4y0m - Revision history

OCA at 18:01, 26 April 2023

OCA — Wed, 26 Apr 2023 18:01:20 GMT

←Older revision		Revision as of 18:01, 26 April 2023
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	==The reduced form of OxyR regulatory domain from Psedomonas aeruginosa==		==The reduced form of OxyR regulatory domain from Psedomonas aeruginosa==
-	<StructureSection load='4y0m' size='340' side='right' caption='[[4y0m]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4y0m' size='340' side='right'caption='[[4y0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y0m]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Y0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y0m]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y0M FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x6g\|4x6g]], [[4xws\|4xws]]</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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [https://pdbe.org/4y0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [https://www.ebi.ac.uk/pdbsum/4y0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0m ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxyR, PA5344 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [~~http~~://pdbe.org/4y0m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4y0m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0m ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9HTL4_PSEAE Q9HTL4_PSEAE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4y0m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4y0m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseae~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ha, N C~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: ~~Jo, I~~]]	+	[[Category: Ha NC]]
-	[[Category: ~~Kim, J S~~]]	+	[[Category: Jo I]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Kim JS]]
-	~~[[Category: Lysr]]~~	+
-	~~[[Category: Oxyr]]~~	+
-	~~[[Category: Peroxide]]~~	+
-	~~[[Category: Transcription regulator~~]]	+

OCA at 05:44, 16 May 2018

OCA — Wed, 16 May 2018 05:44:00 GMT

←Older revision		Revision as of 05:44, 16 May 2018
Line 3:		Line 3:
	<StructureSection load='4y0m' size='340' side='right' caption='[[4y0m]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4y0m' size='340' side='right' caption='[[4y0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y0m]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y0m]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0M FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x6g\|4x6g]], [[4xws\|4xws]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x6g\|4x6g]], [[4xws\|4xws]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oxyR, PA5344 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [http://pdbe.org/4y0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [http://www.ebi.ac.uk/pdbsum/4y0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0m ProSAT]</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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [http://pdbe.org/4y0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [http://www.ebi.ac.uk/pdbsum/4y0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0m ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pseae]]
	[[Category: Ha, N C]]		[[Category: Ha, N C]]
	[[Category: Jo, I]]		[[Category: Jo, I]]
	[[Category: Kim, J S]]		[[Category: Kim, J S]]
		+	[[Category: Dna binding protein]]
	[[Category: Lysr]]		[[Category: Lysr]]
	[[Category: Oxyr]]		[[Category: Oxyr]]
	[[Category: Peroxide]]		[[Category: Peroxide]]
	[[Category: Transcription regulator]]		[[Category: Transcription regulator]]

OCA at 01:45, 10 March 2017

OCA — Fri, 10 Mar 2017 01:45:06 GMT

←Older revision		Revision as of 01:45, 10 March 2017
Line 1:		Line 1:
		+
	==The reduced form of OxyR regulatory domain from Psedomonas aeruginosa==		==The reduced form of OxyR regulatory domain from Psedomonas aeruginosa==
	<StructureSection load='4y0m' size='340' side='right' caption='[[4y0m]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4y0m' size='340' side='right' caption='[[4y0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x6g\|4x6g]], [[4xws\|4xws]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x6g\|4x6g]], [[4xws\|4xws]]</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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [http://www.ebi.ac.uk/pdbsum/4y0m 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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [http://pdbe.org/4y0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [http://www.ebi.ac.uk/pdbsum/4y0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0m ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4y0m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:38, 3 June 2015

OCA — Wed, 03 Jun 2015 06:38:02 GMT

←Older revision		Revision as of 06:38, 3 June 2015
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	<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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [http://www.ebi.ac.uk/pdbsum/4y0m 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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [http://www.ebi.ac.uk/pdbsum/4y0m PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	OxyR, a bacterial peroxide sensor, is a LysR-type transcriptional regulator (LTTR) that regulates the transcription of defense genes in response to a low level of cellular H2O2. Consisting of an N-terminal DNA-binding domain (DBD) and a C-terminal regulatory domain (RD), OxyR senses H2O2 with conserved cysteine residues in the RD. However, the precise mechanism of OxyR is not yet known due to the absence of the full-length (FL) protein structure. Here we determined the crystal structures of the FL protein and RD of Pseudomonas aeruginosa OxyR and its C199D mutant proteins. The FL crystal structures revealed that OxyR has a tetrameric arrangement assembled via two distinct dimerization interfaces. The C199D mutant structures suggested that new interactions that are mediated by cysteine hydroxylation induce a large conformational change, facilitating intramolecular disulfide-bond formation. More importantly, a bound H2O2 molecule was found near the Cys199 site, suggesting the H2O2-driven oxidation mechanism of OxyR. Combined with the crystal structures, a modeling study suggested that a large movement of the DBD is triggered by structural changes in the regulatory domains upon oxidation. Taken together, these findings provide novel concepts for answering key questions regarding OxyR in the H2O2-sensing and oxidation-dependent regulation of antioxidant genes.
		+
		+	Structural details of the OxyR peroxide-sensing mechanism.,Jo I, Chung IY, Bae HW, Kim JS, Song S, Cho YH, Ha NC Proc Natl Acad Sci U S A. 2015 May 19;112(20):6443-8. doi:, 10.1073/pnas.1424495112. Epub 2015 Apr 30. PMID:25931525<ref>PMID:25931525</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:37, 30 April 2015

OCA — Thu, 30 Apr 2015 11:37:52 GMT

←Older revision		Revision as of 11:37, 30 April 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==The reduced form of OxyR regulatory domain from Psedomonas aeruginosa==
-		+	<StructureSection load='4y0m' size='340' side='right' caption='[[4y0m]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~The entry~~ 4y0m is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4y0m]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0M FirstGlance]. <br>
-	~~Authors~~: ~~Jo, I~~.~~, Kim, J~~.S.~~, Ha, N~~.C.	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4x6g\|4x6g]], [[4xws\|4xws]]</td></tr>
-	~~Description~~: ~~The reduced form of OxyR regulatory domain from Psedomonas aeruginosa~~	+	<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=4y0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y0m RCSB], [http://www.ebi.ac.uk/pdbsum/4y0m PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Kim~~, ~~J.S~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Ha, N C]]
	[[Category: Jo, I]]		[[Category: Jo, I]]
-	[[Category: Ha, ~~N.C~~]]	+	[[Category: Kim, J S]]
		+	[[Category: Lysr]]
		+	[[Category: Oxyr]]
		+	[[Category: Peroxide]]
		+	[[Category: Transcription regulator]]

OCA at 10:11, 11 March 2015

OCA — Wed, 11 Mar 2015 10:11:04 GMT

←Older revision		Revision as of 10:11, 11 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y0m is ON HOLD	+	The entry 4y0m is ON HOLD until Paper Publication

	Authors: Jo, I., Kim, J.S., Ha, N.C.		Authors: Jo, I., Kim, J.S., Ha, N.C.

OCA at 09:58, 4 March 2015

OCA — Wed, 04 Mar 2015 09:58:51 GMT

←Older revision		Revision as of 09:58, 4 March 2015
Line 3:		Line 3:
	The entry 4y0m is ON HOLD		The entry 4y0m is ON HOLD

-	Authors: Jo, I., Kim, JS, Ha, NC.	+	Authors: Jo, I., Kim, J.S., Ha, N.C.

-	Description: OxyR regulatory domain ~~C199D mutant~~ from ~~pseudomonas~~ aeruginosa	+	Description: The reduced form of OxyR regulatory domain from Psedomonas aeruginosa
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kim, ~~Js, Ha, Nc~~]]	+	[[Category: Kim, J.S]]
	[[Category: Jo, I]]		[[Category: Jo, I]]
		+	[[Category: Ha, N.C]]

OCA: Protected "4y0m" [edit=sysop:move=sysop]

OCA — Thu, 12 Feb 2015 10:58:10 GMT

Protected "4y0m" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:58, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4y0m is ON HOLD Authors: Jo, I., Kim, JS, Ha, NC. Description: OxyR regulatory domain C199D mutant from pseudomonas aeruginosa [[Category: Unreleas...

OCA — Thu, 12 Feb 2015 10:58:09 GMT

New page: '''Unreleased structure''' The entry 4y0m is ON HOLD Authors: Jo, I., Kim, JS, Ha, NC. Description: OxyR regulatory domain C199D mutant from pseudomonas aeruginosa [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 4y0m is ON HOLD

Authors: Jo, I., Kim, JS, Ha, NC.

Description: OxyR regulatory domain C199D mutant from pseudomonas aeruginosa
[[Category: Unreleased Structures]]
[[Category: Kim, Js, Ha, Nc]]
[[Category: Jo, I]]