[3qll\|3qll]], [[3s8d\|3s8d]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aCH1, y2385, YPO1926, YP_1668 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aCH1, y2385, YPO1926, YP_1668 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis])</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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [http://www.ebi.ac.uk/pdbsum/3qli 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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [http://www.ebi.ac.uk/pdbsum/3qli 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:
	Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis.,Torres R, Swift RV, Chim N, Wheatley N, Lan B, Atwood BR, Pujol C, Sankaran B, Bliska JB, Amaro RE, Goulding CW PLoS One. 2011;6(9):e25084. Epub 2011 Sep 26. PMID:21966419<ref>PMID:21966419</ref>		Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis.,Torres R, Swift RV, Chim N, Wheatley N, Lan B, Atwood BR, Pujol C, Sankaran B, Bliska JB, Amaro RE, Goulding CW PLoS One. 2011;6(9):e25084. Epub 2011 Sep 26. PMID:21966419<ref>PMID:21966419</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 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Yersinia pestis]]		[[Category: Yersinia pestis]]
-	[[Category: Goulding, C W.]]	+	[[Category: Goulding, C W]]
-	[[Category: Torres, R.]]	+	[[Category: Torres, R]]
	[[Category: 4-hydroxybutryrate coenzyme a transferase]]		[[Category: 4-hydroxybutryrate coenzyme a transferase]]
	[[Category: Coenzyme a transferase]]		[[Category: Coenzyme a transferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 05:32, 4 June 2014

OCA — Wed, 04 Jun 2014 05:32:37 GMT

←Older revision		Revision as of 05:32, 4 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3qli.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of RipA from Yersinia pestis==
		+	<StructureSection load='3qli' size='340' side='right' caption='[[3qli]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qli]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QLI FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qlk\|3qlk]], [[3qll\|3qll]], [[3s8d\|3s8d]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aCH1, y2385, YPO1926, YP_1668 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 Yersinia pestis])</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=3qli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qli RCSB], [http://www.ebi.ac.uk/pdbsum/3qli PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 A X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway.

-	~~<!--~~	+	Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis.,Torres R, Swift RV, Chim N, Wheatley N, Lan B, Atwood BR, Pujol C, Sankaran B, Bliska JB, Amaro RE, Goulding CW PLoS One. 2011;6(9):e25084. Epub 2011 Sep 26. PMID:21966419<ref>PMID:21966419</ref>
-	~~The line below this paragraph, containing "STRUCTURE_3qli"~~, ~~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_3qli\| PDB=3qli \| SCENE= }}~~	+

-	~~===Crystal Structure~~ of ~~RipA from Yersinia pestis===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21966419}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21966419 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21966419}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3qli]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021966419<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Yersinia pestis]]		[[Category: Yersinia pestis]]
	[[Category: Goulding, C W.]]		[[Category: Goulding, C W.]]

OCA at 10:44, 18 January 2012

OCA — Wed, 18 Jan 2012 10:44:49 GMT

←Older revision		Revision as of 10:44, 18 January 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3qli.jpg\|left\|200px]]

-	The ~~entry 3qli~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qli", 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_3qli\| PDB=3qli \| SCENE= }}

-	~~Authors: Torres, R., Goulding, C.W.~~	+	===Crystal Structure of RipA from Yersinia pestis===

-	~~Description~~: ~~Crystal~~ Structure ~~of RipA~~ from Yersinia pestis	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21966419}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21966419 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21966419}}
		+
		+	==About this Structure==
		+	[[3qli]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QLI OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021966419</ref><references group="xtra"/>
		+	[[Category: Yersinia pestis]]
		+	[[Category: Goulding, C W.]]
		+	[[Category: Torres, R.]]
		+	[[Category: 4-hydroxybutryrate coenzyme a transferase]]
		+	[[Category: Coenzyme a transferase]]
		+	[[Category: Transferase]]

OCA at 08:36, 6 April 2011

OCA — Wed, 06 Apr 2011 08:36:18 GMT

←Older revision		Revision as of 08:36, 6 April 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3qli is ON HOLD	+	The entry 3qli is ON HOLD until Paper Publication

	Authors: Torres, R., Goulding, C.W.		Authors: Torres, R., Goulding, C.W.

	Description: Crystal Structure of RipA from Yersinia pestis		Description: Crystal Structure of RipA from Yersinia pestis

OCA: Protected "3qli" [edit=sysop:move=sysop]

OCA — Wed, 09 Feb 2011 05:51:46 GMT

Protected "3qli" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:51, 9 February 2011

OCA: New page: '''Unreleased structure''' The entry 3qli is ON HOLD Authors: Torres, R., Goulding, C.W. Description: Crystal Structure of RipA from Yersinia pestis

OCA — Wed, 09 Feb 2011 05:51:45 GMT

New page: '''Unreleased structure''' The entry 3qli is ON HOLD Authors: Torres, R., Goulding, C.W. Description: Crystal Structure of RipA from Yersinia pestis

New page

'''Unreleased structure'''

The entry 3qli is ON HOLD

Authors: Torres, R., Goulding, C.W.

Description: Crystal Structure of RipA from Yersinia pestis