4qba - Revision history

OCA at 10:54, 31 August 2022

OCA — Wed, 31 Aug 2022 10:54:39 GMT

←Older revision		Revision as of 10:54, 31 August 2022
Line 1:		Line 1:

	==Crystal structure of the effector-binding domain of S. aureus CcpE==		==Crystal structure of the effector-binding domain of S. aureus CcpE==
-	<StructureSection load='4qba' size='340' side='right'caption='[[4qba]]~~, [[Resolution\|resolution]] 2.21Å~~' scene=''>	+	<StructureSection load='4qba' size='340' side='right'caption='[[4qba]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[4qba]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QBA FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QBA FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>~~	+	</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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [https://pdbe.org/4qba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [https://www.ebi.ac.uk/pdbsum/4qba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qba ProSAT]</span></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [https://pdbe.org/4qba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [https://www.ebi.ac.uk/pdbsum/4qba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qba ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	An effective metabolism is essential to all living organisms, including the important human pathogen Staphylococcus aureus. To establish successful infection, S. aureus must scavenge nutrients and coordinate its metabolism for proliferation. Meanwhile, it also must produce an array of virulence factors to interfere with host defenses. However, the ways in which S. aureus ties its metabolic state to its virulence regulation remain largely unknown. Here we show that citrate, the first intermediate of the tricarboxylic acid (TCA) cycle, binds to and activates the catabolite control protein E (CcpE) of S. aureus. Using structural and site-directed mutagenesis studies, we demonstrate that two arginine residues (Arg145 and Arg256) within the putative inducer-binding cavity of CcpE are important for its allosteric activation by citrate. Microarray analysis reveals that CcpE tunes the expression of 126 genes that comprise about 4.7% of the S. aureus genome. Intriguingly, although CcpE is a major positive regulator of the TCA-cycle activity, its regulon consists predominantly of genes involved in the pathogenesis of S. aureus. Moreover, inactivation of CcpE results in increased staphyloxanthin production, improved ability to acquire iron, increased resistance to whole-blood-mediated killing, and enhanced bacterial virulence in a mouse model of systemic infection. This study reveals CcpE as an important metabolic sensor that allows S. aureus to sense and adjust its metabolic state and subsequently to coordinate the expression of virulence factors and bacterial virulence.
-
-	Metabolic sensor governing bacterial virulence in Staphylococcus aureus.,Ding Y, Liu X, Chen F, Di H, Xu B, Zhou L, Deng X, Wu M, Yang CG, Lan L Proc Natl Acad Sci U S A. 2014 Nov 3. pii: 201411077. PMID:25368190<ref>PMID:25368190</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4qba" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lan, L]]	+	[[Category: Lan L]]
-	[[Category: Liu, X]]	+	[[Category: Liu X]]
-	[[Category: Yang~~, C G]]~~	+	[[Category: Yang CG]]
-	~~[[Category: Lysr type transcriptional regulator]]~~	+
-	~~[[Category: Transcription regulator~~]]	+

OCA at 05:06, 25 August 2022

OCA — Thu, 25 Aug 2022 05:06:50 GMT

←Older revision		Revision as of 05:06, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='4qba' size='340' side='right'caption='[[4qba]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='4qba' size='340' side='right'caption='[[4qba]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qba]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Staas Staas]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QBA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qba]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QBA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAS0637 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=282459 STAAS])</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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [https://pdbe.org/4qba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [https://www.ebi.ac.uk/pdbsum/4qba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qba 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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [~~http~~://pdbe.org/4qba PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qba PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qba ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Staas]]
	[[Category: Lan, L]]		[[Category: Lan, L]]
	[[Category: Liu, X]]		[[Category: Liu, X]]

OCA at 08:52, 24 April 2019

OCA — Wed, 24 Apr 2019 08:52:32 GMT

←Older revision		Revision as of 08:52, 24 April 2019
Line 1:		Line 1:

	==Crystal structure of the effector-binding domain of S. aureus CcpE==		==Crystal structure of the effector-binding domain of S. aureus CcpE==
-	<StructureSection load='4qba' size='340' side='right' caption='[[4qba]], [[Resolution\|resolution]] 2.21Å' scene=''>	+	<StructureSection load='4qba' size='340' side='right'caption='[[4qba]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qba]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qba]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staas Staas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAS0637 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=282459 STAAS])</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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [http://pdbe.org/4qba PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [http://www.ebi.ac.uk/pdbsum/4qba PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qba 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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [http://pdbe.org/4qba PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [http://www.ebi.ac.uk/pdbsum/4qba PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qba ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Staas]]
	[[Category: Lan, L]]		[[Category: Lan, L]]
	[[Category: Liu, X]]		[[Category: Liu, X]]

OCA at 11:41, 11 August 2016

OCA — Thu, 11 Aug 2016 11:41:44 GMT

←Older revision		Revision as of 11:41, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the effector-binding domain of S. aureus CcpE==		==Crystal structure of the effector-binding domain of S. aureus CcpE==
	<StructureSection load='4qba' size='340' side='right' caption='[[4qba]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='4qba' size='340' side='right' caption='[[4qba]], [[Resolution\|resolution]] 2.21Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [http://www.ebi.ac.uk/pdbsum/4qba 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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [http://pdbe.org/4qba PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [http://www.ebi.ac.uk/pdbsum/4qba PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qba ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4qba" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:37, 19 November 2014

OCA — Wed, 19 Nov 2014 12:37:06 GMT

←Older revision		Revision as of 12:37, 19 November 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of the effector-binding domain of S. aureus CcpE==
		+	<StructureSection load='4qba' size='340' side='right' caption='[[4qba]], [[Resolution\|resolution]] 2.21Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4qba]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4qba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qba OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qba RCSB], [http://www.ebi.ac.uk/pdbsum/4qba PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	An effective metabolism is essential to all living organisms, including the important human pathogen Staphylococcus aureus. To establish successful infection, S. aureus must scavenge nutrients and coordinate its metabolism for proliferation. Meanwhile, it also must produce an array of virulence factors to interfere with host defenses. However, the ways in which S. aureus ties its metabolic state to its virulence regulation remain largely unknown. Here we show that citrate, the first intermediate of the tricarboxylic acid (TCA) cycle, binds to and activates the catabolite control protein E (CcpE) of S. aureus. Using structural and site-directed mutagenesis studies, we demonstrate that two arginine residues (Arg145 and Arg256) within the putative inducer-binding cavity of CcpE are important for its allosteric activation by citrate. Microarray analysis reveals that CcpE tunes the expression of 126 genes that comprise about 4.7% of the S. aureus genome. Intriguingly, although CcpE is a major positive regulator of the TCA-cycle activity, its regulon consists predominantly of genes involved in the pathogenesis of S. aureus. Moreover, inactivation of CcpE results in increased staphyloxanthin production, improved ability to acquire iron, increased resistance to whole-blood-mediated killing, and enhanced bacterial virulence in a mouse model of systemic infection. This study reveals CcpE as an important metabolic sensor that allows S. aureus to sense and adjust its metabolic state and subsequently to coordinate the expression of virulence factors and bacterial virulence.

-	~~The entry 4qba is ON HOLD~~	+	Metabolic sensor governing bacterial virulence in Staphylococcus aureus.,Ding Y, Liu X, Chen F, Di H, Xu B, Zhou L, Deng X, Wu M, Yang CG, Lan L Proc Natl Acad Sci U S A. 2014 Nov 3. pii: 201411077. PMID:25368190<ref>PMID:25368190</ref>

-	~~Authors: Liu~~, X., Lan, L., Yang, C.G.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of the effector-binding domain of S. aureus CcpE~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lan, L]]
		+	[[Category: Liu, X]]
		+	[[Category: Yang, C G]]
		+	[[Category: Lysr type transcriptional regulator]]
		+	[[Category: Transcription regulator]]

OCA at 08:16, 21 May 2014

OCA — Wed, 21 May 2014 08:16:20 GMT

←Older revision		Revision as of 08:16, 21 May 2014
Line 3:		Line 3:
	The entry 4qba is ON HOLD		The entry 4qba is ON HOLD

-	Authors: ~~Xing~~ Liu, ~~Lefu~~ Lan, ~~Cai-Guang~~ Yang	+	Authors: Liu, X., Lan, L., Yang, C.G.

	Description: Crystal structure of the effector-binding domain of S. aureus CcpE		Description: Crystal structure of the effector-binding domain of S. aureus CcpE

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

OCA — Wed, 14 May 2014 07:11:22 GMT

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

←Older revision

Revision as of 07:11, 14 May 2014

OCA: New page: '''Unreleased structure''' The entry 4qba is ON HOLD Authors: Xing Liu, Lefu Lan, Cai-Guang Yang Description: Crystal structure of the effector-binding domain of S. aureus CcpE

OCA — Wed, 14 May 2014 07:11:21 GMT

New page: '''Unreleased structure''' The entry 4qba is ON HOLD Authors: Xing Liu, Lefu Lan, Cai-Guang Yang Description: Crystal structure of the effector-binding domain of S. aureus CcpE

New page

'''Unreleased structure'''

The entry 4qba is ON HOLD

Authors: Xing Liu, Lefu Lan, Cai-Guang Yang

Description: Crystal structure of the effector-binding domain of S. aureus CcpE