4x1e - Revision history

OCA at 10:46, 10 January 2024

OCA — Wed, 10 Jan 2024 10:46:03 GMT

←Older revision		Revision as of 10:46, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_CFT073 Escherichia coli CFT073]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X1E FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_CFT073 Escherichia coli CFT073]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X1E FirstGlance]. <br>
-	</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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [https://pdbe.org/4x1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [https://www.ebi.ac.uk/pdbsum/4x1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1e ProSAT]</span></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]] 2.4Å</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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [https://pdbe.org/4x1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [https://www.ebi.ac.uk/pdbsum/4x1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:06, 12 April 2023

OCA — Wed, 12 Apr 2023 21:06:42 GMT

←Older revision		Revision as of 21:06, 12 April 2023
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	<StructureSection load='4x1e' size='340' side='right'caption='[[4x1e]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4x1e' size='340' side='right'caption='[[4x1e]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecol6 Ecol6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X1E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_CFT073 Escherichia coli CFT073]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X1E FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jyk\|4jyk]], [[3loc\|3loc]]</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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [https://pdbe.org/4x1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [https://www.ebi.ac.uk/pdbsum/4x1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1e ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rutR, c1150 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=199310 ECOL6])</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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [~~http~~://pdbe.org/4x1e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x1e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1e ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RUTR_ECOL6 RUTR_ECOL6]] Master transcription regulator which represses the degradation of pyrimidines (rutABCDEFG) and purines (gcl operon) for maintenance of metabolic balance between pyrimidines and purines. It also regulates the synthesis of pyrimidine nucleotides and arginine from glutamine (carAB) and the supply of glutamate (gadABWX) (By similarity).	+	[https://www.uniprot.org/uniprot/RUTR_ECOL6 RUTR_ECOL6] Master transcription regulator which represses the degradation of pyrimidines (rutABCDEFG) and purines (gcl operon) for maintenance of metabolic balance between pyrimidines and purines. It also regulates the synthesis of pyrimidine nucleotides and arginine from glutamine (carAB) and the supply of glutamate (gadABWX) (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 4x1e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x1e" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecol6~~]]	+	[[Category: Escherichia coli CFT073]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bervoets, I]]	+	[[Category: Bervoets I]]
-	[[Category: Charlier, D]]	+	[[Category: Charlier D]]
-	~~[[Category: Cima, S de~~]]	+	[[Category: Maes D]]
-	[[Category: Maes, D]]	+	[[Category: Nguyen Le Minh P]]
-	[[Category: Minh, P ~~Nguyen Le~~]]	+	[[Category: Rubio V]]
-	[[Category: Rubio, V]]	+	[[Category: De Cima S]]
-	[[Category: ~~Arginine and pyrimidine biosynthesis]]~~	+
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Tetr family member]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcriptional regulator~~]]	+

OCA at 09:00, 23 May 2019

OCA — Thu, 23 May 2019 09:00:06 GMT

←Older revision		Revision as of 09:00, 23 May 2019
Line 1:		Line 1:

	==Crystal structure of unliganded E. coli transcriptional regulator RutR, W167A mutant==		==Crystal structure of unliganded E. coli transcriptional regulator RutR, W167A mutant==
-	<StructureSection load='4x1e' size='340' side='right' caption='[[4x1e]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4x1e' size='340' side='right'caption='[[4x1e]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecol6 Ecol6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1E FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jyk\|4jyk]], [[3loc\|3loc]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jyk\|4jyk]], [[3loc\|3loc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rutR, c1150 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=199310 ECOL6])</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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [http://pdbe.org/4x1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [http://www.ebi.ac.uk/pdbsum/4x1e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1e 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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [http://pdbe.org/4x1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [http://www.ebi.ac.uk/pdbsum/4x1e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1e ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecol6]]
		+	[[Category: Large Structures]]
	[[Category: Bervoets, I]]		[[Category: Bervoets, I]]
	[[Category: Charlier, D]]		[[Category: Charlier, D]]

OCA at 00:20, 26 January 2017

OCA — Thu, 26 Jan 2017 00:20:56 GMT

←Older revision		Revision as of 00:20, 26 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of unliganded E. coli transcriptional regulator RutR, W167A mutant==		==Crystal structure of unliganded E. coli transcriptional regulator RutR, W167A mutant==
	<StructureSection load='4x1e' size='340' side='right' caption='[[4x1e]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4x1e' size='340' side='right' caption='[[4x1e]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1E FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1E FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jyk\|4jyk]], [[3loc\|3loc]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jyk\|4jyk]], [[3loc\|3loc]]</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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [http://www.ebi.ac.uk/pdbsum/4x1e 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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [http://pdbe.org/4x1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [http://www.ebi.ac.uk/pdbsum/4x1e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x1e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	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 4x1e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:21, 4 March 2015

OCA — Wed, 04 Mar 2015 11:21:44 GMT

←Older revision		Revision as of 11:21, 4 March 2015
Line 8:		Line 8:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RUTR_ECOL6 RUTR_ECOL6]] Master transcription regulator which represses the degradation of pyrimidines (rutABCDEFG) and purines (gcl operon) for maintenance of metabolic balance between pyrimidines and purines. It also regulates the synthesis of pyrimidine nucleotides and arginine from glutamine (carAB) and the supply of glutamate (gadABWX) (By similarity).		[[http://www.uniprot.org/uniprot/RUTR_ECOL6 RUTR_ECOL6]] Master transcription regulator which represses the degradation of pyrimidines (rutABCDEFG) and purines (gcl operon) for maintenance of metabolic balance between pyrimidines and purines. It also regulates the synthesis of pyrimidine nucleotides and arginine from glutamine (carAB) and the supply of glutamate (gadABWX) (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RutR is a member of the large family of TetR transcriptional regulators in Escherichia coli. It was originally discovered as the regulator of the rutABCDEFG operon encoding a novel pathway for pyrimidine utilization, but its highest affinity target is the control region of the carAB operon, encoding carbamoylphosphate synthase. Unlike most other TetR-like regulators, RutR exerts both positive and negative effects on promoter activity. Furthermore, RutR exhibits a very narrow ligand binding specificity, unlike the broad effector specificity that characterizes some of the well-studied multidrug resistance regulators of the family. Here we focus on ligand binding and ligand specificity of RutR. We construct single alanine substitution mutants of amino acid residues of the ligand-binding pocket, study their effect on in vitro DNA binding in absence and presence of potential ligands, and analyse their effect on positive regulation of the carP1 promoter and negative autoregulation in vivo. Although RutR structures have been determined previously, they were deposited in the Protein Data Bank without accompanying publications. All of them have uracil bound in the effector-binding site, representing the inactive form of the regulator. We determined the crystal structure of an unliganded mutant RutR protein and provide a structural basis for the use of uracil as sole effector molecule and the exclusion of the very similar thymine from the ligand-binding pocket.
		+
		+	Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli.,Nguyen Le Minh P, de Cima S, Bervoets I, Maes D, Rubio V, Charlier D FEBS Open Bio. 2015 Jan 28;5:76-84. doi: 10.1016/j.fob.2015.01.002. eCollection, 2015. PMID:25685666<ref>PMID:25685666</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:01, 21 January 2015

OCA — Wed, 21 Jan 2015 17:01:22 GMT

←Older revision		Revision as of 17:01, 21 January 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of unliganded E. coli transcriptional regulator RutR, W167A mutant==
-		+	<StructureSection load='4x1e' size='340' side='right' caption='[[4x1e]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~The entry~~ 4x1e is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4x1e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X1E FirstGlance]. <br>
-	~~Authors~~: ~~Nguyen Le Minh, P~~.~~, de Cima, S~~.~~, Bervoets, I~~.~~, Maes, D~~.~~, Rubio, V~~.~~, Charlier, D~~.	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jyk\|4jyk]], [[3loc\|3loc]]</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=4x1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x1e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4x1e RCSB], [http://www.ebi.ac.uk/pdbsum/4x1e PDBsum]</span></td></tr>
-	~~Description:~~	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	== Function ==
-	[[~~Category~~: ~~Rubio~~, V]]	+	[[http://www.uniprot.org/uniprot/RUTR_ECOL6 RUTR_ECOL6]] Master transcription regulator which represses the degradation of pyrimidines (rutABCDEFG) and purines (gcl operon) for maintenance of metabolic balance between pyrimidines and purines. It also regulates the synthesis of pyrimidine nucleotides and arginine from glutamine (carAB) and the supply of glutamate (gadABWX) (By similarity).
-	[[~~Category~~: ~~Maes, D~~]]	+	__TOC__
		+	</StructureSection>
	[[Category: Bervoets, I]]		[[Category: Bervoets, I]]
	[[Category: Charlier, D]]		[[Category: Charlier, D]]
-	[[Category: De Cima, S]]	+	[[Category: Cima, S de]]
-	[[Category: ~~Nguyen Le~~ Minh, P]]	+	[[Category: Maes, D]]
		+	[[Category: Minh, P Nguyen Le]]
		+	[[Category: Rubio, V]]
		+	[[Category: Arginine and pyrimidine biosynthesis]]
		+	[[Category: Dna binding]]
		+	[[Category: Tetr family member]]
		+	[[Category: Transcription]]
		+	[[Category: Transcriptional regulator]]

OCA at 20:19, 24 December 2014

OCA — Wed, 24 Dec 2014 20:19:32 GMT

←Older revision		Revision as of 20:19, 24 December 2014
Line 5:		Line 5:
	Authors: Nguyen Le Minh, P., de Cima, S., Bervoets, I., Maes, D., Rubio, V., Charlier, D.		Authors: Nguyen Le Minh, P., de Cima, S., Bervoets, I., Maes, D., Rubio, V., Charlier, D.

-	Description:	+	Description:
		+	[[Category: Unreleased Structures]]
		+	[[Category: Rubio, V]]
		+	[[Category: Maes, D]]
		+	[[Category: Bervoets, I]]
		+	[[Category: Charlier, D]]
		+	[[Category: De Cima, S]]
		+	[[Category: Nguyen Le Minh, P]]

OCA: Protected "4x1e" [edit=sysop:move=sysop]

OCA — Wed, 03 Dec 2014 08:45:19 GMT

Protected "4x1e" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:45, 3 December 2014

OCA: New page: '''Unreleased structure''' The entry 4x1e is ON HOLD until Paper Publication Authors: Nguyen Le Minh, P., de Cima, S., Bervoets, I., Maes, D., Rubio, V., Charlier, D. Description:

OCA — Wed, 03 Dec 2014 08:45:18 GMT

New page: '''Unreleased structure''' The entry 4x1e is ON HOLD until Paper Publication Authors: Nguyen Le Minh, P., de Cima, S., Bervoets, I., Maes, D., Rubio, V., Charlier, D. Description:

New page

'''Unreleased structure'''

The entry 4x1e is ON HOLD until Paper Publication

Authors: Nguyen Le Minh, P., de Cima, S., Bervoets, I., Maes, D., Rubio, V., Charlier, D.

Description: