6c28 - Revision history

OCA at 14:25, 13 March 2024

2024-03-13T14:25:54Z

←Older revision		Revision as of 14:25, 13 March 2024
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	==Transcriptional repressor, CouR, bound to p-coumaroyl-CoA==		==Transcriptional repressor, CouR, bound to p-coumaroyl-CoA==
-	<StructureSection load='6c28' size='340' side='right' caption='[[6c28]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='6c28' size='340' side='right'caption='[[6c28]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c28]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhopa Rhopa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C28 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6C28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c28]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris_CGA009 Rhodopseudomonas palustris CGA009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C28 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=WCA:P~~-~~COUMAROYL-COA'>WCA</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]] 2.09Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~couR, RPA1794 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=258594 RHOPA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=WCA:P-COUMAROYL-COA'>WCA</scene></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=6c28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c28 OCA], [~~http~~://pdbe.org/6c28 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6c28 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6c28 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6c28 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=6c28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c28 OCA], [https://pdbe.org/6c28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c28 RCSB], [https://www.ebi.ac.uk/pdbsum/6c28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c28 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q6N8V9_RHOPA Q6N8V9_RHOPA]
-	The MarR-family transcriptional regulator CouR, from the soil bacterium Rhodopseudomonas palustris CGA009, has recently been shown to negatively regulate a p-coumarate catabolic operon. Unlike most characterized MarR repressors that respond to small metabolites at concentrations in the millimolar range, repression by CouR is alleviated by the 800 Da ligand p-coumaroyl-CoA with high affinity and specificity. Here we report the crystal structures of ligand free CouR as well as the complex with p-coumaroyl-CoA, each to 2.1 A resolution, and the 2.85 A resolution cocrystal structure of CouR bound to an oligonucleotide bearing the cognate DNA operator sequence. In combination with binding experiments which uncover specific residues important for ligand and DNA recognition, these structures provide glimpses of a MarR family repressor in all possible states, allowing for an understanding for the molecular basis of DNA binding and the conformation alterations that accompany ligand-induced dissociation for activation of the operon.	+

-	Structural basis of transcriptional regulation by CouR, a repressor of coumarate catabolism in Rhodopseudomonas palustris.,Cogan DP, Baraquet C, Harwood CS, Nair SK J Biol Chem. 2018 May 23. pii: RA118.003561. doi: 10.1074/jbc.RA118.003561. PMID:29794028<ref>PMID:29794028</ref>	+	==See Also==
-		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6c28" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhopa~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Cogan, D P~~]]	+	[[Category: Rhodopseudomonas palustris CGA009]]
-	[[Category: ~~Nair, S K~~]]	+	[[Category: Cogan DP]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Nair SK]]
-	~~[[Category: Marr family]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Transcriptional regulation~~]]	+

OCA at 08:09, 14 June 2018

2018-06-14T08:09:40Z

←Older revision		Revision as of 08:09, 14 June 2018
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	<StructureSection load='6c28' size='340' side='right' caption='[[6c28]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='6c28' size='340' side='right' caption='[[6c28]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c28]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c28]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhopa Rhopa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C28 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=WCA:P-COUMAROYL-COA'>WCA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=WCA:P-COUMAROYL-COA'>WCA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">couR, RPA1794 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=258594 RHOPA])</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=6c28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c28 OCA], [http://pdbe.org/6c28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c28 RCSB], [http://www.ebi.ac.uk/pdbsum/6c28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c28 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=6c28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c28 OCA], [http://pdbe.org/6c28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c28 RCSB], [http://www.ebi.ac.uk/pdbsum/6c28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c28 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The MarR-family transcriptional regulator CouR, from the soil bacterium Rhodopseudomonas palustris CGA009, has recently been shown to negatively regulate a p-coumarate catabolic operon. Unlike most characterized MarR repressors that respond to small metabolites at concentrations in the millimolar range, repression by CouR is alleviated by the 800 Da ligand p-coumaroyl-CoA with high affinity and specificity. Here we report the crystal structures of ligand free CouR as well as the complex with p-coumaroyl-CoA, each to 2.1 A resolution, and the 2.85 A resolution cocrystal structure of CouR bound to an oligonucleotide bearing the cognate DNA operator sequence. In combination with binding experiments which uncover specific residues important for ligand and DNA recognition, these structures provide glimpses of a MarR family repressor in all possible states, allowing for an understanding for the molecular basis of DNA binding and the conformation alterations that accompany ligand-induced dissociation for activation of the operon.
		+
		+	Structural basis of transcriptional regulation by CouR, a repressor of coumarate catabolism in Rhodopseudomonas palustris.,Cogan DP, Baraquet C, Harwood CS, Nair SK J Biol Chem. 2018 May 23. pii: RA118.003561. doi: 10.1074/jbc.RA118.003561. PMID:29794028<ref>PMID:29794028</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6c28" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Rhopa]]
	[[Category: Cogan, D P]]		[[Category: Cogan, D P]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]

OCA at 05:33, 30 May 2018

2018-05-30T05:33:13Z

←Older revision		Revision as of 05:33, 30 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6c28 is ~~ON HOLD until Paper Publication~~	+	==Transcriptional repressor, CouR, bound to p-coumaroyl-CoA==
-		+	<StructureSection load='6c28' size='340' side='right' caption='[[6c28]], [[Resolution\|resolution]] 2.09Å' scene=''>
-	~~Authors~~: ~~Cogan~~, D.P., ~~Nair~~, S.K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6c28]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C28 FirstGlance]. <br>
-	~~Description~~: ~~Transcriptional repressor~~, ~~CouR, bound to p~~-~~coumaroyl-CoA~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=WCA:P-COUMAROYL-COA'>WCA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6c28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c28 OCA], [http://pdbe.org/6c28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c28 RCSB], [http://www.ebi.ac.uk/pdbsum/6c28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c28 ProSAT]</span></td></tr>
-	[[Category: Nair, S.K]]	+	</table>
-	[[Category: ~~Cogan, D.P~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Cogan, D P]]
		+	[[Category: Nair, S K]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Marr family]]
		+	[[Category: Repressor]]
		+	[[Category: Transcriptional regulation]]

OCA at 03:58, 25 April 2018

2018-04-25T03:58:30Z

←Older revision		Revision as of 03:58, 25 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6c28 is ON HOLD	+	The entry 6c28 is ON HOLD until Paper Publication

	Authors: Cogan, D.P., Nair, S.K.		Authors: Cogan, D.P., Nair, S.K.
Line 7:		Line 7:
	Description: Transcriptional repressor, CouR, bound to p-coumaroyl-CoA		Description: Transcriptional repressor, CouR, bound to p-coumaroyl-CoA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Cogan, D.P]]
	[[Category: Nair, S.K]]		[[Category: Nair, S.K]]
		+	[[Category: Cogan, D.P]]

OCA: Protected "6c28" [edit=sysop:move=sysop]

2018-01-17T05:42:59Z

Protected "6c28" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:42, 17 January 2018

OCA: New page: '''Unreleased structure''' The entry 6c28 is ON HOLD Authors: Cogan, D.P., Nair, S.K. Description: Transcriptional repressor, CouR, bound to p-coumaroyl-CoA [[Category: Unreleased Stru...

2018-01-17T05:42:58Z

New page: '''Unreleased structure''' The entry 6c28 is ON HOLD Authors: Cogan, D.P., Nair, S.K. Description: Transcriptional repressor, CouR, bound to p-coumaroyl-CoA [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 6c28 is ON HOLD

Authors: Cogan, D.P., Nair, S.K.

Description: Transcriptional repressor, CouR, bound to p-coumaroyl-CoA
[[Category: Unreleased Structures]]
[[Category: Cogan, D.P]]
[[Category: Nair, S.K]]