5ey2 - Revision history

OCA at 08:32, 12 July 2023

2023-07-12T08:32:52Z

←Older revision		Revision as of 08:32, 12 July 2023
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	<StructureSection load='5ey2' size='340' side='right'caption='[[5ey2]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5ey2' size='340' side='right'caption='[[5ey2]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ey2]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baccr Baccr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EY2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ey2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_ATCC_14579 Bacillus cereus ATCC 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EY2 FirstGlance]. <br>
-	</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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ey0\|5ey0]]~~, [[~~5ey1~~\|~~5ey1~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~codY, BC_3826 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226900 BACCR])~~</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=5ey2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey2 OCA], [https://pdbe.org/5ey2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ey2 RCSB], [https://www.ebi.ac.uk/pdbsum/5ey2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey2 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=5ey2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey2 OCA], [~~http~~://pdbe.org/5ey2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ey2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ey2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey2 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CODY_BACCR CODY_BACCR]] 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_BACCR CODY_BACCR] 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baccr~~]]	+	[[Category: Bacillus cereus ATCC 14579]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Han, A]]	+	[[Category: Han A]]
-	[[Category: Hwang~~, K Y~~]]	+	[[Category: Hwang KY]]
-	[[Category: Kim~~, S H~~]]	+	[[Category: Kim SH]]
-	[[Category: Lee~~, W C~~]]	+	[[Category: Lee WC]]
-	[[Category: Son, J]]	+	[[Category: Son J]]
-	~~[[Category: Auto-inhibition]]~~	+
-	~~[[Category: Gtp-sensing]]~~	+
-	~~[[Category: Pleiotropic transcription regulator]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 07:14, 19 February 2020

2020-02-19T07:14:22Z

←Older revision		Revision as of 07:14, 19 February 2020
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	==Crystal structure of CodY from Bacillus cereus==		==Crystal structure of CodY from Bacillus cereus==
-	<StructureSection load='5ey2' size='340' side='right' caption='[[5ey2]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5ey2' size='340' side='right'caption='[[5ey2]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ey2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EY2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ey2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baccr Baccr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EY2 FirstGlance]. <br>
	</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>		</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ey0\|5ey0]], [[5ey1\|5ey1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ey0\|5ey0]], [[5ey1\|5ey1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">codY, BC_3826 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226900 BACCR])</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=5ey2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey2 OCA], [http://pdbe.org/5ey2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ey2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ey2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey2 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=5ey2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey2 OCA], [http://pdbe.org/5ey2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ey2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ey2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey2 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baccr]]
		+	[[Category: Large Structures]]
	[[Category: Han, A]]		[[Category: Han, A]]
	[[Category: Hwang, K Y]]		[[Category: Hwang, K Y]]

OCA at 06:17, 21 September 2016

2016-09-21T06:17:18Z

←Older revision		Revision as of 06:17, 21 September 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CODY_BACCR CODY_BACCR]] 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_BACCR CODY_BACCR]] 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 5ey2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:30, 14 September 2016

2016-09-14T15:30:23Z

←Older revision		Revision as of 15:30, 14 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ey2 is ~~ON HOLD~~	+	==Crystal structure of CodY from Bacillus cereus==
-		+	<StructureSection load='5ey2' size='340' side='right' caption='[[5ey2]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors~~: ~~Han~~, A., ~~Lee, W~~.C., ~~Son~~, J., ~~Kim, S~~.H., ~~Hwang, K~~.Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ey2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EY2 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~CodY~~ from ~~Bacillus cereus~~	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ey0\|5ey0]], [[5ey1\|5ey1]]</td></tr>
-	[[Category: Kim, S.H]]	+	<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=5ey2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ey2 OCA], [http://pdbe.org/5ey2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ey2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ey2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ey2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CODY_BACCR CODY_BACCR]] 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: Hwang, K Y]]
		+	[[Category: Kim, S H]]
		+	[[Category: Lee, W C]]
	[[Category: Son, J]]		[[Category: Son, J]]
-	[[Category: ~~Lee, W.C~~]]	+	[[Category: Auto-inhibition]]
-	[[Category: ~~Hwang, K.Y~~]]	+	[[Category: Gtp-sensing]]
-	[[Category: ~~Han, A~~]]	+	[[Category: Pleiotropic transcription regulator]]
		+	[[Category: Transcription]]

OCA at 11:04, 9 September 2016

2016-09-09T11:04:55Z

←Older revision		Revision as of 11:04, 9 September 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ey2 is ON HOLD ~~until Paper Publication~~	+	The entry 5ey2 is ON HOLD

	Authors: Han, A., Lee, W.C., Son, J., Kim, S.H., Hwang, K.Y.		Authors: Han, A., Lee, W.C., Son, J., Kim, S.H., Hwang, K.Y.

OCA at 17:18, 30 December 2015

2015-12-30T17:18:13Z

←Older revision		Revision as of 17:18, 30 December 2015
Line 3:		Line 3:
	The entry 5ey2 is ON HOLD until Paper Publication		The entry 5ey2 is ON HOLD until Paper Publication

-	Authors: Han, A., Lee, W.C., Son, J.H., Kim, S.H., Hwang, K.Y.	+	Authors: Han, A., Lee, W.C., Son, J., Kim, S.H., Hwang, K.Y.

	Description: Crystal structure of CodY from Bacillus cereus		Description: Crystal structure of CodY from Bacillus cereus
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kim, S.H]]		[[Category: Kim, S.H]]
		+	[[Category: Son, J]]
	[[Category: Lee, W.C]]		[[Category: Lee, W.C]]
	[[Category: Hwang, K.Y]]		[[Category: Hwang, K.Y]]
	[[Category: Han, A]]		[[Category: Han, A]]
-	[[Category: Son, J.H]]

OCA at 12:21, 9 December 2015

2015-12-09T12:21:24Z

←Older revision		Revision as of 12:21, 9 December 2015
Line 3:		Line 3:
	The entry 5ey2 is ON HOLD until Paper Publication		The entry 5ey2 is ON HOLD until Paper Publication

-	Authors: Han, A., Lee, W.C., Hwang, K.Y.	+	Authors: Han, A., Lee, W.C., Son, J.H., Kim, S.H., Hwang, K.Y.

	Description: Crystal structure of CodY from Bacillus cereus		Description: Crystal structure of CodY from Bacillus cereus
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Kim, S.H]]
	[[Category: Lee, W.C]]		[[Category: Lee, W.C]]
	[[Category: Hwang, K.Y]]		[[Category: Hwang, K.Y]]
	[[Category: Han, A]]		[[Category: Han, A]]
		+	[[Category: Son, J.H]]

OCA: Protected "5ey2" [edit=sysop:move=sysop]

2015-12-02T15:08:51Z

Protected "5ey2" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:08, 2 December 2015

OCA: New page: '''Unreleased structure''' The entry 5ey2 is ON HOLD until Paper Publication Authors: Han, A., Lee, W.C., Hwang, K.Y. Description: Crystal structure of CodY from Bacillus cereus [[Cate...

2015-12-02T15:08:49Z

New page: '''Unreleased structure''' The entry 5ey2 is ON HOLD until Paper Publication Authors: Han, A., Lee, W.C., Hwang, K.Y. Description: Crystal structure of CodY from Bacillus cereus [[Cate...

New page

'''Unreleased structure'''

The entry 5ey2 is ON HOLD until Paper Publication

Authors: Han, A., Lee, W.C., Hwang, K.Y.

Description: Crystal structure of CodY from Bacillus cereus
[[Category: Unreleased Structures]]
[[Category: Lee, W.C]]
[[Category: Hwang, K.Y]]
[[Category: Han, A]]