1xwr - Revision history

OCA at 13:37, 13 March 2024

OCA — Wed, 13 Mar 2024 13:37:11 GMT

←Older revision		Revision as of 13:37, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1xwr' size='340' side='right'caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='1xwr' size='340' side='right'caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacteriophage_lambda Bacteriophage lambda~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XWR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XWR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</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]] 2.56Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=10710 Bacteriophage lambda])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [~~http~~://pdbe.org/1xwr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xwr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xwr 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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [https://pdbe.org/1xwr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [https://www.ebi.ac.uk/pdbsum/1xwr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xwr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RPC2_LAMBD RPC2_LAMBD]] This protein and protein CIII form a complex that is involved in the initiation of lysogeny. The complex binds at either of the cy regulatory sites preceding the CI repressor protein and integrase coding regions and induces transcription of these genes.	+	[https://www.uniprot.org/uniprot/RPC2_LAMBD RPC2_LAMBD] This protein and protein CIII form a complex that is involved in the initiation of lysogeny. The complex binds at either of the cy regulatory sites preceding the CI repressor protein and integrase coding regions and induces transcription of these genes.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xwr ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xwr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The temperate coliphage lambda, after infecting its host bacterium Escherichia coli, can develop either along the lytic or the lysogenic pathway. Crucial to the lysis/lysogeny decision is the homotetrameric transcription-activator protein CII (4 x 11 kDa) of the phage that binds to a unique direct-repeat sequence T-T-G-C-N6-T-T-G-C at each of the three phage promoters it activates: p(E), p(I), and p(aQ). Several regions of CII have been identified for its various functions (DNA binding, oligomerization, and susceptibility to host protease), but the crystal structure of the protein long remained elusive. Here, we present the three-dimensional structure of CII at 2.6-angstroms resolution. The CII monomer is comprised of four alpha helices and a disordered C terminus. The first three helices (alpha1-alpha3) form a compact domain, whereas the fourth helix (alpha4) protrudes in different orientations in each subunit. A four-helix bundle, formed by alpha4 from each subunit, holds the tetramer. The quaternary structure can be described as a dimer of dimers, but the tetramer does not exhibit a closed symmetry. This unusual quaternary arrangement allows the placement of the helix-turn-helix motifs of two of the four CII subunits for interaction with successive major grooves of B-DNA, from one face of DNA. This structure provides a simple explanation for how a homotetrameric protein may recognize a direct-repeat DNA sequence rather than the inverted-repeat sequences of most prokaryotic activators.
-
-	Structure of lambda CII: implications for recognition of direct-repeat DNA by an unusual tetrameric organization.,Datta AB, Panjikar S, Weiss MS, Chakrabarti P, Parrack P Proc Natl Acad Sci U S A. 2005 Aug 9;102(32):11242-7. Epub 2005 Aug 1. PMID:16061804<ref>PMID:16061804</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1xwr" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacteriophage lambda~~]]	+	[[Category: Escherichia virus Lambda]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chakrabarti, P]]	+	[[Category: Chakrabarti P]]
-	[[Category: Datta~~, A B~~]]	+	[[Category: Datta AB]]
-	[[Category: Panjikar, S]]	+	[[Category: Panjikar S]]
-	[[Category: Parrack, P]]	+	[[Category: Parrack P]]
-	[[Category: Weiss~~, M S]]~~	+	[[Category: Weiss MS]]
-	~~[[Category: All-alpha fold]]~~	+
-	~~[[Category: Dna binding protein~~]]	+

OCA at 10:24, 6 January 2021

OCA — Wed, 06 Jan 2021 10:24:18 GMT

←Older revision		Revision as of 10:24, 6 January 2021
Line 1:		Line 1:

	==Crystal structure of the coliphage lambda transcription activator protein CII==		==Crystal structure of the coliphage lambda transcription activator protein CII==
-	<StructureSection load='1xwr' size='340' side='right' caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>	+	<StructureSection load='1xwr' size='340' side='right'caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XWR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XWR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://pdbe.org/1xwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xwr ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://pdbe.org/1xwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xwr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Bacteriophage lambda]]		[[Category: Bacteriophage lambda]]
		+	[[Category: Large Structures]]
	[[Category: Chakrabarti, P]]		[[Category: Chakrabarti, P]]
	[[Category: Datta, A B]]		[[Category: Datta, A B]]

OCA at 07:13, 18 April 2018

OCA — Wed, 18 Apr 2018 07:13:32 GMT

←Older revision		Revision as of 07:13, 18 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of the coliphage lambda transcription activator protein CII==		==Crystal structure of the coliphage lambda transcription activator protein CII==
	<StructureSection load='1xwr' size='340' side='right' caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='1xwr' size='340' side='right' caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://pdbe.org/1xwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr 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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://pdbe.org/1xwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xwr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xw/1xwr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xw/1xwr_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xwr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:40, 12 September 2015

OCA — Sat, 12 Sep 2015 00:40:10 GMT

←Older revision		Revision as of 00:40, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1xwr' size='340' side='right' caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='1xwr' size='340' side='right' caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_lambda Enterobacteria phage~~ lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XWR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XWR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 ~~Enterobacteria phage~~ lambda])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr 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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://pdbe.org/1xwr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1xwr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage~~ lambda]]	+	[[Category: Bacteriophage lambda]]
	[[Category: Chakrabarti, P]]		[[Category: Chakrabarti, P]]
	[[Category: Datta, A B]]		[[Category: Datta, A B]]

OCA at 21:32, 25 December 2014

OCA — Thu, 25 Dec 2014 21:32:28 GMT

←Older revision		Revision as of 21:32, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XWR FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XWR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Enterobacteria phage lambda])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Enterobacteria phage lambda])</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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr 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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPC2_LAMBD RPC2_LAMBD]] This protein and protein CIII form a complex that is involved in the initiation of lysogeny. The complex binds at either of the cy regulatory sites preceding the CI repressor protein and integrase coding regions and induces transcription of these genes.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Enterobacteria phage lambda]]		[[Category: Enterobacteria phage lambda]]
-	[[Category: Chakrabarti, P.]]	+	[[Category: Chakrabarti, P]]
-	[[Category: Datta, A B.]]	+	[[Category: Datta, A B]]
-	[[Category: Panjikar, S.]]	+	[[Category: Panjikar, S]]
-	[[Category: Parrack, P.]]	+	[[Category: Parrack, P]]
-	[[Category: Weiss, M S.]]	+	[[Category: Weiss, M S]]
	[[Category: All-alpha fold]]		[[Category: All-alpha fold]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]

OCA at 20:56, 29 September 2014

OCA — Mon, 29 Sep 2014 20:56:08 GMT

←Older revision		Revision as of 20:56, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xwr.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the coliphage lambda transcription activator protein CII==
		+	<StructureSection load='1xwr' size='340' side='right' caption='[[1xwr]], [[Resolution\|resolution]] 2.56Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xwr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XWR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Enterobacteria phage lambda])</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=1xwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xwr RCSB], [http://www.ebi.ac.uk/pdbsum/1xwr PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xw/1xwr_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The temperate coliphage lambda, after infecting its host bacterium Escherichia coli, can develop either along the lytic or the lysogenic pathway. Crucial to the lysis/lysogeny decision is the homotetrameric transcription-activator protein CII (4 x 11 kDa) of the phage that binds to a unique direct-repeat sequence T-T-G-C-N6-T-T-G-C at each of the three phage promoters it activates: p(E), p(I), and p(aQ). Several regions of CII have been identified for its various functions (DNA binding, oligomerization, and susceptibility to host protease), but the crystal structure of the protein long remained elusive. Here, we present the three-dimensional structure of CII at 2.6-angstroms resolution. The CII monomer is comprised of four alpha helices and a disordered C terminus. The first three helices (alpha1-alpha3) form a compact domain, whereas the fourth helix (alpha4) protrudes in different orientations in each subunit. A four-helix bundle, formed by alpha4 from each subunit, holds the tetramer. The quaternary structure can be described as a dimer of dimers, but the tetramer does not exhibit a closed symmetry. This unusual quaternary arrangement allows the placement of the helix-turn-helix motifs of two of the four CII subunits for interaction with successive major grooves of B-DNA, from one face of DNA. This structure provides a simple explanation for how a homotetrameric protein may recognize a direct-repeat DNA sequence rather than the inverted-repeat sequences of most prokaryotic activators.

-	~~{{STRUCTURE_1xwr\| PDB=1xwr \| SCENE= }}~~	+	Structure of lambda CII: implications for recognition of direct-repeat DNA by an unusual tetrameric organization.,Datta AB, Panjikar S, Weiss MS, Chakrabarti P, Parrack P Proc Natl Acad Sci U S A. 2005 Aug 9;102(32):11242-7. Epub 2005 Aug 1. PMID:16061804<ref>PMID:16061804</ref>

-	~~===Crystal structure~~ of the ~~coliphage lambda transcription activator protein CII===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16061804}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xwr]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016061804<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Enterobacteria phage lambda]]		[[Category: Enterobacteria phage lambda]]
	[[Category: Chakrabarti, P.]]		[[Category: Chakrabarti, P.]]

OCA: Protected "1xwr" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:52:59 GMT

Protected "1xwr" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:52, 5 January 2013

OCA at 11:52, 5 January 2013

OCA — Sat, 05 Jan 2013 11:52:56 GMT

←Older revision		Revision as of 11:52, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xwr.png\|left\|200px]]		[[Image:1xwr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xwr", 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_1xwr\| PDB=1xwr \| SCENE= }}		{{STRUCTURE_1xwr\| PDB=1xwr \| SCENE= }}

	===Crystal structure of the coliphage lambda transcription activator protein CII===		===Crystal structure of the coliphage lambda transcription activator protein CII===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16061804}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16061804 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16061804}}		{{ABSTRACT_PUBMED_16061804}}

	==About this Structure==		==About this Structure==
-	~~1XWR~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA].	+	[[1xwr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16061804~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016061804</ref><references group="xtra"/>
	[[Category: Enterobacteria phage lambda]]		[[Category: Enterobacteria phage lambda]]
	[[Category: Chakrabarti, P.]]		[[Category: Chakrabarti, P.]]
Line 31:		Line 19:
	[[Category: Weiss, M S.]]		[[Category: Weiss, M S.]]
	[[Category: All-alpha fold]]		[[Category: All-alpha fold]]
-	[[Category: Dna-binding protein]]	+	[[Category: Dna binding protein]]
-		+
-	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:24:38 2009''~~	+

OCA at 06:24, 18 February 2009

OCA — Wed, 18 Feb 2009 06:24:41 GMT

←Older revision		Revision as of 06:24, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1XWR is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA].	+	1XWR is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWR OCA].

	==Reference==		==Reference==
-	Structure of lambda CII: implications for recognition of direct-repeat DNA by an unusual tetrameric organization., Datta AB, Panjikar S, Weiss MS, Chakrabarti P, Parrack P, Proc Natl Acad Sci U S A. 2005 Aug 9;102(32):11242-7. Epub 2005 Aug 1. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16061804 16061804]~~	+	<ref group="xtra">PMID:16061804</ref><references group="xtra"/>
	[[Category: Enterobacteria phage lambda]]		[[Category: Enterobacteria phage lambda]]
-	[[Category: Single protein]]
	[[Category: Chakrabarti, P.]]		[[Category: Chakrabarti, P.]]
	[[Category: Datta, A B.]]		[[Category: Datta, A B.]]
Line 34:		Line 33:
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 14~~:43:~~03 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:24:38 2009''

OCA at 11:43, 29 July 2008

OCA — Tue, 29 Jul 2008 11:43:07 GMT

←Older revision		Revision as of 11:43, 29 July 2008
Line 1:		Line 1:
-	[[Image:1xwr.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1xwr.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1xwr\| PDB=1xwr \| SCENE= }}		{{STRUCTURE_1xwr\| PDB=1xwr \| SCENE= }}

-	~~'''~~Crystal structure of the coliphage lambda transcription activator protein CII~~'''~~	+	===Crystal structure of the coliphage lambda transcription activator protein CII===


-	~~==Overview==~~	+	<!--
-	The ~~temperate coliphage lambda~~, ~~after infecting its host bacterium Escherichia coli~~, ~~can develop either along~~ the ~~lytic or the lysogenic pathway. Crucial~~ to the ~~lysis/lysogeny decision is the homotetrameric transcription-activator protein CII~~ (~~4 x 11 kDa) of the phage that binds to a unique direct-repeat sequence T-T-G-C-N6-T-T-G-C~~ at ~~each of the three phage promoters it activates~~: ~~p(E), p(I), and p(aQ)~~. ~~Several regions of CII have been identified for its various functions (DNA binding, oligomerization, and susceptibility to host protease~~), ~~but the crystal structure of the protein long remained elusive. Here, we present the three-dimensional structure of CII at 2.6-angstroms resolution. The CII monomer~~ is ~~comprised of four alpha helices and a disordered C terminus. The first three helices (alpha1-alpha3) form a compact domain, whereas~~ the ~~fourth helix (alpha4) protrudes in different orientations in each subunit~~. ~~A four~~-helix bundle, formed by alpha4 from each subunit, holds the tetramer. The quaternary structure can be described as a dimer of dimers, but the tetramer does not exhibit a closed symmetry. This unusual quaternary arrangement allows the placement of the helix-turn-helix motifs of two of the four CII subunits for interaction with successive major grooves of B-DNA, from one face of DNA. This structure provides a simple explanation for how a homotetrameric protein may recognize a direct-repeat DNA sequence rather than the inverted-repeat sequences of most prokaryotic activators.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16061804}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16061804 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16061804}}

	==About this Structure==		==About this Structure==
Line 29:		Line 33:
	[[Category: All-alpha fold]]		[[Category: All-alpha fold]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 15~~:36:16 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:43:03 2008''