2lev - Revision history

OCA at 06:55, 1 May 2024

2024-05-01T06:55:24Z

← Older revision		Revision as of 06:55, 1 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LEV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LEV 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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [https://pdbe.org/2lev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [https://www.ebi.ac.uk/pdbsum/2lev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lev ProSAT]</span></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Solution NMR , X-ray solution scattering</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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [https://pdbe.org/2lev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [https://www.ebi.ac.uk/pdbsum/2lev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lev ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q7DB51_ECO57 Q7DB51_ECO57]		[https://www.uniprot.org/uniprot/Q7DB51_ECO57 Q7DB51_ECO57]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family.

	Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler.,Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado P, Griesinger C, Garcia J, Pons M PLoS Pathog. 2011 Nov;7(11):e1002380. Epub 2011 Nov 17. PMID:22114557<ref>PMID:22114557</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2lev" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:55, 15 February 2023

2023-02-15T10:55:40Z

← Older revision		Revision as of 10:55, 15 February 2023
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	==Structure of the DNA complex of the C-Terminal domain of Ler==		==Structure of the DNA complex of the C-Terminal domain of Ler==
	<StructureSection load='2lev' size='340' side='right'caption='[[2lev~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>		<StructureSection load='2lev' size='340' side='right'caption='[[2lev]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LEV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LEV FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [https://pdbe.org/2lev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [https://www.ebi.ac.uk/pdbsum/2lev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lev 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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [https://pdbe.org/2lev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [https://www.ebi.ac.uk/pdbsum/2lev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lev ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q7DB51_ECO57 Q7DB51_ECO57]
	<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: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bernado, P]]		[[Category: Bernado P]]
	[[Category: Cordeiro~~, T N~~]]		[[Category: Cordeiro TN]]
	[[Category: Garcia, J]]		[[Category: Garcia J]]
	[[Category: Grisienger, C]]		[[Category: Grisienger C]]
	[[Category: Juarez, A]]		[[Category: Juarez A]]
	[[Category: Madrid, C]]		[[Category: Madrid C]]
	[[Category: Pons, M]]		[[Category: Pons M]]
	[[Category: Schimdt, H]]		[[Category: Schimdt H]]
	~~[[Category: Arginine-minor-groove recognition]]~~
	~~[[Category: Horizontal gene transfer]]~~
	~~[[Category: Indirect readout]]~~
	~~[[Category: Nucleoid associated protein]]~~
	~~[[Category: Transcription regulator-dna complex~~]]

OCA at 10:09, 12 May 2021

2021-05-12T10:09:27Z

← Older revision		Revision as of 10:09, 12 May 2021
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	==Structure of the DNA complex of the C-Terminal domain of Ler==		==Structure of the DNA complex of the C-Terminal domain of Ler==
	<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lev' size='340' side='right'caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2LEV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LEV FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [~~http~~://pdbe.org/2lev PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2lev PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2lev 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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [https://pdbe.org/2lev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [https://www.ebi.ac.uk/pdbsum/2lev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lev ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
			[[Category: Large Structures]]
	[[Category: Bernado, P]]		[[Category: Bernado, P]]
	[[Category: Cordeiro, T N]]		[[Category: Cordeiro, T N]]

OCA at 19:38, 1 August 2018

2018-08-01T19:38:16Z

← Older revision		Revision as of 19:38, 1 August 2018
Line 1:		Line 1:

	==Structure of the DNA complex of the C-Terminal domain of Ler==		==Structure of the DNA complex of the C-Terminal domain of Ler==
	<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LEV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LEV FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://pdbe.org/2lev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev 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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://pdbe.org/2lev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lev ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:40, 11 September 2015

2015-09-11T10:40:36Z

← Older revision		Revision as of 10:40, 11 September 2015
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	<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LEV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LEV FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev 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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://pdbe.org/2lev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	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 2lev" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Bernado, P]]		[[Category: Bernado, P]]
	[[Category: Cordeiro, T N]]		[[Category: Cordeiro, T N]]

OCA at 05:20, 22 December 2014

2014-12-22T05:20:25Z

← Older revision		Revision as of 05:20, 22 December 2014
Line 2:		Line 2:
	<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. <br>		<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LEV FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev PDBsum]</span></td></tr>
	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev PDBsum]</span></td></tr>		</table>
	<table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler.,Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado P, Griesinger C, Garcia J, Pons M PLoS Pathog. 2011 Nov;7(11):e1002380. Epub 2011 Nov 17. PMID:22114557<ref>PMID:22114557</ref>		Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler.,Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado P, Griesinger C, Garcia J, Pons M PLoS Pathog. 2011 Nov;7(11):e1002380. Epub 2011 Nov 17. PMID:22114557<ref>PMID:22114557</ref>

	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 20:		Line 19:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Bernado, P.]]		[[Category: Bernado, P]]
	[[Category: Cordeiro, T N.]]		[[Category: Cordeiro, T N]]
	[[Category: Garcia, J.]]		[[Category: Garcia, J]]
	[[Category: Grisienger, C.]]		[[Category: Grisienger, C]]
	[[Category: Juarez, A.]]		[[Category: Juarez, A]]
	[[Category: Madrid, C.]]		[[Category: Madrid, C]]
	[[Category: Pons, M.]]		[[Category: Pons, M]]
	[[Category: Schimdt, H.]]		[[Category: Schimdt, H]]
	[[Category: Arginine-minor-groove recognition]]		[[Category: Arginine-minor-groove recognition]]
	[[Category: Horizontal gene transfer]]		[[Category: Horizontal gene transfer]]

OCA at 09:58, 1 May 2014

2014-05-01T09:58:52Z

← Older revision		Revision as of 09:58, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. <br>		<table><tr><td colspan='2'>[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. <br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ler ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev PDBsum]</span><br>		<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family.		Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family.
Line 11:		Line 14:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
			</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:24, 30 April 2014

2014-04-30T10:24:31Z

← Older revision		Revision as of 10:24, 30 April 2014
Line 4:		Line 4:
	[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. <br>		[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. <br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
			<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lev OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lev RCSB], [http://www.ebi.ac.uk/pdbsum/2lev PDBsum]</span><br>
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family.		Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family.

OCA at 08:41, 30 April 2014

2014-04-30T08:41:30Z

← Older revision		Revision as of 08:41, 30 April 2014
Line 1:		Line 1:
	[[~~Image~~:~~2lev~~.~~jpg\|left\|200px~~]]		==Structure of the DNA complex of the C-Terminal domain of Ler==
			<StructureSection load='2lev' size='340' side='right' caption='[[2lev]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
			== Structural highlights ==
			[[2lev]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA]. <br>
			<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
			== Publication Abstract from PubMed ==
			Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family.

	<!--		Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler.,Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado P, Griesinger C, Garcia J, Pons M PLoS Pathog. 2011 Nov;7(11):e1002380. Epub 2011 Nov 17. PMID:22114557<ref>PMID:22114557</ref>
	~~The line below this paragraph~~, ~~containing "STRUCTURE_2lev"~~, ~~creates the "Structure Box" on the page~~.
	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display~~.
	-->
	~~{{STRUCTURE_2lev\| PDB=2lev \| SCENE= }}~~

	~~===Structure of the DNA complex of the C-Terminal domain~~ of ~~Ler===~~		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
			== References ==
			<references/>
	~~<!--~~		__TOC__
	~~The line below this paragraph, {{ABSTRACT_PUBMED_22114557}}, adds the Publication Abstract to~~ the ~~page~~		</StructureSection>
	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22114557 is the PubMed ID number~~.
	-->
	~~{{ABSTRACT_PUBMED_22114557}}~~

	==~~About this Structure~~==
	~~[[2lev]] is a 3 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEV OCA].~~

	~~==Reference==~~
	<~~ref group="xtra">PMID:022114557</ref><references group="xtra"~~/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Bernado, P.]]		[[Category: Bernado, P.]]

OCA at 08:03, 7 December 2011

2011-12-07T08:03:32Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:2lev.jpg|left|200px]]
-The entry 2lev is ON HOLD  until Paper Publication
+<!--
-Authors: Cordeiro, T.N., Schimdt, H., Madrid, C., Juarez, A., Bernado, P., Grisienger, C., Garcia, J., Pons, M.
+===Structure of the DNA complex of the C-Terminal domain of Ler===
-Description: Structure of the DNA complex of the C-Terminal domain of Ler