5x0q - Revision history

OCA at 07:52, 22 November 2023

OCA — Wed, 22 Nov 2023 07:52:41 GMT

←Older revision		Revision as of 07:52, 22 November 2023
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	<StructureSection load='5x0q' size='340' side='right'caption='[[5x0q]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5x0q' size='340' side='right'caption='[[5x0q]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x0q]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_27562 Atcc 27562~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X0Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X0Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x0q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X0Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X0Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.55Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5x0v\|5x0v]]~~, ~~[[5b70\|5b70]], [[5b7d\|5b7d]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=5x0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0q OCA], [~~http~~://pdbe.org/5x0q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x0q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x0q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0q 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=5x0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0q OCA], [https://pdbe.org/5x0q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x0q RCSB], [https://www.ebi.ac.uk/pdbsum/5x0q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A087I947_VIBVL A0A087I947_VIBVL]
	<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: Atcc 27562]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ha, N C~~]]	+	[[Category: Vibrio vulnificus]]
-	[[Category: ~~Jo, I]]~~	+	[[Category: Ha N-C]]
-	~~[[Category: Dna binding protein]]~~	+	[[Category: Jo I]]
-	~~[[Category: H2o2]]~~	+
-	~~[[Category: Lttr]]~~	+
-	~~[[Category: Lysr~~-~~type transcription regulator~~]]	+
-	[[Category: ~~Oxyr~~]]	+

OCA at 07:21, 7 October 2020

OCA — Wed, 07 Oct 2020 07:21:26 GMT

←Older revision		Revision as of 07:21, 7 October 2020
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	==OxyR2 E204G variant (Cl-bound) from Vibrio vulnificus==		==OxyR2 E204G variant (Cl-bound) from Vibrio vulnificus==
-	<StructureSection load='5x0q' size='340' side='right' caption='[[5x0q]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5x0q' size='340' side='right'caption='[[5x0q]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x0q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X0Q OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X0Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x0q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_27562 Atcc 27562]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X0Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X0Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x0v\|5x0v]], [[5b70\|5b70]], [[5b7d\|5b7d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x0v\|5x0v]], [[5b70\|5b70]], [[5b7d\|5b7d]]</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=5x0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0q OCA], [http://pdbe.org/5x0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x0q RCSB], [http://www.ebi.ac.uk/pdbsum/5x0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0q 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=5x0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0q OCA], [http://pdbe.org/5x0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x0q RCSB], [http://www.ebi.ac.uk/pdbsum/5x0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0q ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5x0q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x0q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 27562]]
		+	[[Category: Large Structures]]
	[[Category: Ha, N C]]		[[Category: Ha, N C]]
	[[Category: Jo, I]]		[[Category: Jo, I]]

OCA at 21:09, 15 March 2017

OCA — Wed, 15 Mar 2017 21:09:15 GMT

←Older revision		Revision as of 21:09, 15 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x0q is ~~ON HOLD until Paper~~ Publication	+	==OxyR2 E204G variant (Cl-bound) from Vibrio vulnificus==
		+	<StructureSection load='5x0q' size='340' side='right' caption='[[5x0q]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x0q]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X0Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X0Q FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x0v\|5x0v]], [[5b70\|5b70]], [[5b7d\|5b7d]]</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=5x0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x0q OCA], [http://pdbe.org/5x0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x0q RCSB], [http://www.ebi.ac.uk/pdbsum/5x0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x0q ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Most Gram-negative bacteria respond to excessive levels of H2O2 using the peroxide-sensing transcriptional regulator OxyR, which can induce the expression of antioxidant genes to restore normality. Vibrio vulnificus has two distinct OxyRs (OxyR1 and OxyR2), which are sensitive to different levels of H2O2 and induce expression of two different peroxidases, Prx1 and Prx2. While OxyR1 has both high sequence similarity and comparable H2O2 sensitivity to other OxyR proteins, OxyR2 exhibits limited sequence similarity and is more sensitive to H2O2 To investigate the basis for this difference, we determined crystal structures and carried out biochemical analyses of OxyR2. The determined structure of OxyR2 revealed a flipped conformation of the peptide bond before Glu204, a position occupied by glycine in other OxyR proteins. Activity assays showed that the sensitivity to H2O2 was reduced to the level of other OxyR proteins by the E204G mutation. We solved the structure of the OxyR2-E204G mutant with the same packing environment. The structure of the mutant revealed a dual conformation of the peptide bond before Gly204, indicating the structural flexibility of the region. This structural duality extended to the backbone atoms of Gly204 and the imidazole ring of His205, which interact with H2O2 and invariant water molecules near the peroxidatic cysteine, respectively. Structural comparison suggests that Glu204 in OxyR2 provides rigidity to the region that is important in H2O2 sensing, compared to the E204G structure or other OxyR proteins. Our findings provide a structural basis for the higher sensitivity of OxyR2 to H2O2 and also suggest a molecular mechanism for bacterial regulation of expression of antioxidant genes at divergent concentrations of cellular H2O2.

-	~~Authors: Jo~~, I., Ha, N.-C.	+	The hydrogen peroxide hypersensitivity of OxyR2 in Vibrio vulnificus depends on conformational constraints.,Jo I, Kim D, Bang YJ, Ahn J, Choi SH, Ha NC J Biol Chem. 2017 Mar 6. pii: jbc.M116.743765. doi: 10.1074/jbc.M116.743765. PMID:28264933<ref>PMID:28264933</ref>

-	~~Description: OxyR2 E204G variant (Cl-bound) from Vibrio vulnificus~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Ha, N.-C]]	+	<div class="pdbe-citations 5x0q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ha, N C]]
	[[Category: Jo, I]]		[[Category: Jo, I]]
		+	[[Category: Dna binding protein]]
		+	[[Category: H2o2]]
		+	[[Category: Lttr]]
		+	[[Category: Lysr-type transcription regulator]]
		+	[[Category: Oxyr]]

OCA at 15:32, 9 March 2017

OCA — Thu, 09 Mar 2017 15:32:46 GMT

←Older revision		Revision as of 15:32, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x0q is ON HOLD	+	The entry 5x0q is ON HOLD until Paper Publication

	Authors: Jo, I., Ha, N.-C.		Authors: Jo, I., Ha, N.-C.

OCA: Protected "5x0q" [edit=sysop:move=sysop]

OCA — Wed, 01 Feb 2017 17:09:02 GMT

Protected "5x0q" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:09, 1 February 2017

OCA: New page: '''Unreleased structure''' The entry 5x0q is ON HOLD Authors: Jo, I., Ha, N.-C. Description: OxyR2 E204G variant (Cl-bound) from Vibrio vulnificus Category: Unreleased Structures [...

OCA — Wed, 01 Feb 2017 17:09:00 GMT

New page: '''Unreleased structure''' The entry 5x0q is ON HOLD Authors: Jo, I., Ha, N.-C. Description: OxyR2 E204G variant (Cl-bound) from Vibrio vulnificus Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 5x0q is ON HOLD

Authors: Jo, I., Ha, N.-C.

Description: OxyR2 E204G variant (Cl-bound) from Vibrio vulnificus
[[Category: Unreleased Structures]]
[[Category: Ha, N.-C]]
[[Category: Jo, I]]