2dql - Revision history

OCA at 13:47, 13 March 2024

2024-03-13T13:47:58Z

← Older revision		Revision as of 13:47, 13 March 2024
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	<StructureSection load='2dql' size='340' side='right'caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2dql' size='340' side='right'caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Anabaena_7120 Anabaena~~ 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nostoc_sp._PCC_7120_=_FACHB-418 Nostoc sp. PCC 7120 = FACHB-418]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.7Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [https://pdbe.org/2dql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [https://www.ebi.ac.uk/pdbsum/2dql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql 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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [https://pdbe.org/2dql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [https://www.ebi.ac.uk/pdbsum/2dql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q8YQ56_NOSS1 Q8YQ56_NOSS1]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2dql 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=2dql ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Pex, a clock-related protein involved in the input pathway of the cyanobacterial circadian clock system, suppresses the expression of clock gene kaiA and lengthens the circadian period. Here, we determined the crystal structure of Anabaena Pex (AnaPex; Anabaena sp. strain PCC 7120) and Synechococcus Pex (SynPex; Synechococcus sp. strain PCC 7942). Pex is a homodimer that forms a winged-helix structure. Using the DNase I protection and electrophoresis mobility shift assays on a Synechococcus kaiA upstream region, we identified a minimal 25-bp sequence that contained an imperfectly inverted repeat sequence as the Pex-binding sequence. Based on crystal structure, we predicted the amino acid residues essential for Pex's DNA-binding activity and examined the effects of various Ala-substitutions in the alpha3 helix and wing region of Pex on in vitro DNA-binding activity and in vivo rhythm functions. Mutant AnaPex proteins carrying a substitution in the wing region displayed no specific DNA-binding activity, whereas those carrying a substitution in the alpha3 helix did display specific binding activity. But the latter were less thermostable than wild-type AnaPex and their in vitro functions were defective. We concluded that Pex binds a kaiA upstream DNA sequence via its wing region and that its alpha3 helix is probably important to its stability.

	Functionally important structural elements of the cyanobacterial clock-related protein Pex.,Kurosawa S, Murakami R, Onai K, Morishita M, Hasegawa D, Iwase R, Uzumaki T, Hayashi F, Kitajima-Ihara T, Sakata S, Murakami M, Kouyama T, Ishiura M Genes Cells. 2009 Jan;14(1):1-16. Epub 2008 Nov 21. PMID:19032344<ref>PMID:19032344</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2dql" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Anabaena 7120]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Kouyama, T~~]]		[[Category: Nostoc sp. PCC 7120 = FACHB-418]]
	[[Category: ~~Kurosawa, S~~]]		[[Category: Kouyama T]]
	[[Category: ~~Circadian clock associated protein]]~~		[[Category: Kurosawa S]]
	~~[[Category: Circadian clock protein~~]]

OCA at 10:54, 6 April 2022

2022-04-06T10:54:09Z

← Older revision		Revision as of 10:54, 6 April 2022
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	<StructureSection load='2dql' size='340' side='right'caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2dql' size='340' side='right'caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Anabaena_7120 Anabaena 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2DQL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anabaena_7120 Anabaena 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [~~http~~://pdbe.org/2dql PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dql PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql 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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [https://pdbe.org/2dql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [https://www.ebi.ac.uk/pdbsum/2dql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:05, 1 July 2020

2020-07-01T08:05:21Z

← Older revision		Revision as of 08:05, 1 July 2020
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	==Crystal structure of the circadian clock associated protein Pex from anabaena==		==Crystal structure of the circadian clock associated protein Pex from anabaena==
	<StructureSection load='2dql' size='340' side='right' caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2dql' size='340' side='right'caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anabaena_7120 Anabaena 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DQL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anabaena_7120 Anabaena 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2DQL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://pdbe.org/2dql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql 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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://pdbe.org/2dql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Anabaena 7120]]		[[Category: Anabaena 7120]]
			[[Category: Large Structures]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Kurosawa, S]]		[[Category: Kurosawa, S]]
	[[Category: Circadian clock associated protein]]		[[Category: Circadian clock associated protein]]
	[[Category: Circadian clock protein]]		[[Category: Circadian clock protein]]

OCA at 09:00, 26 September 2018

2018-09-26T09:00:40Z

← Older revision		Revision as of 09:00, 26 September 2018
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	<StructureSection load='2dql' size='340' side='right' caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2dql' size='340' side='right' caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anabaena_7120 Anabaena 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://pdbe.org/2dql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://pdbe.org/2dql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql ProSAT]</span></td></tr>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/2dql_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/2dql_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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Anabaena 7120]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Kurosawa, S]]		[[Category: Kurosawa, S]]
	[[Category: Circadian clock associated protein]]		[[Category: Circadian clock associated protein]]
	[[Category: Circadian clock protein]]		[[Category: Circadian clock protein]]

OCA at 14:28, 22 December 2016

2016-12-22T14:28:55Z

← Older revision		Revision as of 14:28, 22 December 2016
Line 1:		Line 1:
	==~~Crytal~~ structure of the circadian clock associated protein Pex from anabaena==
			==Crystal structure of the circadian clock associated protein Pex from anabaena==
	<StructureSection load='2dql' size='340' side='right' caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2dql' size='340' side='right' caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Anabaena_7120 Anabaena 7120]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://pdbe.org/2dql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql 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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://pdbe.org/2dql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dql ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Anabaena 7120]]~~
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Kurosawa, S]]		[[Category: Kurosawa, S]]
	[[Category: Circadian clock associated protein]]		[[Category: Circadian clock associated protein]]
	[[Category: Circadian clock protein]]		[[Category: Circadian clock protein]]

OCA at 21:22, 8 February 2016

2016-02-08T21:22:47Z

← Older revision		Revision as of 21:22, 8 February 2016
Line 14:		Line 14:
	<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=2dql ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:31, 10 September 2015

2015-09-10T15:31:04Z

← Older revision		Revision as of 15:31, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dql' size='340' side='right' caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='2dql' size='340' side='right' caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Nostoc_sp._pcc_7120 Nostoc sp. pcc~~ 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anabaena_7120 Anabaena 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql 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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://pdbe.org/2dql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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 2dql" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Nostoc sp. pcc~~ 7120]]		[[Category: Anabaena 7120]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Kurosawa, S]]		[[Category: Kurosawa, S]]
	[[Category: Circadian clock associated protein]]		[[Category: Circadian clock associated protein]]
	[[Category: Circadian clock protein]]		[[Category: Circadian clock protein]]

OCA at 17:34, 15 January 2015

2015-01-15T17:34:04Z

← Older revision		Revision as of 17:34, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Nostoc_sp._pcc_7120 Nostoc sp. pcc 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Nostoc_sp._pcc_7120 Nostoc sp. pcc 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql 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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Nostoc sp. pcc 7120]]		[[Category: Nostoc sp. pcc 7120]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T]]
	[[Category: Kurosawa, S.]]		[[Category: Kurosawa, S]]
	[[Category: Circadian clock associated protein]]		[[Category: Circadian clock associated protein]]
	[[Category: Circadian clock protein]]		[[Category: Circadian clock protein]]

OCA at 02:26, 30 September 2014

2014-09-30T02:26:23Z

← Older revision		Revision as of 02:26, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2dql~~.~~png~~\|~~left~~\|~~200px~~]]		==Crytal structure of the circadian clock associated protein Pex from anabaena==
			<StructureSection load='2dql' size='340' side='right' caption='[[2dql]], [[Resolution\|resolution]] 1.70Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dql]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Nostoc_sp._pcc_7120 Nostoc sp. pcc 7120]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQL FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
			<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=2dql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dql OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dql RCSB], [http://www.ebi.ac.uk/pdbsum/2dql 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/dq/2dql_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 ==
			Pex, a clock-related protein involved in the input pathway of the cyanobacterial circadian clock system, suppresses the expression of clock gene kaiA and lengthens the circadian period. Here, we determined the crystal structure of Anabaena Pex (AnaPex; Anabaena sp. strain PCC 7120) and Synechococcus Pex (SynPex; Synechococcus sp. strain PCC 7942). Pex is a homodimer that forms a winged-helix structure. Using the DNase I protection and electrophoresis mobility shift assays on a Synechococcus kaiA upstream region, we identified a minimal 25-bp sequence that contained an imperfectly inverted repeat sequence as the Pex-binding sequence. Based on crystal structure, we predicted the amino acid residues essential for Pex's DNA-binding activity and examined the effects of various Ala-substitutions in the alpha3 helix and wing region of Pex on in vitro DNA-binding activity and in vivo rhythm functions. Mutant AnaPex proteins carrying a substitution in the wing region displayed no specific DNA-binding activity, whereas those carrying a substitution in the alpha3 helix did display specific binding activity. But the latter were less thermostable than wild-type AnaPex and their in vitro functions were defective. We concluded that Pex binds a kaiA upstream DNA sequence via its wing region and that its alpha3 helix is probably important to its stability.

	~~{{STRUCTURE_2dql\| PDB=2dql \| SCENE= }}~~		Functionally important structural elements of the cyanobacterial clock-related protein Pex.,Kurosawa S, Murakami R, Onai K, Morishita M, Hasegawa D, Iwase R, Uzumaki T, Hayashi F, Kitajima-Ihara T, Sakata S, Murakami M, Kouyama T, Ishiura M Genes Cells. 2009 Jan;14(1):1-16. Epub 2008 Nov 21. PMID:19032344<ref>PMID:19032344</ref>

	~~===Crytal structure~~ of the ~~circadian clock associated protein Pex from anabaena===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_19032344}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2dql]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Nostoc_sp~~.~~_pcc_7120 Nostoc sp. pcc 7120]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DQL OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:019032344<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Nostoc sp. pcc 7120]]		[[Category: Nostoc sp. pcc 7120]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T.]]

OCA: Protected "2dql" [edit=sysop:move=sysop]

2013-01-06T11:38:45Z

Protected "2dql" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:38, 6 January 2013
(No difference)