4n8l - Revision history

OCA at 16:49, 20 September 2023

OCA — Wed, 20 Sep 2023 16:49:24 GMT

←Older revision		Revision as of 16:49, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4n8l]] 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=4N8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N8L FirstGlance]. <br>		<table><tr><td colspan='2'>[[4n8l]] 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=4N8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N8L FirstGlance]. <br>
-	</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=4n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8l OCA], [https://pdbe.org/4n8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n8l RCSB], [https://www.ebi.ac.uk/pdbsum/4n8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8l ProSAT]</span></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]] 2.817Å</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=4n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8l OCA], [https://pdbe.org/4n8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n8l RCSB], [https://www.ebi.ac.uk/pdbsum/4n8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:14, 11 January 2023

OCA — Wed, 11 Jan 2023 08:14:40 GMT

←Older revision		Revision as of 08:14, 11 January 2023
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	==E249D mutant, RipA structure==		==E249D mutant, RipA structure==
-	<StructureSection load='4n8l' size='340' side='right' caption='[[4n8l]], [[Resolution\|resolution]] 2.82Å' scene=''>	+	<StructureSection load='4n8l' size='340' side='right'caption='[[4n8l]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4n8l]] 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=4N8L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4N8L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4n8l]] 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=4N8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N8L FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n8h\|4n8h]], [[4n8i\|4n8i]], [[4n8j\|4n8j]], [[4n8k\|4n8k]]</td></tr>~~	+	</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=4n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8l OCA], [https://pdbe.org/4n8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n8l RCSB], [https://www.ebi.ac.uk/pdbsum/4n8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8l ProSAT]</span></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=4n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8l OCA], [~~http~~://pdbe.org/4n8l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4n8l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4n8l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8l ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9ZC36_YERPE Q9ZC36_YERPE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Goulding, C W~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Torres, R~~]]	+	[[Category: Yersinia pestis]]
-	[[Category: ~~Coenzyme a transferase~~]]	+	[[Category: Goulding CW]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Torres R]]

OCA at 14:44, 11 August 2016

OCA — Thu, 11 Aug 2016 14:44:38 GMT

←Older revision		Revision as of 14:44, 11 August 2016
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		+
	==E249D mutant, RipA structure==		==E249D mutant, RipA structure==
	<StructureSection load='4n8l' size='340' side='right' caption='[[4n8l]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='4n8l' size='340' side='right' caption='[[4n8l]], [[Resolution\|resolution]] 2.82Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n8h\|4n8h]], [[4n8i\|4n8i]], [[4n8j\|4n8j]], [[4n8k\|4n8k]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n8h\|4n8h]], [[4n8i\|4n8i]], [[4n8j\|4n8j]], [[4n8k\|4n8k]]</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 ([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=4n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n8l RCSB], [http://www.ebi.ac.uk/pdbsum/4n8l 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=4n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8l OCA], [http://pdbe.org/4n8l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n8l RCSB], [http://www.ebi.ac.uk/pdbsum/4n8l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8l ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 4n8l" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:59, 5 January 2015

OCA — Mon, 05 Jan 2015 08:59:51 GMT

←Older revision		Revision as of 08:59, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4n8l~~\| ~~PDB~~=4n8l \| ~~SCENE~~= }}	+	==E249D mutant, RipA structure==
-	===~~E249D mutant~~, ~~RipA structure~~===	+	<StructureSection load='4n8l' size='340' side='right' caption='[[4n8l]], [[Resolution\|resolution]] 2.82Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24699651}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4n8l]] 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=4N8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N8L FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n8h\|4n8h]], [[4n8i\|4n8i]], [[4n8j\|4n8j]], [[4n8k\|4n8k]]</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=4n8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n8l RCSB], [http://www.ebi.ac.uk/pdbsum/4n8l PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon gamma-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully understand the function of the acyl-group binding pocket in substrate specificity.

-	~~==About this Structure==~~	+	Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase.,Torres R, Lan B, Latif Y, Chim N, Goulding CW Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):1074-85. doi:, 10.1107/S1399004714000911. Epub 2014 Mar 20. PMID:24699651<ref>PMID:24699651</ref>
-	~~[[4n8l]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4N8L OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024699651</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Goulding, C W.]]	+	== References ==
-	[[Category: Torres, R.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Goulding, C W]]
		+	[[Category: Torres, R]]
	[[Category: Coenzyme a transferase]]		[[Category: Coenzyme a transferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:47, 16 April 2014

OCA — Wed, 16 Apr 2014 07:47:50 GMT

←Older revision		Revision as of 07:47, 16 April 2014
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	{{STRUCTURE_4n8l\| PDB=4n8l \| SCENE= }}		{{STRUCTURE_4n8l\| PDB=4n8l \| SCENE= }}
	===E249D mutant, RipA structure===		===E249D mutant, RipA structure===
		+	{{ABSTRACT_PUBMED_24699651}}

	==About this Structure==		==About this Structure==
	[[4n8l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N8L OCA].		[[4n8l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N8L OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024699651</ref><references group="xtra"/><references/>
	[[Category: Goulding, C W.]]		[[Category: Goulding, C W.]]
	[[Category: Torres, R.]]		[[Category: Torres, R.]]
	[[Category: Coenzyme a transferase]]		[[Category: Coenzyme a transferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:45, 9 April 2014

OCA — Wed, 09 Apr 2014 06:45:11 GMT

←Older revision		Revision as of 06:45, 9 April 2014
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-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4n8l\| PDB=4n8l \| SCENE= }}
		+	===E249D mutant, RipA structure===

-	~~The entry~~ 4n8l is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4n8l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N8L OCA].
-	~~Authors~~: ~~Torres, R~~., Goulding, C.W.	+	[[Category: Goulding, C W.]]
-		+	[[Category: Torres, R.]]
-	~~Description~~: ~~E249D mutant~~, ~~RipA structure~~	+	[[Category: Coenzyme a transferase]]
		+	[[Category: Transferase]]

OCA at 12:55, 20 November 2013

OCA — Wed, 20 Nov 2013 12:55:59 GMT

←Older revision		Revision as of 12:55, 20 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4n8l is ON HOLD	+	The entry 4n8l is ON HOLD until Paper Publication

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

	Description: E249D mutant, RipA structure		Description: E249D mutant, RipA structure

OCA at 07:03, 6 November 2013

OCA — Wed, 06 Nov 2013 07:03:49 GMT

←Older revision		Revision as of 07:03, 6 November 2013
Line 3:		Line 3:
	The entry 4n8l is ON HOLD		The entry 4n8l is ON HOLD

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

	Description: E249D mutant, RipA structure		Description: E249D mutant, RipA structure

OCA: Protected "4n8l" [edit=sysop:move=sysop]

OCA — Wed, 23 Oct 2013 06:18:40 GMT

Protected "4n8l" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:18, 23 October 2013

OCA: New page: '''Unreleased structure''' The entry 4n8l is ON HOLD Authors: Torres, R, Goulding, C.W. Description: E249D mutant, RipA structure

OCA — Wed, 23 Oct 2013 06:18:39 GMT

New page: '''Unreleased structure''' The entry 4n8l is ON HOLD Authors: Torres, R, Goulding, C.W. Description: E249D mutant, RipA structure

New page

'''Unreleased structure'''

The entry 4n8l is ON HOLD

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

Description: E249D mutant, RipA structure