5o8y - Revision history

OCA at 09:37, 6 December 2023

OCA — Wed, 06 Dec 2023 09:37:16 GMT

←Older revision		Revision as of 09:37, 6 December 2023
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	==Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.==		==Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.==
-	<StructureSection load='5o8y' size='340' side='right' caption='[[5o8y]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5o8y' size='340' side='right'caption='[[5o8y]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o8y]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Salty Salty~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O8Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O8Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o8y]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O8Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rcsB, STM2270 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5o8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o8y OCA], [~~http~~://pdbe.org/5o8y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o8y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o8y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o8y 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=5o8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o8y OCA], [https://pdbe.org/5o8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o8y RCSB], [https://www.ebi.ac.uk/pdbsum/5o8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o8y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RCSB_SALTY RCSB_SALTY]] Component of the Rcs signaling system, which controls transcription of numerous genes. RcsB is the response regulator that binds to regulatory DNA regions. Can function both in an RcsA-dependent or RcsA-independent manner.[HAMAP-Rule:MF_00981]	+	[https://www.uniprot.org/uniprot/RCSB_SALTY RCSB_SALTY] Component of the Rcs signaling system, which controls transcription of numerous genes. RcsB is the response regulator that binds to regulatory DNA regions. Can function both in an RcsA-dependent or RcsA-independent manner.[HAMAP-Rule:MF_00981]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Salty~~]]	+	[[Category: Large Structures]]
-	[[Category: Casino, P]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
-	[[Category: Huesa, J]]	+	[[Category: Casino P]]
-	[[Category: Marina, A]]	+	[[Category: Huesa J]]
-	[[Category: Miguel-Romero, L]]	+	[[Category: Marina A]]
-	~~[[Category: Response regulator transcriptional factor]]~~	+	[[Category: Miguel-Romero L]]
-	~~[[Category: Transcription~~]]	+

OCA at 07:29, 13 December 2017

OCA — Wed, 13 Dec 2017 07:29:42 GMT

←Older revision		Revision as of 07:29, 13 December 2017
Line 3:		Line 3:
	<StructureSection load='5o8y' size='340' side='right' caption='[[5o8y]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5o8y' size='340' side='right' caption='[[5o8y]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o8y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O8Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o8y]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O8Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rcsB, STM2270 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=5o8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o8y OCA], [http://pdbe.org/5o8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o8y RCSB], [http://www.ebi.ac.uk/pdbsum/5o8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o8y 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=5o8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o8y OCA], [http://pdbe.org/5o8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o8y RCSB], [http://www.ebi.ac.uk/pdbsum/5o8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o8y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RCSB_SALTY RCSB_SALTY]] Component of the Rcs signaling system, which controls transcription of numerous genes. RcsB is the response regulator that binds to regulatory DNA regions. Can function both in an RcsA-dependent or RcsA-independent manner.[HAMAP-Rule:MF_00981]		[[http://www.uniprot.org/uniprot/RCSB_SALTY RCSB_SALTY]] Component of the Rcs signaling system, which controls transcription of numerous genes. RcsB is the response regulator that binds to regulatory DNA regions. Can function both in an RcsA-dependent or RcsA-independent manner.[HAMAP-Rule:MF_00981]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The RcsCDB phosphorelay system controls an extremely large regulon in Enterobacteriaceae that involves processes such as biofilm formation, flagella production, synthesis of extracellular capsules and cell division. Therefore, fine-tuning of this system is essential for virulence in pathogenic microorganisms of this group. The final master effector of the RcsCDB system is the response regulator (RR) RcsB, which activates or represses multiple genes by binding to different promoter regions. This regulatory activity of RcsB can be done alone or in combination with additional transcriptional factors in phosphorylated or dephosphorylated states. The capacity of RcsB to interact with multiple promoters and partners, either dephosphorylated or phosphorylated, suggests an extremely conformational dynamism for this RR. To shed light on the activation mechanism of RcsB and its implication on promoter recognition, we solved the crystal structure of full-length RcsB from Salmonella enterica serovar Typhimurium in the presence and absence of a phosphomimetic molecule BeF3-. These two novel structures have guided an extensive site-directed mutagenesis study at the structural and functional level that confirms RcsB conformational plasticity and dynamism. Our data allowed us to propose a beta5-T switch mechanism where phosphorylation is coupled to alternative DNA binding ways and which highlights the conformational dynamism of RcsB to be so pleiotropic.
		+
		+	Conformational dynamism for DNA interaction in the Salmonella RcsB response regulator.,Casino P, Miguel-Romero L, Huesa J, Garcia P, Garcia-Del Portillo F, Marina A Nucleic Acids Res. 2017 Nov 23. pii: 4653532. doi: 10.1093/nar/gkx1164. PMID:29186528<ref>PMID:29186528</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5o8y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Salty]]
	[[Category: Casino, P]]		[[Category: Casino, P]]
	[[Category: Huesa, J]]		[[Category: Huesa, J]]

OCA at 07:29, 15 November 2017

OCA — Wed, 15 Nov 2017 07:29:00 GMT

←Older revision		Revision as of 07:29, 15 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5o8y ~~is ON HOLD until Paper Publication~~	+	==Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.==
-		+	<StructureSection load='5o8y' size='340' side='right' caption='[[5o8y]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~: ~~Casino, P~~., ~~Marina, A~~., ~~Miguel~~-~~Romero~~, L., ~~Huesa~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5o8y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O8Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O8Y FirstGlance]. <br>
-	~~Description~~: ~~Conformational dynamism for DNA interaction in Salmonella typhimurium~~ RcsB response regulator.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5o8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o8y OCA], [http://pdbe.org/5o8y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o8y RCSB], [http://www.ebi.ac.uk/pdbsum/5o8y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o8y ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RCSB_SALTY RCSB_SALTY]] Component of the Rcs signaling system, which controls transcription of numerous genes. RcsB is the response regulator that binds to regulatory DNA regions. Can function both in an RcsA-dependent or RcsA-independent manner.[HAMAP-Rule:MF_00981]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Casino, P]]
	[[Category: Huesa, J]]		[[Category: Huesa, J]]
		+	[[Category: Marina, A]]
	[[Category: Miguel-Romero, L]]		[[Category: Miguel-Romero, L]]
-	[[Category: ~~Casino, P~~]]	+	[[Category: Response regulator transcriptional factor]]
-	[[Category: ~~Marina, A~~]]	+	[[Category: Transcription]]

OCA: Protected "5o8y" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:10:09 GMT

Protected "5o8y" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:10, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5o8y is ON HOLD until Paper Publication Authors: Casino, P., Marina, A., Miguel-Romero, L., Huesa, J. Description: Conformational dynamism for DNA ...

OCA — Wed, 27 Sep 2017 12:10:08 GMT

New page: '''Unreleased structure''' The entry 5o8y is ON HOLD until Paper Publication Authors: Casino, P., Marina, A., Miguel-Romero, L., Huesa, J. Description: Conformational dynamism for DNA ...

New page

'''Unreleased structure'''

The entry 5o8y is ON HOLD until Paper Publication

Authors: Casino, P., Marina, A., Miguel-Romero, L., Huesa, J.

Description: Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.
[[Category: Unreleased Structures]]
[[Category: Huesa, J]]
[[Category: Miguel-Romero, L]]
[[Category: Casino, P]]
[[Category: Marina, A]]