4xqj - Revision history

OCA at 15:30, 8 November 2023

OCA — Wed, 08 Nov 2023 15:30:38 GMT

←Older revision		Revision as of 15:30, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xqj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XQJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xqj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XQJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene></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=4xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqj OCA], [https://pdbe.org/4xqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xqj RCSB], [https://www.ebi.ac.uk/pdbsum/4xqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqj 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=4xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqj OCA], [https://pdbe.org/4xqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xqj RCSB], [https://www.ebi.ac.uk/pdbsum/4xqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqj ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:47, 26 April 2023

OCA — Wed, 26 Apr 2023 17:47:54 GMT

←Older revision		Revision as of 17:47, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xqj' size='340' side='right'caption='[[4xqj]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4xqj' size='340' side='right'caption='[[4xqj]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xqj]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staac Staac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xqj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XQJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqn\|4xqn]], [[4xqq\|4xqq]]</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=4xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqj OCA], [https://pdbe.org/4xqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xqj RCSB], [https://www.ebi.ac.uk/pdbsum/4xqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqj ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">agrA, SACOL2026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])~~</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=4xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqj OCA], [~~http~~://pdbe.org/4xqj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xqj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xqj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AGRA_STAAC AGRA_STAAC]] Required for high-level post-exponential phase expression of a series of secreted proteins.	+	[https://www.uniprot.org/uniprot/AGRA_STAAC AGRA_STAAC] Required for high-level post-exponential phase expression of a series of secreted proteins.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Staac~~]]	+	[[Category: Staphylococcus aureus subsp. aureus COL]]
-	[[Category: ~~Gopal, B~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Rajasree, K~~]]	+	[[Category: Gopal B]]
-	[[Category: ~~Dna binding protein-dna complex]]~~	+	[[Category: Rajasree K]]
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 08:42, 18 December 2019

OCA — Wed, 18 Dec 2019 08:42:49 GMT

←Older revision		Revision as of 08:42, 18 December 2019
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/AGRA_STAAC AGRA_STAAC]] Required for high-level post-exponential phase expression of a series of secreted proteins.		[[http://www.uniprot.org/uniprot/AGRA_STAAC AGRA_STAAC]] Required for high-level post-exponential phase expression of a series of secreted proteins.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The intracellular trigger for the quorum sensing response mechanism in Staphylococcus aureus involves the phosphorylation of the response regulator AgrA by the membrane anchored histidine kinase AgrC. AgrA activates transcription from three promoter sequences (P1-P3). The promoter strength, conditional association of AgrA with these promoter elements and temporal delay in AgrA-mediated changes in gene expression contribute to the diversity of the quorum sensing response in different S. aureus strains. AgrA promoters comprise of imperfect direct repeats of DNA with a consensus sequence- [TA][AC][CA]GTTN[AG][TG]. Here we describe crystal structures of the DNA-binding (LytTR) domain of AgrA with different cognate DNA sequences that reveal a hitherto unanticipated feature of AgrA-DNA interactions. AgrA promoter interactions are asymmetric with fewer interactions at the binding site proximal to the -35 promoter element. Biochemical assays to evaluate AgrA-promoter interactions suggests that phosphorylation induced dimerization of AgrA can compensate for the asymmetry in AgrA-DNA interactions. The structures also provide a basis to rationalize mutations that were noted to alter AgrA activity without affecting protein-DNA interactions. Put together, the structural data, gene expression and mutational analysis reveal that promoter strength and AgrA phosphorylation enable quorum-sensing triggered transcriptional changes leading to a transition from the persistent to virulent phenotype.
		+
		+	Conformational features of the Staphylococcus aureus AgrA-promoter interactions rationalize quorum-sensing triggered gene expression.,Rajasree K, Fasim A, Gopal B Biochem Biophys Rep. 2016 Mar 23;6:124-134. doi: 10.1016/j.bbrep.2016.03.012., eCollection 2016 Jul. PMID:28955870<ref>PMID:28955870</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4xqj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 00:09, 6 June 2019

OCA — Thu, 06 Jun 2019 00:09:42 GMT

←Older revision		Revision as of 00:09, 6 June 2019
Line 1:		Line 1:

	==Crystal structure of AgrA LytTR domain in complex with promoters==		==Crystal structure of AgrA LytTR domain in complex with promoters==
-	<StructureSection load='4xqj' size='340' side='right' caption='[[4xqj]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4xqj' size='340' side='right'caption='[[4xqj]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xqj]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xqj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Staac Staac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XQJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqn\|4xqn]], [[4xqq\|4xqq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqn\|4xqn]], [[4xqq\|4xqq]]</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=4xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqj OCA], [http://pdbe.org/4xqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xqj RCSB], [http://www.ebi.ac.uk/pdbsum/4xqj PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">agrA, SACOL2026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</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=4xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqj OCA], [http://pdbe.org/4xqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xqj RCSB], [http://www.ebi.ac.uk/pdbsum/4xqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Staac]]
	[[Category: Gopal, B]]		[[Category: Gopal, B]]
	[[Category: Rajasree, K]]		[[Category: Rajasree, K]]
	[[Category: Dna binding protein-dna complex]]		[[Category: Dna binding protein-dna complex]]
	[[Category: Protein-dna complex]]		[[Category: Protein-dna complex]]

OCA at 04:01, 12 May 2016

OCA — Thu, 12 May 2016 04:01:37 GMT

←Older revision		Revision as of 04:01, 12 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4xqj is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of AgrA LytTR domain in complex with promoters==
-		+	<StructureSection load='4xqj' size='340' side='right' caption='[[4xqj]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~: ~~Gopal~~, B., ~~Rajasree~~, K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4xqj]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XQJ FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~AgrA LytTR domain in complex with promoters~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqn\|4xqn]], [[4xqq\|4xqq]]</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=4xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqj OCA], [http://pdbe.org/4xqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xqj RCSB], [http://www.ebi.ac.uk/pdbsum/4xqj PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AGRA_STAAC AGRA_STAAC]] Required for high-level post-exponential phase expression of a series of secreted proteins.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gopal, B]]
	[[Category: Rajasree, K]]		[[Category: Rajasree, K]]
-	[[Category: ~~Gopal, B~~]]	+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Protein-dna complex]]

OCA at 12:17, 25 February 2015

OCA — Wed, 25 Feb 2015 12:17:39 GMT

←Older revision		Revision as of 12:17, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Gopal, B., Rajasree, K.		Authors: Gopal, B., Rajasree, K.

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

OCA — Wed, 28 Jan 2015 15:42:14 GMT

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

←Older revision

Revision as of 15:42, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xqj is ON HOLD Authors: Gopal, B., Rajasree, K. Description: Crystal structure of AgrA LytTR domain in complex with promoters [[Category: Unreleas...

OCA — Wed, 28 Jan 2015 15:42:13 GMT

New page: '''Unreleased structure''' The entry 4xqj is ON HOLD Authors: Gopal, B., Rajasree, K. Description: Crystal structure of AgrA LytTR domain in complex with promoters [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 4xqj is ON HOLD

Authors: Gopal, B., Rajasree, K.

Description: Crystal structure of AgrA LytTR domain in complex with promoters
[[Category: Unreleased Structures]]
[[Category: Rajasree, K]]
[[Category: Gopal, B]]