4xqn - Revision history

OCA at 09:02, 20 March 2024

2024-03-20T09:02:42Z

←Older revision		Revision as of 09:02, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xqn]] is a 12 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=4XQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XQN FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xqn]] is a 12 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=4XQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XQN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [https://pdbe.org/4xqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [https://www.ebi.ac.uk/pdbsum/4xqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqn 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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [https://pdbe.org/4xqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [https://www.ebi.ac.uk/pdbsum/4xqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://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;">
-	== 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 4xqn" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:47, 26 April 2023

2023-04-26T17:47:59Z

←Older revision		Revision as of 17:47, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xqn' size='340' side='right'caption='[[4xqn]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4xqn' size='340' side='right'caption='[[4xqn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xqn]] is a 12 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=4XQN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XQN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xqn]] is a 12 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=4XQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XQN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqj\|4xqj]], [[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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [https://pdbe.org/4xqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [https://www.ebi.ac.uk/pdbsum/4xqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqn 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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [~~http~~://pdbe.org/4xqn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xqn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqn 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 ==
Line 25:		Line 23:
	</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-dna binding protein complex~~]]	+	[[Category: Rajasree K]]

OCA at 08:42, 18 December 2019

2019-12-18T08:42:49Z

←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 4xqn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 23:36, 5 June 2019

2019-06-05T23:36:32Z

←Older revision		Revision as of 23:36, 5 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='4xqn' size='340' side='right' caption='[[4xqn]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4xqn' size='340' side='right'caption='[[4xqn]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xqn]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XQN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xqn]] is a 12 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=4XQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XQN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqj\|4xqj]], [[4xqq\|4xqq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqj\|4xqj]], [[4xqq\|4xqq]]</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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [http://pdbe.org/4xqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [http://www.ebi.ac.uk/pdbsum/4xqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqn 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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [http://pdbe.org/4xqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [http://www.ebi.ac.uk/pdbsum/4xqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqn ProSAT]</span></td></tr>
	</table>		</table>
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-dna binding protein complex]]		[[Category: Dna-dna binding protein complex]]

OCA at 09:53, 22 March 2017

2017-03-22T09:53:20Z

←Older revision		Revision as of 09:53, 22 March 2017
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqj\|4xqj]], [[4xqq\|4xqq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqj\|4xqj]], [[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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [http://pdbe.org/4xqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [http://www.ebi.ac.uk/pdbsum/4xqn 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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [http://pdbe.org/4xqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [http://www.ebi.ac.uk/pdbsum/4xqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 04:01, 12 May 2016

2016-05-12T04:01:38Z

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

-	~~The entry~~ 4xqn is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of AgrA LytTR domain in complex with promoters==
-		+	<StructureSection load='4xqn' size='340' side='right' caption='[[4xqn]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~: ~~Gopal~~, B., ~~Rajasree~~, K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4xqn]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XQN 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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xqj\|4xqj]], [[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=4xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqn OCA], [http://pdbe.org/4xqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xqn RCSB], [http://www.ebi.ac.uk/pdbsum/4xqn 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-dna binding protein complex]]

OCA at 09:26, 24 June 2015

2015-06-24T09:26:04Z

←Older revision		Revision as of 09:26, 24 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

OCA at 11:35, 17 June 2015

2015-06-17T11:35:15Z

←Older revision		Revision as of 11:35, 17 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xqn is ON HOLD ~~until Paper Publication~~	+	The entry 4xqn is ON HOLD

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

OCA at 12:17, 25 February 2015

2015-02-25T12:17:52Z

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

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

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

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

2015-01-28T15:42:43Z

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

←Older revision

Revision as of 15:42, 28 January 2015