1suy - Revision history

OCA at 08:35, 1 May 2024

2024-05-01T08:35:48Z

←Older revision		Revision as of 08:35, 1 May 2024
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	==NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)==		==NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)==
-	<StructureSection load='1suy' size='340' side='right'caption='[[1suy~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1suy' size='340' side='right'caption='[[1suy]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Theeb Theeb~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SUY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SUY FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1q6a\|1q6a]], [[1sv1\|1sv1]]</div></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB])</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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [https://pdbe.org/1suy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [https://www.ebi.ac.uk/pdbsum/1suy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1suy 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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [~~http~~://pdbe.org/1suy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1suy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1suy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~KAIA_THEEB KAIA_THEEB~~]~~] Component~~ of the KaiABC ~~clock protein~~ complex, which constitutes the main circadian regulator in cyanobacteria. ~~The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on~~ the ~~state of chromosome compaction. In the complex, it enhances the phosphorylation status of~~ KaiC. ~~In contrast, the presence of KaiB in the complex decreases the phosphorylation status of~~ KaiC, ~~suggesting that~~ KaiB ~~acts by antagonizing the interaction between~~ KaiA ~~and~~ KaiC. A KaiA ~~dimer is sufficient~~ to ~~enhance~~ KaiC ~~hexamer phosphorylation. [[http~~:~~//www~~.~~uniprot.org/uniprot/KAIC_THEEB KAIC_THEEB]] Core component~~ of the ~~KaiABC clock protein~~ complex, ~~which constitutes~~ the ~~main circadian regulator in cyanobacteria~~. ~~Binds to DNA. The KaiABC complex may act as~~ a ~~promoter-nonspecific transcription regulator~~ that ~~represses transcription~~, ~~possibly by acting on~~ the ~~state~~ of ~~chromosome compaction~~ (By similarity).[~~HAMAP~~-~~Rule~~:~~MF_01836~~]	+	[https://www.uniprot.org/uniprot/KAIA_THEVB KAIA_THEVB] Key component of the KaiABC oscillator complex, which constitutes the main circadian regulator in cyanobacteria. Complex composition changes during the circadian cycle to control KaiC phosphorylation. KaiA stimulates KaiC autophosphorylation, while KaiB sequesters KaiA, leading to KaiC autodephosphorylation. KaiA binding to the KaiC CII domain during the subjective day yields KaiA(2-4):KaiC(6) complexes which stimulate KaiC autophosphorylation. Phospho-Ser-431 KaiC accumulation triggers binding of KaiB during the subjective night to form the KaiB(6):KaiC(6) complex, leading to changes in the output regulators CikA and SasA. KaiB(6):KaiC(6) formation exposes a site for KaiA binding on KaiB that sequesters KaiA from KaiC's CII domain, making the KaiC(6):KaiB(6):KaiA(12) complex resulting in KaiC autodephosphorylation. Complete dephosphorylation of KaiC leads to dissociation of KaiA(2):KaiB(1), completing 1 cycle of the Kai oscillator (By similarity). Formation of the KaiB:KaiC complex is promoted by KaiA, helping switch KaiC from its autophosphorylation to autodephosphatase function (PubMed:24112939).[UniProtKB:Q79PF6]<ref>PMID:24112939</ref> Binds oxidized quinones via the N-terminal PsR domain, allowing it to sense redox changes and possibly mediate clock input.[UniProtKB:Q79PF6]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 19:
	</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=1suy 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=1suy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Circadian clocks are widespread endogenous mechanisms that control the temporal pattern of diverse biological processes, including gene transcription. KaiA is the positive element of the cyanobacterial clock because KaiA overexpression elevates transcription levels of clock components. Recently, we showed that the structure of KaiA is that of a domain-swapped homodimer. The N-terminal domain is a pseudo-receiver; thus, it is likely to be involved in signal transduction in the clock-resetting pathway. The C-terminal domain of KaiA is structurally novel and enhances the KaiC autokinase activity directly. Here, we report the NMR structure of the C-terminal domain of KaiA (ThKaiA180C) in complex with a KaiC-derived peptide from the cyanobacterium Thermosynechococcus elongatus BP-1. The protein-peptide interface is revealed to be different from a model that was proposed earlier, is stabilized by a combination of hydrophobic and electrostatic interactions, and includes many residues known to produce a circadian-period phenotype upon substitution. Although the structure of the monomeric subunit of ThKaiA180C is largely unchanged upon peptide binding, the intersubunit dimerization angle changes. It is proposed that modulation of the C-terminal KaiA domain dimerization angle regulates KaiA-KaiC interactions.
-
-	Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation.,Vakonakis I, LiWang AC Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10925-30. Epub 2004 Jul 15. PMID:15256595<ref>PMID:15256595</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1suy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Theeb~~]]	+	[[Category: Thermosynechococcus vestitus BP-1]]
-	[[Category: LiWang~~, A C~~]]	+	[[Category: LiWang AC]]
-	[[Category: Vakonakis, I]]	+	[[Category: Vakonakis I]]
-	~~[[Category: Circadian clock protein]]~~	+
-	~~[[Category: Protein-peptide complex]]~~	+
-	~~[[Category: X-class four helix bundle~~]]	+

OCA at 11:34, 24 December 2020

2020-12-24T11:34:37Z

←Older revision		Revision as of 11:34, 24 December 2020
Line 1:		Line 1:

	==NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)==		==NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)==
-	<StructureSection load='1suy' size='340' side='right' caption='[[1suy]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1suy' size='340' side='right'caption='[[1suy]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Theeb Theeb]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SUY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Theeb Theeb]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SUY FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6a\|1q6a]], [[1sv1\|1sv1]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q6a\|1q6a]], [[1sv1\|1sv1]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB])</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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://pdbe.org/1suy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1suy 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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://pdbe.org/1suy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1suy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Circadian clock protein\|Circadian clock protein]]	+	*[[Circadian clock protein 3D structures\|Circadian clock protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Theeb]]		[[Category: Theeb]]
	[[Category: LiWang, A C]]		[[Category: LiWang, A C]]

OCA at 07:26, 14 March 2018

2018-03-14T07:26:25Z

←Older revision		Revision as of 07:26, 14 March 2018
Line 1:		Line 1:
		+
	==NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)==		==NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)==
	<StructureSection load='1suy' size='340' side='right' caption='[[1suy]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1suy' size='340' side='right' caption='[[1suy]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6a\|1q6a]], [[1sv1\|1sv1]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6a\|1q6a]], [[1sv1\|1sv1]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB])</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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://pdbe.org/1suy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy 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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://pdbe.org/1suy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1suy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/su/1suy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/su/1suy_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>

OCA at 07:07, 8 February 2016

2016-02-08T07:07:02Z

←Older revision		Revision as of 07:07, 8 February 2016
Line 17:		Line 17:
	<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=1suy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:06, 10 September 2015

2015-09-10T09:06:42Z

←Older revision		Revision as of 09:06, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1suy' size='340' side='right' caption='[[1suy]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1suy' size='340' side='right' caption='[[1suy]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermosynechococcus_elongatus_bp-1 Thermosynechococcus elongatus bp-1~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SUY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Theeb Theeb]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SUY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6a\|1q6a]], [[1sv1\|1sv1]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6a\|1q6a]], [[1sv1\|1sv1]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 ~~Thermosynechococcus elongatus BP-1~~]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 ~~Thermosynechococcus elongatus BP-1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 THEEB])</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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy 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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://pdbe.org/1suy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~KAIA_SYNEL KAIA_SYNEL~~]] Component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. In the complex, it enhances the phosphorylation status of KaiC. In contrast, the presence of KaiB in the complex decreases the phosphorylation status of KaiC, suggesting that KaiB acts by antagonizing the interaction between KaiA and KaiC. A KaiA dimer is sufficient to enhance KaiC hexamer phosphorylation. [[http://www.uniprot.org/uniprot/KAIC_THEEB KAIC_THEEB]] Core component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. Binds to DNA. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction (By similarity).[HAMAP-Rule:MF_01836]	+	[[http://www.uniprot.org/uniprot/KAIA_THEEB KAIA_THEEB]] Component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. In the complex, it enhances the phosphorylation status of KaiC. In contrast, the presence of KaiB in the complex decreases the phosphorylation status of KaiC, suggesting that KaiB acts by antagonizing the interaction between KaiA and KaiC. A KaiA dimer is sufficient to enhance KaiC hexamer phosphorylation. [[http://www.uniprot.org/uniprot/KAIC_THEEB KAIC_THEEB]] Core component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. Binds to DNA. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction (By similarity).[HAMAP-Rule:MF_01836]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 1suy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermosynechococcus elongatus bp-1~~]]	+	[[Category: Theeb]]
	[[Category: LiWang, A C]]		[[Category: LiWang, A C]]
	[[Category: Vakonakis, I]]		[[Category: Vakonakis, I]]

OCA at 21:32, 24 December 2014

2014-12-24T21:32:23Z

←Older revision		Revision as of 21:32, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_bp-1 Thermosynechococcus elongatus bp-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SUY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_bp-1 Thermosynechococcus elongatus bp-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SUY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6a\|1q6a]], [[1sv1\|1sv1]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6a\|1q6a]], [[1sv1\|1sv1]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 Thermosynechococcus elongatus BP-1]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 Thermosynechococcus elongatus BP-1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 Thermosynechococcus elongatus BP-1]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 Thermosynechococcus elongatus BP-1])</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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy 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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KAIA_SYNEL KAIA_SYNEL]] Component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. In the complex, it enhances the phosphorylation status of KaiC. In contrast, the presence of KaiB in the complex decreases the phosphorylation status of KaiC, suggesting that KaiB acts by antagonizing the interaction between KaiA and KaiC. A KaiA dimer is sufficient to enhance KaiC hexamer phosphorylation. [[http://www.uniprot.org/uniprot/KAIC_THEEB KAIC_THEEB]] Core component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. Binds to DNA. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction (By similarity).[HAMAP-Rule:MF_01836]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Thermosynechococcus elongatus bp-1]]		[[Category: Thermosynechococcus elongatus bp-1]]
-	[[Category: LiWang, A C.]]	+	[[Category: LiWang, A C]]
-	[[Category: Vakonakis, I.]]	+	[[Category: Vakonakis, I]]
	[[Category: Circadian clock protein]]		[[Category: Circadian clock protein]]
	[[Category: Protein-peptide complex]]		[[Category: Protein-peptide complex]]
	[[Category: X-class four helix bundle]]		[[Category: X-class four helix bundle]]

OCA at 17:16, 29 September 2014

2014-09-29T17:16:19Z

←Older revision		Revision as of 17:16, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1suy.~~png~~\|~~left~~\|200px]]	+	==NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)==
		+	<StructureSection load='1suy' size='340' side='right' caption='[[1suy]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1suy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_bp-1 Thermosynechococcus elongatus bp-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SUY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q6a\|1q6a]], [[1sv1\|1sv1]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KaiA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 Thermosynechococcus elongatus BP-1]), KaiC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197221 Thermosynechococcus elongatus BP-1])</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=1suy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1suy RCSB], [http://www.ebi.ac.uk/pdbsum/1suy 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/su/1suy_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 widespread endogenous mechanisms that control the temporal pattern of diverse biological processes, including gene transcription. KaiA is the positive element of the cyanobacterial clock because KaiA overexpression elevates transcription levels of clock components. Recently, we showed that the structure of KaiA is that of a domain-swapped homodimer. The N-terminal domain is a pseudo-receiver; thus, it is likely to be involved in signal transduction in the clock-resetting pathway. The C-terminal domain of KaiA is structurally novel and enhances the KaiC autokinase activity directly. Here, we report the NMR structure of the C-terminal domain of KaiA (ThKaiA180C) in complex with a KaiC-derived peptide from the cyanobacterium Thermosynechococcus elongatus BP-1. The protein-peptide interface is revealed to be different from a model that was proposed earlier, is stabilized by a combination of hydrophobic and electrostatic interactions, and includes many residues known to produce a circadian-period phenotype upon substitution. Although the structure of the monomeric subunit of ThKaiA180C is largely unchanged upon peptide binding, the intersubunit dimerization angle changes. It is proposed that modulation of the C-terminal KaiA domain dimerization angle regulates KaiA-KaiC interactions.

-	~~{{STRUCTURE_1suy\| PDB=1suy \| SCENE= }}~~	+	Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation.,Vakonakis I, LiWang AC Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10925-30. Epub 2004 Jul 15. PMID:15256595<ref>PMID:15256595</ref>

-	~~===NMR structure~~ of the ~~ThKaiA180C-CIIABD complex (average minimized structure)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_15256595}}~~	+	==See Also==
-		+	*[[Circadian clock protein\|Circadian clock protein]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1suy~~]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_bp-1 Thermosynechococcus elongatus bp-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:015256595<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Thermosynechococcus elongatus bp-1]]		[[Category: Thermosynechococcus elongatus bp-1]]
	[[Category: LiWang, A C.]]		[[Category: LiWang, A C.]]

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

2013-01-04T10:00:27Z

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

←Older revision

Revision as of 10:00, 4 January 2013

OCA at 10:00, 4 January 2013

2013-01-04T10:00:24Z

←Older revision		Revision as of 10:00, 4 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1suy.png\|left\|200px]]		[[Image:1suy.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1suy", 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_1suy\| PDB=1suy \| SCENE= }}		{{STRUCTURE_1suy\| PDB=1suy \| SCENE= }}

	===NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)===		===NMR structure of the ThKaiA180C-CIIABD complex (average minimized structure)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15256595}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15256595 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15256595}}		{{ABSTRACT_PUBMED_15256595}}

	==About this Structure==		==About this Structure==
-	~~1SUY~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Bacteria Bacteria~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA].	+	[[1suy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_bp-1 Thermosynechococcus elongatus bp-1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15256595~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015256595</ref><references group="xtra"/>
-	[[Category: ~~Bacteria~~]]	+	[[Category: Thermosynechococcus elongatus bp-1]]
	[[Category: LiWang, A C.]]		[[Category: LiWang, A C.]]
	[[Category: Vakonakis, I.]]		[[Category: Vakonakis, I.]]
		+	[[Category: Circadian clock protein]]
	[[Category: Protein-peptide complex]]		[[Category: Protein-peptide complex]]
	[[Category: X-class four helix bundle]]		[[Category: X-class four helix bundle]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:03:57 2009''

OCA at 18:03, 16 February 2009

2009-02-16T18:03:58Z

←Older revision		Revision as of 18:03, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1SUY is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA].	+	1SUY is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUY OCA].

	==Reference==		==Reference==
-	Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation., Vakonakis I, LiWang AC, Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10925-30. Epub 2004 Jul 15. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15256595 15256595]~~	+	<ref group="xtra">PMID:15256595</ref><references group="xtra"/>
	[[Category: Bacteria]]		[[Category: Bacteria]]
-	[[Category: Protein complex]]
	[[Category: LiWang, A C.]]		[[Category: LiWang, A C.]]
	[[Category: Vakonakis, I.]]		[[Category: Vakonakis, I.]]
Line 31:		Line 30:
	[[Category: X-class four helix bundle]]		[[Category: X-class four helix bundle]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 00~~:11:~~31 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:03:57 2009''