5ey1 - Revision history

OCA at 08:32, 12 July 2023

OCA — Wed, 12 Jul 2023 08:32:50 GMT

←Older revision		Revision as of 08:32, 12 July 2023
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	<StructureSection load='5ey1' size='340' side='right'caption='[[5ey1]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5ey1' size='340' side='right'caption='[[5ey1]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ey1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staa1 Staa1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ey1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu3 Staphylococcus aureus subsp. aureus Mu3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EY1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GTP:GUANOSINE~~-~~5-TRIPHOSPHATE'>GTP</scene>~~, ~~<scene name='pdbligand=ILE:ISOLEUCINE'>ILE</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5ey0\|5ey0]], [[5ey2\|5ey2]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=ILE:ISOLEUCINE'>ILE</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">codY, SAHV_1245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=418127 STAA1])~~</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=5ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey1 OCA], [https://pdbe.org/5ey1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ey1 RCSB], [https://www.ebi.ac.uk/pdbsum/5ey1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey1 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey1 OCA], [~~http~~://pdbe.org/5ey1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ey1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ey1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey1 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~CODY_STAA1 CODY_STAA1]~~] DNA-binding ~~protein that represses~~ the expression of ~~many~~ genes ~~that are induced as cells make the transition from~~ rapid exponential growth to ~~stationary phase~~. It is a ~~GTP~~-binding ~~protein that senses~~ the ~~intracellular GTP concentration as an indicator~~ of ~~nutritional limitations~~. ~~At low GTP concentration it no longer binds GTP~~ and ~~stop to act as~~ a transcriptional ~~repressor~~.	+	[https://www.uniprot.org/uniprot/CODY_STAA8 CODY_STAA8] DNA-binding global transcriptional regulator which is involved in the adaptive response to starvation and acts by directly or indirectly controlling the expression of numerous genes in response to nutrient availability. During rapid exponential growth, CodY is highly active and represses genes whose products allow adaptation to nutrient depletion.[HAMAP-Rule:MF_00621]<ref>PMID:27116338</ref> In S.aureus, targets include over 200 genes (PubMed:20363936, PubMed:27116338). Acts mainly as a repressor of genes involved in amino acid transport and metabolism, including the branched-chain amino acids (BCAAs) biosynthetic operon (PubMed:19251851, PubMed:20363936, PubMed:27116338, PubMed:29357354). Several genes involved in nucleotide synthesis and transport are activated (PubMed:19251851). Binds to a 21-bp conserved DNA motif, the CodY-binding site (PubMed:20363936). Additionally, in pathogenic bacteria, CodY also regulates virulence gene expression and provides a regulatory link between metabolism and pathogenesis (PubMed:18156263, PubMed:19251851, PubMed:20363936, PubMed:27116338, PubMed:29378891). Genes encoding virulence and defense factors are either up- or down-regulated by CodY (PubMed:19251851). Among others, is involved in the repression of the accessory gene regulator (agr), the hemolytic alpha-toxin (hla) gene, and the icaADBC operon, responsible for the production of polysaccharide intercellular adhesin (PIA), a major contributor to biofilm formation in S.aureus (PubMed:18156263, PubMed:19251851). Also regulates the expression of thermonuclease (nuc) via the Sae two-component system, by binding directly to the sae P1 promoter region and blocking the binding of the positive regulator SaeR (PubMed:27116338, PubMed:29378891). It restrains Sae-dependent production of leukocidins (PubMed:29378891). CodY also controls the sae locus indirectly through Agr and Rot-mediated repression of the sae P1 promoter (PubMed:29378891). The virulence genes regulated by CodY fall into three groups: one group is regulated directly by CodY, a second group is indirectly regulated by CodY, in particular through its repression of the agr and sae loci, and a third group is regulated in two ways, by direct repression and by repression via another regulator (PubMed:19251851, PubMed:20363936, PubMed:29378891). S.aureus may use CodY to limit host damage to only the most severe starvation conditions (PubMed:27116338). Modulation of central metabolism, virulence gene expression, and biofilm-associated genes to optimize growth on preferred carbon sources until starvation sets in may require coordinated action of CodY and the carbon catabolite protein A (CcpA), another global transcriptional regulator (PubMed:35735992).<ref>PMID:18156263</ref> <ref>PMID:19251851</ref> <ref>PMID:20363936</ref> <ref>PMID:27116338</ref> <ref>PMID:29357354</ref> <ref>PMID:29378891</ref> <ref>PMID:35735992</ref>
	<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: ~~Staa1~~]]	+	[[Category: Staphylococcus aureus subsp. aureus Mu3]]
-	[[Category: Han, A]]	+	[[Category: Han A]]
-	[[Category: Hwang~~, K Y]]~~	+	[[Category: Hwang KY]]
-	~~[[Category: Gtp sensing]]~~	+
-	~~[[Category: Pleiotropic transcription regulator]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 07:50, 29 April 2020

OCA — Wed, 29 Apr 2020 07:50:09 GMT

←Older revision		Revision as of 07:50, 29 April 2020
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	==Crystal structure of CodY from Staphylococcus aureus with GTP and Ile==		==Crystal structure of CodY from Staphylococcus aureus with GTP and Ile==
-	<StructureSection load='5ey1' size='340' side='right' caption='[[5ey1]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5ey1' size='340' side='right'caption='[[5ey1]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ey1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ey1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staa1 Staa1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EY1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=ILE:ISOLEUCINE'>ILE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=ILE:ISOLEUCINE'>ILE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ey0\|5ey0]], [[5ey2\|5ey2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ey0\|5ey0]], [[5ey2\|5ey2]]</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=5ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey1 OCA], [http://pdbe.org/5ey1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ey1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey1 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">codY, SAHV_1245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=418127 STAA1])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey1 OCA], [http://pdbe.org/5ey1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ey1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Staa1]]
	[[Category: Han, A]]		[[Category: Han, A]]
	[[Category: Hwang, K Y]]		[[Category: Hwang, K Y]]

OCA at 06:35, 21 September 2016

OCA — Wed, 21 Sep 2016 06:35:24 GMT

←Older revision		Revision as of 06:35, 21 September 2016
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CODY_STAA1 CODY_STAA1]] DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase. It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor.		[[http://www.uniprot.org/uniprot/CODY_STAA1 CODY_STAA1]] DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase. It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	GTP and branched-chain amino acids (BCAAs) are metabolic sensors that are indispensable for the determination of the metabolic status of cells. However, their molecular sensing mechanism remains unclear. CodY is a unique global transcription regulator that recognizes GTP and BCAAs as specific signals and affects expression of more than 100 genes associated with metabolism. Herein, we report the first crystal structures of the full-length CodY complex with sensing molecules and describe their functional states. We observed two different oligomeric states of CodY: a dimeric complex of CodY from Staphylococcus aureus with the two metabolites GTP and isoleucine, and a tetrameric form (apo) of CodY from Bacillus cereus Notably, the tetrameric state shows in an auto-inhibitory manner by blocking the GTP-binding site, whereas the binding sites of GTP and isoleucine are clearly visible in the dimeric state. The GTP is located at a hinge site between the long helical region and the metabolite-binding site. Together, data from structural and electrophoretic mobility shift assay analyses improve understanding of how CodY senses GTP and operates as a DNA-binding protein and a pleiotropic transcription regulator.
		+
		+	The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism.,Han AR, Kang HR, Son J, Kwon DH, Kim S, Lee WC, Song HK, Song MJ, Hwang KY Nucleic Acids Res. 2016 Sep 4. pii: gkw775. PMID:27596595<ref>PMID:27596595</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ey1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:30, 14 September 2016

OCA — Wed, 14 Sep 2016 15:30:17 GMT

←Older revision		Revision as of 15:30, 14 September 2016
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-	'''Unreleased structure'''

-	~~The entry 5ey1 is ON HOLD until Paper Publication~~	+	==Crystal structure of CodY from Staphylococcus aureus with GTP and Ile==
-		+	<StructureSection load='5ey1' size='340' side='right' caption='[[5ey1]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors: Han, A., Hwang, K.Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ey1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EY1 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of CodY from Staphylococcus aureus with GTP and Ile	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=ILE:ISOLEUCINE'>ILE</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ey0\|5ey0]], [[5ey2\|5ey2]]</td></tr>
-	[[~~Category~~: ~~Hwang~~, K.Y]]	+	<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=5ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey1 OCA], [http://pdbe.org/5ey1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ey1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ey1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CODY_STAA1 CODY_STAA1]] DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase. It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor.
		+	__TOC__
		+	</StructureSection>
	[[Category: Han, A]]		[[Category: Han, A]]
		+	[[Category: Hwang, K Y]]
		+	[[Category: Gtp sensing]]
		+	[[Category: Pleiotropic transcription regulator]]
		+	[[Category: Transcription]]

OCA at 12:21, 9 December 2015

OCA — Wed, 09 Dec 2015 12:21:22 GMT

←Older revision		Revision as of 12:21, 9 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ey1 is ON HOLD	+	The entry 5ey1 is ON HOLD until Paper Publication

	Authors: Han, A., Hwang, K.Y.		Authors: Han, A., Hwang, K.Y.

OCA: Protected "5ey1" [edit=sysop:move=sysop]

OCA — Wed, 02 Dec 2015 15:08:48 GMT

Protected "5ey1" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:08, 2 December 2015

OCA: New page: '''Unreleased structure''' The entry 5ey1 is ON HOLD Authors: Han, A., Hwang, K.Y. Description: Crystal structure of CodY from Staphylococcus aureus with GTP and Ile [[Category: Unrele...

OCA — Wed, 02 Dec 2015 15:08:47 GMT

New page: '''Unreleased structure''' The entry 5ey1 is ON HOLD Authors: Han, A., Hwang, K.Y. Description: Crystal structure of CodY from Staphylococcus aureus with GTP and Ile [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 5ey1 is ON HOLD

Authors: Han, A., Hwang, K.Y.

Description: Crystal structure of CodY from Staphylococcus aureus with GTP and Ile
[[Category: Unreleased Structures]]
[[Category: Hwang, K.Y]]
[[Category: Han, A]]