6d6l - Revision history

OCA at 14:32, 13 March 2024

OCA — Wed, 13 Mar 2024 14:32:50 GMT

←Older revision		Revision as of 14:32, 13 March 2024
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	==The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 14==		==The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 14==
-	<StructureSection load='6d6l' size='340' side='right' caption='[[6d6l]], [[Resolution\|resolution]] 1.63Å' scene=''>	+	<StructureSection load='6d6l' size='340' side='right'caption='[[6d6l]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d6l]] is a 4 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=6D6L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6D6L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d6l]] is a 4 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=6D6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D6L FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=FY4:2~~,~~4-dibromo-6-{~~[~~(2-nitrobenzene-~~1~~-carbonyl)amino]methyl}phenyl+4-chlorobenzoate'>FY4</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]] 1.63Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6d6a\|6d6a]], [[6d6b\|6d6b]], [[6d6c\|6d6c]], [[6d6d\|6d6d]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FY4:2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl+4-chlorobenzoate'>FY4</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><b>[~~[Gene\|Gene:~~]~~]</b~~></td>~~<td class="sblockDat">lasR, PA1430 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=6d6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d6l OCA], [https://pdbe.org/6d6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d6l RCSB], [https://www.ebi.ac.uk/pdbsum/6d6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d6l 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=6d6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d6l OCA], [~~http~~://pdbe.org/6d6l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6d6l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6d6l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6d6l ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LASR_PSEAE LASR_PSEAE]] Transcriptional activator of elastase structural gene (LasB). Binds to the PAI autoinducer.	+	[https://www.uniprot.org/uniprot/LASR_PSEAE LASR_PSEAE] Transcriptional activator of elastase structural gene (LasB). Binds to the PAI autoinducer.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Chemical strategies to block quorum sensing (QS) could provide a route to attenuate virulence in bacterial pathogens. Considerable research has focused on this approach in Pseudomonas aeruginosa, which uses the LuxR-type receptor LasR to regulate much of its QS network. Non-native ligands that antagonize LasR have been developed, yet we have little understanding of the mode by which these compounds interact with LasR and alter its function, as the receptor is unstable in their presence. Herein, we report an approach to circumvent this challenge through the study of a series of synthetic LasR agonists with varying levels of potency. Structural investigations of these ligands with the LasR ligand-binding domain reveal that certain agonists can enforce a conformation that deviates from that observed for other, often more potent agonists. These results, when combined with cell-based and biophysical analyses, suggest a functional model for LasR that could guide future ligand design.	+
-		+
-	Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop "Out" Conformation for LasR.,O'Reilly MC, Dong SH, Rossi FM, Karlen KM, Kumar RS, Nair SK, Blackwell HE Cell Chem Biol. 2018 Jul 11. pii: S2451-9456(18)30221-6. doi:, 10.1016/j.chembiol.2018.06.007. PMID:30033130<ref>PMID:30033130</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6d6l" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
-	*[[Transcriptional activator\|Transcriptional activator]]	+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseae~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Dong, S H~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: ~~Nair, S K~~]]	+	[[Category: Dong SH]]
-	[[Category: ~~Luxr receptor]]~~	+	[[Category: Nair SK]]
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Signaling protein-agonist complex~~]]	+

OCA at 08:46, 3 October 2018

OCA — Wed, 03 Oct 2018 08:46:09 GMT

←Older revision		Revision as of 08:46, 3 October 2018
Line 3:		Line 3:
	<StructureSection load='6d6l' size='340' side='right' caption='[[6d6l]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='6d6l' size='340' side='right' caption='[[6d6l]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d6l]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D6L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d6l]] is a 4 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=6D6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D6L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FY4:2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl+4-chlorobenzoate'>FY4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FY4:2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl+4-chlorobenzoate'>FY4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6d6a\|6d6a]], [[6d6b\|6d6b]], [[6d6c\|6d6c]], [[6d6d\|6d6d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6d6a\|6d6a]], [[6d6b\|6d6b]], [[6d6c\|6d6c]], [[6d6d\|6d6d]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lasR, PA1430 ([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=6d6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d6l OCA], [http://pdbe.org/6d6l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d6l RCSB], [http://www.ebi.ac.uk/pdbsum/6d6l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d6l 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=6d6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d6l OCA], [http://pdbe.org/6d6l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d6l RCSB], [http://www.ebi.ac.uk/pdbsum/6d6l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d6l ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6d6l" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6d6l" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator\|Transcriptional activator]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pseae]]
	[[Category: Dong, S H]]		[[Category: Dong, S H]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]

OCA at 21:48, 9 August 2018

OCA — Thu, 09 Aug 2018 21:48:28 GMT

←Older revision		Revision as of 21:48, 9 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6d6l is ~~ON HOLD until Paper~~ Publication	+	==The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 14==
		+	<StructureSection load='6d6l' size='340' side='right' caption='[[6d6l]], [[Resolution\|resolution]] 1.63Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6d6l]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D6L FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FY4:2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl+4-chlorobenzoate'>FY4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6d6a\|6d6a]], [[6d6b\|6d6b]], [[6d6c\|6d6c]], [[6d6d\|6d6d]]</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=6d6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d6l OCA], [http://pdbe.org/6d6l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d6l RCSB], [http://www.ebi.ac.uk/pdbsum/6d6l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d6l ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LASR_PSEAE LASR_PSEAE]] Transcriptional activator of elastase structural gene (LasB). Binds to the PAI autoinducer.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chemical strategies to block quorum sensing (QS) could provide a route to attenuate virulence in bacterial pathogens. Considerable research has focused on this approach in Pseudomonas aeruginosa, which uses the LuxR-type receptor LasR to regulate much of its QS network. Non-native ligands that antagonize LasR have been developed, yet we have little understanding of the mode by which these compounds interact with LasR and alter its function, as the receptor is unstable in their presence. Herein, we report an approach to circumvent this challenge through the study of a series of synthetic LasR agonists with varying levels of potency. Structural investigations of these ligands with the LasR ligand-binding domain reveal that certain agonists can enforce a conformation that deviates from that observed for other, often more potent agonists. These results, when combined with cell-based and biophysical analyses, suggest a functional model for LasR that could guide future ligand design.

-	~~Authors:~~ Dong, ~~S.H.~~, Nair, S.K.	+	Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop "Out" Conformation for LasR.,O'Reilly MC, Dong SH, Rossi FM, Karlen KM, Kumar RS, Nair SK, Blackwell HE Cell Chem Biol. 2018 Jul 11. pii: S2451-9456(18)30221-6. doi:, 10.1016/j.chembiol.2018.06.007. PMID:30033130<ref>PMID:30033130</ref>

-	~~Description: The structure~~ of ~~ligand binding domain~~ of ~~LasR in complex with TP~~-~~1 homolog, compound 14~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Nair, S.K]]	+	<div class="pdbe-citations 6d6l" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Dong, S.H~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dong, S H]]
		+	[[Category: Nair, S K]]
		+	[[Category: Luxr receptor]]
		+	[[Category: Signaling protein]]
		+	[[Category: Signaling protein-agonist complex]]

OCA at 04:01, 16 May 2018

OCA — Wed, 16 May 2018 04:01:21 GMT

←Older revision		Revision as of 04:01, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6d6l is ON HOLD	+	The entry 6d6l is ON HOLD until Paper Publication

	Authors: Dong, S.H., Nair, S.K.		Authors: Dong, S.H., Nair, S.K.
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	Description: The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 14		Description: The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 14
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Dong, S.H]]
	[[Category: Nair, S.K]]		[[Category: Nair, S.K]]
		+	[[Category: Dong, S.H]]

OCA: Protected "6d6l" [edit=sysop:move=sysop]

OCA — Wed, 02 May 2018 06:44:40 GMT

Protected "6d6l" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:44, 2 May 2018

OCA: New page: '''Unreleased structure''' The entry 6d6l is ON HOLD Authors: Dong, S.H., Nair, S.K. Description: The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound ...

OCA — Wed, 02 May 2018 06:44:38 GMT

New page: '''Unreleased structure''' The entry 6d6l is ON HOLD Authors: Dong, S.H., Nair, S.K. Description: The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound ...

New page

'''Unreleased structure'''

The entry 6d6l is ON HOLD

Authors: Dong, S.H., Nair, S.K.

Description: The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 14
[[Category: Unreleased Structures]]
[[Category: Dong, S.H]]
[[Category: Nair, S.K]]