2l8n - Revision history

OCA at 05:40, 15 May 2024

OCA — Wed, 15 May 2024 05:40:04 GMT

←Older revision		Revision as of 05:40, 15 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_536 Escherichia coli 536]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_536 Escherichia coli 536]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L8N 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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [https://pdbe.org/2l8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [https://www.ebi.ac.uk/pdbsum/2l8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8n ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [https://pdbe.org/2l8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [https://www.ebi.ac.uk/pdbsum/2l8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8n ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:26, 18 January 2023

OCA — Wed, 18 Jan 2023 08:26:33 GMT

←Older revision		Revision as of 08:26, 18 January 2023
Line 1:		Line 1:

	==NMR structure of the cytidine repressor DNA binding domain in presence of operator half-site DNA==		==NMR structure of the cytidine repressor DNA binding domain in presence of operator half-site DNA==
-	<StructureSection load='2l8n' size='340' side='right'caption='[[2l8n~~]], [[NMR_Ensembles_of_Models \| 11 NMR models~~]]' scene=''>	+	<StructureSection load='2l8n' size='340' side='right'caption='[[2l8n]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecol5 Ecol5~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_536 Escherichia coli 536]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L8N FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B3934, CYTR, ECP_4143, JW3905 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=362663 ECOL5])</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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [https://pdbe.org/2l8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [https://www.ebi.ac.uk/pdbsum/2l8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8n 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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [https://pdbe.org/2l8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [https://www.ebi.ac.uk/pdbsum/2l8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8n ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecol5~~]]	+	[[Category: Escherichia coli 536]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cocco~~, M J~~]]	+	[[Category: Cocco MJ]]
-	[[Category: Moody~~, C L~~]]	+	[[Category: Moody CL]]
-	[[Category: Senear~~, D F~~]]	+	[[Category: Senear DF]]
-	[[Category: Tretyachenko-Ladokhina, V]]	+	[[Category: Tretyachenko-Ladokhina V]]
-	~~[[Category: Bacterial gene repressor]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Helix turn helix binding domain]]~~	+
-	~~[[Category: Lacr family]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription regulator~~]]	+

OCA at 07:38, 14 April 2021

OCA — Wed, 14 Apr 2021 07:38:24 GMT

←Older revision		Revision as of 07:38, 14 April 2021
Line 1:		Line 1:

	==NMR structure of the cytidine repressor DNA binding domain in presence of operator half-site DNA==		==NMR structure of the cytidine repressor DNA binding domain in presence of operator half-site DNA==
-	<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>	+	<StructureSection load='2l8n' size='340' side='right'caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecol5 Ecol5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2L8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecol5 Ecol5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L8N FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B3934, CYTR, ECP_4143, JW3905 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=362663 ECOL5])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B3934, CYTR, ECP_4143, JW3905 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=362663 ECOL5])</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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [~~http~~://pdbe.org/2l8n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2l8n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8n 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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [https://pdbe.org/2l8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [https://www.ebi.ac.uk/pdbsum/2l8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8n ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Ecol5]]		[[Category: Ecol5]]
		+	[[Category: Large Structures]]
	[[Category: Cocco, M J]]		[[Category: Cocco, M J]]
	[[Category: Moody, C L]]		[[Category: Moody, C L]]

OCA at 20:09, 1 August 2018

OCA — Wed, 01 Aug 2018 20:09:02 GMT

←Older revision		Revision as of 20:09, 1 August 2018
Line 1:		Line 1:
		+
	==NMR structure of the cytidine repressor DNA binding domain in presence of operator half-site DNA==		==NMR structure of the cytidine repressor DNA binding domain in presence of operator half-site DNA==
	<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>		<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecol5 Ecol5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecol5 Ecol5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L8N FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B3934, CYTR, ECP_4143, JW3905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=362663 ECOL5])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B3934, CYTR, ECP_4143, JW3905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=362663 ECOL5])</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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://pdbe.org/2l8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n 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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://pdbe.org/2l8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8n ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:07, 11 September 2015

OCA — Fri, 11 Sep 2015 08:07:30 GMT

←Older revision		Revision as of 08:07, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>		<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l8n]] is a 1 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=2L8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2l8n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecol5 Ecol5]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L8N FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B3934, CYTR, ECP_4143, JW3905 ([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">B3934, CYTR, ECP_4143, JW3905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=362663 ECOL5])</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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n 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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://pdbe.org/2l8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n 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 2l8n" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecol5]]
	[[Category: Cocco, M J]]		[[Category: Cocco, M J]]
	[[Category: Moody, C L]]		[[Category: Moody, C L]]

OCA at 22:19, 3 January 2015

OCA — Sat, 03 Jan 2015 22:19:05 GMT

←Older revision		Revision as of 22:19, 3 January 2015
Line 2:		Line 2:
	<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>		<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2l8n]] is a 1 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=2L8N OCA]. <br>	+	<table><tr><td colspan='2'>[[2l8n]] is a 1 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=2L8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L8N FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B3934, CYTR, ECP_4143, JW3905 ([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">B3934, CYTR, ECP_4143, JW3905 ([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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n 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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n PDBsum]</span></td></tr>	+	</table>
-	<table>	+
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 12:
	Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One Upon Recognition of a Specific DNA Surface.,Moody CL, Tretyachenko-Ladokhina V, Laue TM, Senear DF, Cocco MJ Biochemistry. 2011 Jun 21. PMID:21688840<ref>PMID:21688840</ref>		Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One Upon Recognition of a Specific DNA Surface.,Moody CL, Tretyachenko-Ladokhina V, Laue TM, Senear DF, Cocco MJ Biochemistry. 2011 Jun 21. PMID:21688840<ref>PMID:21688840</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: Cocco, M J.]]	+	[[Category: Cocco, M J]]
-	[[Category: Moody, C L.]]	+	[[Category: Moody, C L]]
-	[[Category: Senear, D F.]]	+	[[Category: Senear, D F]]
-	[[Category: Tretyachenko-Ladokhina, V.]]	+	[[Category: Tretyachenko-Ladokhina, V]]
	[[Category: Bacterial gene repressor]]		[[Category: Bacterial gene repressor]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]

OCA at 10:00, 1 May 2014

OCA — Thu, 01 May 2014 10:00:12 GMT

←Older revision		Revision as of 10:00, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>		<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[2l8n]] is a 1 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=2L8N OCA]. <br>	+	<table><tr><td colspan='2'>[[2l8n]] is a 1 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=2L8N 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">B3934, CYTR, ECP_4143, JW3905 ([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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n 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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, in spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR targets. Such coupling is a common feature of sequence-specific DNA-binding proteins including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used NMR spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties.		The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, in spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR targets. Such coupling is a common feature of sequence-specific DNA-binding proteins including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used NMR spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties.
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 10:25, 30 April 2014

OCA — Wed, 30 Apr 2014 10:25:47 GMT

←Older revision		Revision as of 10:25, 30 April 2014
Line 4:		Line 4:
	[[2l8n]] is a 1 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=2L8N OCA]. <br>		[[2l8n]] is a 1 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=2L8N 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=2l8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l8n RCSB], [http://www.ebi.ac.uk/pdbsum/2l8n PDBsum]</span><br>
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, in spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR targets. Such coupling is a common feature of sequence-specific DNA-binding proteins including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used NMR spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties.		The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, in spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR targets. Such coupling is a common feature of sequence-specific DNA-binding proteins including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used NMR spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties.

OCA at 08:42, 30 April 2014

OCA — Wed, 30 Apr 2014 08:42:57 GMT

←Older revision		Revision as of 08:42, 30 April 2014
Line 1:		Line 1:
-	[[~~Image:~~2l8n~~.png~~\|~~left\|200px~~]]	+	==NMR structure of the cytidine repressor DNA binding domain in presence of operator half-site DNA==
		+	<StructureSection load='2l8n' size='340' side='right' caption='[[2l8n]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	[[2l8n]] is a 1 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=2L8N 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 ==
		+	The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, in spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR targets. Such coupling is a common feature of sequence-specific DNA-binding proteins including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used NMR spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties.

-	<!--	+	Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One Upon Recognition of a Specific DNA Surface.,Moody CL, Tretyachenko-Ladokhina V, Laue TM, Senear DF, Cocco MJ Biochemistry. 2011 Jun 21. PMID:21688840<ref>PMID:21688840</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2l8n"~~, ~~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_2l8n\| PDB=2l8n \| SCENE= }}~~	+

-	~~===NMR structure~~ of the ~~cytidine repressor DNA binding domain in presence of operator half-site DNA===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	== References ==
-		+	<references/>
-	~~<!--~~	+	__TOC__
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21688840}}, adds the Publication Abstract to the page~~	+	</StructureSection>
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21688840 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21688840}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~[[2l8n]] is a 1 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=2L8N OCA].~~	+
-		+
-	~~==Reference==~~	+
-	<~~ref group="xtra">PMID:021688840</ref><references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Cocco, M J.]]		[[Category: Cocco, M J.]]

OCA at 06:38, 17 August 2011

OCA — Wed, 17 Aug 2011 06:38:10 GMT

←Older revision		Revision as of 06:38, 17 August 2011
Line 1:		Line 1:
-	[[Image:2l8n.~~jpg~~\|left\|200px]]	+	[[Image:2l8n.png\|left\|200px]]

	<!--		<!--