4n8i - Revision history

OCA at 16:49, 20 September 2023

2023-09-20T16:49:22Z

←Older revision		Revision as of 16:49, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4n8i]] 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=4N8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N8I FirstGlance]. <br>		<table><tr><td colspan='2'>[[4n8i]] 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=4N8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N8I 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>, <scene name='pdbligand=COA:COENZYME+A'>COA</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]] 2.011Å</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>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></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=4n8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8i OCA], [https://pdbe.org/4n8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n8i RCSB], [https://www.ebi.ac.uk/pdbsum/4n8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8i 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=4n8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8i OCA], [https://pdbe.org/4n8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n8i RCSB], [https://www.ebi.ac.uk/pdbsum/4n8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8i ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:14, 11 January 2023

2023-01-11T08:14:33Z

←Older revision		Revision as of 08:14, 11 January 2023
Line 1:		Line 1:

	==M31G mutant, RipA structure==		==M31G mutant, RipA structure==
-	<StructureSection load='4n8i' size='340' side='right' caption='[[4n8i]], [[Resolution\|resolution]] 2.01Å' scene=''>	+	<StructureSection load='4n8i' size='340' side='right'caption='[[4n8i]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4n8i]] 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=4N8I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4N8I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4n8i]] 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=4N8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N8I 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>, <scene name='pdbligand=COA:COENZYME+A'>COA</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>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n8h\|4n8h]], [[4n8j\|4n8j]], [[4n8k\|4n8k]], [[4n8l\|4n8l]]</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=4n8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8i OCA], [https://pdbe.org/4n8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n8i RCSB], [https://www.ebi.ac.uk/pdbsum/4n8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8i 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=4n8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8i OCA], [~~http~~://pdbe.org/4n8i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4n8i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4n8i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8i 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 ==
Line 22:		Line 22:
	__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 13:40, 11 August 2016

2016-08-11T13:40:56Z

←Older revision		Revision as of 13:40, 11 August 2016
Line 1:		Line 1:
		+
	==M31G mutant, RipA structure==		==M31G mutant, RipA structure==
	<StructureSection load='4n8i' size='340' side='right' caption='[[4n8i]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='4n8i' size='340' side='right' caption='[[4n8i]], [[Resolution\|resolution]] 2.01Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n8h\|4n8h]], [[4n8j\|4n8j]], [[4n8k\|4n8k]], [[4n8l\|4n8l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n8h\|4n8h]], [[4n8j\|4n8j]], [[4n8k\|4n8k]], [[4n8l\|4n8l]]</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=4n8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n8i RCSB], [http://www.ebi.ac.uk/pdbsum/4n8i 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=4n8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8i OCA], [http://pdbe.org/4n8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n8i RCSB], [http://www.ebi.ac.uk/pdbsum/4n8i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n8i 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 4n8i" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:31, 5 January 2015

2015-01-05T09:31:44Z

←Older revision		Revision as of 09:31, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4n8i~~\| ~~PDB~~=4n8i \| ~~SCENE~~= }}	+	==M31G mutant, RipA structure==
-	===~~M31G mutant~~, ~~RipA structure~~===	+	<StructureSection load='4n8i' size='340' side='right' caption='[[4n8i]], [[Resolution\|resolution]] 2.01Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24699651}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4n8i]] 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=4N8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N8I 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>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4n8h\|4n8h]], [[4n8j\|4n8j]], [[4n8k\|4n8k]], [[4n8l\|4n8l]]</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=4n8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n8i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n8i RCSB], [http://www.ebi.ac.uk/pdbsum/4n8i 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>
-	~~[[4n8i]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4N8I 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 08:34, 16 April 2014

2014-04-16T08:34:19Z

←Older revision		Revision as of 08:34, 16 April 2014
Line 1:		Line 1:
	{{STRUCTURE_4n8i\| PDB=4n8i \| SCENE= }}		{{STRUCTURE_4n8i\| PDB=4n8i \| SCENE= }}
	===M31G mutant, RipA structure===		===M31G mutant, RipA structure===
		+	{{ABSTRACT_PUBMED_24699651}}

	==About this Structure==		==About this Structure==
	[[4n8i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N8I OCA].		[[4n8i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N8I 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 06:44, 9 April 2014

2014-04-09T06:44:57Z

←Older revision		Revision as of 06:44, 9 April 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4n8i\| PDB=4n8i \| SCENE= }}
		+	===M31G mutant, RipA structure===

-	~~The entry~~ 4n8i is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4n8i]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N8I OCA].
-	~~Authors~~: ~~Torres, R~~., Goulding, C.W.	+	[[Category: Goulding, C W.]]
-		+	[[Category: Torres, R.]]
-	~~Description~~: ~~M31G mutant~~, ~~RipA structure~~	+	[[Category: Coenzyme a transferase]]
		+	[[Category: Transferase]]

OCA at 07:41, 13 November 2013

2013-11-13T07:41:23Z

←Older revision		Revision as of 07:41, 13 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4n8i is ON HOLD	+	The entry 4n8i is ON HOLD until Paper Publication

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

	Description: M31G mutant, RipA structure		Description: M31G mutant, RipA structure

OCA at 07:03, 6 November 2013

2013-11-06T07:03:43Z

←Older revision		Revision as of 07:03, 6 November 2013
Line 3:		Line 3:
	The entry 4n8i is ON HOLD		The entry 4n8i is ON HOLD

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

	Description: M31G mutant, RipA structure		Description: M31G mutant, RipA structure

OCA: Protected "4n8i" [edit=sysop:move=sysop]

2013-10-23T06:18:32Z

Protected "4n8i" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:18, 23 October 2013

OCA: New page: '''Unreleased structure''' The entry 4n8i is ON HOLD Authors: Torres, R, Goulding, C.W. Description: M31G mutant, RipA structure

2013-10-23T06:18:31Z

New page: '''Unreleased structure''' The entry 4n8i is ON HOLD Authors: Torres, R, Goulding, C.W. Description: M31G mutant, RipA structure

New page

'''Unreleased structure'''

The entry 4n8i is ON HOLD

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

Description: M31G mutant, RipA structure