2e1n - Revision history

OCA at 13:48, 13 March 2024

OCA — Wed, 13 Mar 2024 13:48:47 GMT

←Older revision		Revision as of 13:48, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2e1n' size='340' side='right'caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2e1n' size='340' side='right'caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Anacystis_nidulans_r2 Anacystis nidulans r2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_7942_=_FACHB-805 Synechococcus elongatus PCC 7942 = FACHB-805]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~pex ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1140 Anacystis nidulans R2])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [https://pdbe.org/2e1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [https://www.ebi.ac.uk/pdbsum/2e1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1n 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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [https://pdbe.org/2e1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [https://www.ebi.ac.uk/pdbsum/2e1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1n ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q31QG0_SYNE7 Q31QG0_SYNE7]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		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=2e1n 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=2e1n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Circadian clocks are self-sustained biochemical oscillators. The oscillator of cyanobacteria comprises the products of three kai genes (kaiA, kaiB, and kaiC). The autophosphorylation cycle of KaiC oscillates robustly in the cell with a 24-h period and is essential for the basic timing of the cyanobacterial circadian clock. Recently, period extender (pex), mutants of which show a short period phenotype, was classified as a resetting-related gene. In fact, pex mRNA and the pex protein (Pex) increase during the dark period, and a pex mutant subjected to diurnal light-dark cycles shows a 3-h advance in rhythm phase. Here, we report the x-ray crystallographic analysis and biochemical characterization of Pex from cyanobacterium Synechococcus elongatus PCC 7942. The molecule has an (alpha+beta) structure with a winged-helix motif and is indicated to function as a dimer. The subunit arrangement in the dimer is unique and has not been seen in other winged-helix proteins. Electrophoresis mobility shift assay using a 25-base pair complementary oligonucleotide incorporating the kaiA upstream sequence demonstrates that Pex has an affinity for the double-stranded DNA. Furthermore, mutation analysis shows that Pex uses the wing region to recognize the DNA. The in vivo rhythm assay of Pex shows that the constitutive expression of the pex gene harboring the mutation that fails to bind to DNA lacks the period-prolongation activity in the pex-deficient Synechococcus, suggesting that Pex is a DNA-binding transcription factor.
-
-	Structural and biochemical characterization of a cyanobacterium circadian clock-modifier protein.,Arita K, Hashimoto H, Igari K, Akaboshi M, Kutsuna S, Sato M, Shimizu T J Biol Chem. 2007 Jan 12;282(2):1128-35. Epub 2006 Nov 10. PMID:17098741<ref>PMID:17098741</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2e1n" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Anacystis nidulans r2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Arita, K~~]]	+	[[Category: Synechococcus elongatus PCC 7942 = FACHB-805]]
-	[[Category: ~~Shimizu, T~~]]	+	[[Category: Arita K]]
-	[[Category: ~~Circadian clock]]~~	+	[[Category: Shimizu T]]
-	~~[[Category: Circadian clock protein]]~~	+
-	~~[[Category: Dna binding protein~~]]	+

OCA at 11:44, 10 February 2021

OCA — Wed, 10 Feb 2021 11:44:31 GMT

←Older revision		Revision as of 11:44, 10 February 2021
Line 1:		Line 1:

	==Crystal structure of the Cyanobacterium circadian clock modifier Pex==		==Crystal structure of the Cyanobacterium circadian clock modifier Pex==
-	<StructureSection load='2e1n' size='340' side='right' caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2e1n' size='340' side='right'caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Anacystis_nidulans_r2 Anacystis nidulans r2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2E1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anacystis_nidulans_r2 Anacystis nidulans r2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Anacystis nidulans R2])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Anacystis nidulans R2])</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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [~~http~~://pdbe.org/2e1n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2e1n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1n 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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [https://pdbe.org/2e1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [https://www.ebi.ac.uk/pdbsum/2e1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1n ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Anacystis nidulans r2]]		[[Category: Anacystis nidulans r2]]
		+	[[Category: Large Structures]]
	[[Category: Arita, K]]		[[Category: Arita, K]]
	[[Category: Shimizu, T]]		[[Category: Shimizu, T]]

OCA at 07:05, 6 June 2018

OCA — Wed, 06 Jun 2018 07:05:30 GMT

←Older revision		Revision as of 07:05, 6 June 2018
Line 1:		Line 1:
		+
	==Crystal structure of the Cyanobacterium circadian clock modifier Pex==		==Crystal structure of the Cyanobacterium circadian clock modifier Pex==
	<StructureSection load='2e1n' size='340' side='right' caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2e1n' size='340' side='right' caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Anacystis nidulans R2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Anacystis nidulans R2])</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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [http://pdbe.org/2e1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [http://www.ebi.ac.uk/pdbsum/2e1n 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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [http://pdbe.org/2e1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [http://www.ebi.ac.uk/pdbsum/2e1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1n ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e1/2e1n_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e1/2e1n_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=2e1n ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:15, 11 September 2015

OCA — Fri, 11 Sep 2015 13:15:37 GMT

←Older revision		Revision as of 13:15, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2e1n' size='340' side='right' caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2e1n' size='340' side='right' caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Synechococcus_elongatus_pcc_7942 Synechococcus elongatus pcc 7942~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anacystis_nidulans_r2 Anacystis nidulans r2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 ~~Synechococcus elongatus PCC 7942~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Anacystis nidulans R2])</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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [http://www.ebi.ac.uk/pdbsum/2e1n 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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [http://pdbe.org/2e1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [http://www.ebi.ac.uk/pdbsum/2e1n PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 2e1n" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Synechococcus elongatus pcc 7942~~]]	+	[[Category: Anacystis nidulans r2]]
	[[Category: Arita, K]]		[[Category: Arita, K]]
	[[Category: Shimizu, T]]		[[Category: Shimizu, T]]

OCA at 18:22, 15 January 2015

OCA — Thu, 15 Jan 2015 18:22:51 GMT

←Older revision		Revision as of 18:22, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechococcus_elongatus_pcc_7942 Synechococcus elongatus pcc 7942]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1N FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechococcus_elongatus_pcc_7942 Synechococcus elongatus pcc 7942]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1N FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Synechococcus elongatus PCC 7942])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Synechococcus elongatus PCC 7942])</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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [http://www.ebi.ac.uk/pdbsum/2e1n 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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [http://www.ebi.ac.uk/pdbsum/2e1n PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Synechococcus elongatus pcc 7942]]		[[Category: Synechococcus elongatus pcc 7942]]
-	[[Category: Arita, K.]]	+	[[Category: Arita, K]]
-	[[Category: Shimizu, T.]]	+	[[Category: Shimizu, T]]
	[[Category: Circadian clock]]		[[Category: Circadian clock]]
	[[Category: Circadian clock protein]]		[[Category: Circadian clock protein]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]

OCA at 02:56, 30 September 2014

OCA — Tue, 30 Sep 2014 02:56:29 GMT

←Older revision		Revision as of 02:56, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2e1n.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the Cyanobacterium circadian clock modifier Pex==
		+	<StructureSection load='2e1n' size='340' side='right' caption='[[2e1n]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2e1n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechococcus_elongatus_pcc_7942 Synechococcus elongatus pcc 7942]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E1N FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pex ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Synechococcus elongatus PCC 7942])</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=2e1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e1n RCSB], [http://www.ebi.ac.uk/pdbsum/2e1n 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/e1/2e1n_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 ==
		+	Circadian clocks are self-sustained biochemical oscillators. The oscillator of cyanobacteria comprises the products of three kai genes (kaiA, kaiB, and kaiC). The autophosphorylation cycle of KaiC oscillates robustly in the cell with a 24-h period and is essential for the basic timing of the cyanobacterial circadian clock. Recently, period extender (pex), mutants of which show a short period phenotype, was classified as a resetting-related gene. In fact, pex mRNA and the pex protein (Pex) increase during the dark period, and a pex mutant subjected to diurnal light-dark cycles shows a 3-h advance in rhythm phase. Here, we report the x-ray crystallographic analysis and biochemical characterization of Pex from cyanobacterium Synechococcus elongatus PCC 7942. The molecule has an (alpha+beta) structure with a winged-helix motif and is indicated to function as a dimer. The subunit arrangement in the dimer is unique and has not been seen in other winged-helix proteins. Electrophoresis mobility shift assay using a 25-base pair complementary oligonucleotide incorporating the kaiA upstream sequence demonstrates that Pex has an affinity for the double-stranded DNA. Furthermore, mutation analysis shows that Pex uses the wing region to recognize the DNA. The in vivo rhythm assay of Pex shows that the constitutive expression of the pex gene harboring the mutation that fails to bind to DNA lacks the period-prolongation activity in the pex-deficient Synechococcus, suggesting that Pex is a DNA-binding transcription factor.

-	~~{{STRUCTURE_2e1n\| PDB=2e1n \| SCENE= }}~~	+	Structural and biochemical characterization of a cyanobacterium circadian clock-modifier protein.,Arita K, Hashimoto H, Igari K, Akaboshi M, Kutsuna S, Sato M, Shimizu T J Biol Chem. 2007 Jan 12;282(2):1128-35. Epub 2006 Nov 10. PMID:17098741<ref>PMID:17098741</ref>

-	~~===Crystal structure~~ of the ~~Cyanobacterium circadian clock modifier Pex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17098741}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2e1n]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Synechococcus_elongatus_pcc_7942 Synechococcus elongatus pcc 7942]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017098741<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Synechococcus elongatus pcc 7942]]		[[Category: Synechococcus elongatus pcc 7942]]
	[[Category: Arita, K.]]		[[Category: Arita, K.]]

OCA: Protected "2e1n" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 12:06:52 GMT

Protected "2e1n" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:06, 6 January 2013

OCA at 12:06, 6 January 2013

OCA — Sun, 06 Jan 2013 12:06:49 GMT

←Older revision		Revision as of 12:06, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2e1n.png\|left\|200px]]		[[Image:2e1n.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2e1n", 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_2e1n\| PDB=2e1n \| SCENE= }}		{{STRUCTURE_2e1n\| PDB=2e1n \| SCENE= }}

	===Crystal structure of the Cyanobacterium circadian clock modifier Pex===		===Crystal structure of the Cyanobacterium circadian clock modifier Pex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17098741}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17098741 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17098741}}		{{ABSTRACT_PUBMED_17098741}}

	==About this Structure==		==About this Structure==
-	~~2E1N~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Synechococcus_sp.~~ Synechococcus ~~sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA].	+	[[2e1n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synechococcus_elongatus_pcc_7942 Synechococcus elongatus pcc 7942]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17098741~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017098741</ref><references group="xtra"/>
-	[[Category: Synechococcus ~~sp.~~]]	+	[[Category: Synechococcus elongatus pcc 7942]]
	[[Category: Arita, K.]]		[[Category: Arita, K.]]
	[[Category: Shimizu, T.]]		[[Category: Shimizu, T.]]
	[[Category: Circadian clock]]		[[Category: Circadian clock]]
		+	[[Category: Circadian clock protein]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:27:04 2009''

OCA at 20:27, 17 February 2009

OCA — Tue, 17 Feb 2009 20:27:06 GMT

←Older revision		Revision as of 20:27, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2E1N is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA].	+	2E1N is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1N OCA].

	==Reference==		==Reference==
-	Structural and biochemical characterization of a cyanobacterium circadian clock-modifier protein., Arita K, Hashimoto H, Igari K, Akaboshi M, Kutsuna S, Sato M, Shimizu T, J Biol Chem. 2007 Jan 12;282(2):1128-35. Epub 2006 Nov 10. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17098741 17098741]~~	+	<ref group="xtra">PMID:17098741</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Synechococcus sp.]]		[[Category: Synechococcus sp.]]
	[[Category: Arita, K.]]		[[Category: Arita, K.]]
Line 31:		Line 30:
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 06~~:39:~~52 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:27:04 2009''

OCA at 03:39, 29 July 2008

OCA — Tue, 29 Jul 2008 03:39:57 GMT

←Older revision		Revision as of 03:39, 29 July 2008
Line 1:		Line 1:
-	[[Image:2e1n.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2e1n.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2e1n\| PDB=2e1n \| SCENE= }}		{{STRUCTURE_2e1n\| PDB=2e1n \| SCENE= }}

-	~~'''~~Crystal structure of the Cyanobacterium circadian clock modifier Pex~~'''~~	+	===Crystal structure of the Cyanobacterium circadian clock modifier Pex===


-	~~==Overview==~~	+	<!--
-	~~Circadian clocks are self-sustained biochemical oscillators.~~ The ~~oscillator of cyanobacteria comprises the products of three kai genes (kaiA~~, ~~kaiB~~, ~~and kaiC). The autophosphorylation cycle of KaiC oscillates robustly in~~ the ~~cell with a 24-h period and is essential for~~ the ~~basic timing of the cyanobacterial circadian clock. Recently, period extender~~ (~~pex), mutants of which show a short period phenotype, was classified~~ as ~~a resetting-related gene~~. ~~In fact, pex mRNA and the pex protein (Pex~~) ~~increase during the dark period~~, and a pex mutant subjected to diurnal light-dark cycles shows a 3-h advance in rhythm phase. Here, we report the x-ray crystallographic analysis and biochemical characterization of Pex from cyanobacterium Synechococcus elongatus PCC 7942. The molecule has an (alpha+beta) structure with a winged-helix motif and is ~~indicated to function as a dimer. The subunit arrangement in~~ the ~~dimer is unique and has not been seen in other winged-helix proteins~~. ~~Electrophoresis mobility shift assay using a 25~~-~~base pair complementary oligonucleotide incorporating the kaiA upstream sequence demonstrates that Pex has an affinity for the double~~-stranded DNA. Furthermore, mutation analysis shows that Pex uses the wing region to recognize the DNA. The in vivo rhythm assay of Pex shows that the constitutive expression of the pex gene harboring the mutation that fails to bind to DNA lacks the period-prolongation activity in the pex-deficient Synechococcus, suggesting that Pex is a DNA-binding transcription factor.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17098741}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17098741 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17098741}}

	==About this Structure==		==About this Structure==
Line 26:		Line 30:
	[[Category: Circadian clock]]		[[Category: Circadian clock]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 01~~:45:15 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:39:52 2008''