5yz8 - Revision history

OCA at 08:41, 22 November 2023

OCA — Wed, 22 Nov 2023 08:41:27 GMT

←Older revision		Revision as of 08:41, 22 November 2023
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	<StructureSection load='5yz8' size='340' side='right'caption='[[5yz8]], [[Resolution\|resolution]] 2.81Å' scene=''>		<StructureSection load='5yz8' size='340' side='right'caption='[[5yz8]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yz8]] is a 6 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=5YZ8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yz8]] is a 6 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=5YZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZ8 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID~~-~~ADENYLATE+ESTER'>ANP</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.81Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~KAIC, SYNPCC7942_1216, SEE0011 ([http://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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </~~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=5yz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz8 OCA], [https://pdbe.org/5yz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yz8 RCSB], [https://www.ebi.ac.uk/pdbsum/5yz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz8 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=5yz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz8 OCA], [~~http~~://pdbe.org/5yz8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yz8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yz8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KAIC_SYNE7 KAIC_SYNE7]] 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.<ref>PMID:9727980</ref> <ref>PMID:14709675</ref>	+	[https://www.uniprot.org/uniprot/KAIC_SYNE7 KAIC_SYNE7] 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.<ref>PMID:9727980</ref> <ref>PMID:14709675</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Anacystis nidulans r2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Non~~-~~specific serine/threonine protein kinase~~]]	+	[[Category: Synechococcus elongatus PCC 7942 = FACHB-805]]
-	[[Category: Abe, J]]	+	[[Category: Abe J]]
-	[[Category: Akiyama, S]]	+	[[Category: Akiyama S]]
-	[[Category: Furuike, Y]]	+	[[Category: Furuike Y]]
-	[[Category: Mukaiyama, A]]	+	[[Category: Mukaiyama A]]
-	~~[[Category: Clock protein]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:24, 21 August 2019

OCA — Wed, 21 Aug 2019 06:24:49 GMT

←Older revision		Revision as of 06:24, 21 August 2019
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	==Crystal Structure of N-terminal C1 domain of KaiC==		==Crystal Structure of N-terminal C1 domain of KaiC==
-	<StructureSection load='5yz8' size='340' side='right' caption='[[5yz8]], [[Resolution\|resolution]] 2.81Å' scene=''>	+	<StructureSection load='5yz8' size='340' side='right'caption='[[5yz8]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yz8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yz8]] is a 6 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=5YZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZ8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KAIC, SYNPCC7942_1216, SEE0011 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1140 Anacystis nidulans R2])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=5yz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz8 OCA], [http://pdbe.org/5yz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz8 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz8 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=5yz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz8 OCA], [http://pdbe.org/5yz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz8 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz8 ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/KAIC_SYNE7 KAIC_SYNE7]] 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.<ref>PMID:9727980</ref> <ref>PMID:14709675</ref>		[[http://www.uniprot.org/uniprot/KAIC_SYNE7 KAIC_SYNE7]] 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.<ref>PMID:9727980</ref> <ref>PMID:14709675</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	KaiC, the core oscillator of the cyanobacterial circadian clock, is composed of an N-terminal C1 domain and a C-terminal C2 domain, and assembles into a double-ring hexamer upon ATP binding. Cyclic phosphorylation and dephosphorylation at Ser431 and Thr432 in the C2 domain proceed with a period of approximately 24 h in the presence of other clock proteins, KaiA and KaiB, but recent studies have revealed a crucial role for the C1 ring in determining the cycle period. In this study, we mapped dynamic structural changes of the C1 ring in solution using a combination of site-directed tryptophan mutagenesis and fluorescence spectroscopy. We found that the C1 ring undergoes a structural transition, coupled with ATPase activity and the phosphorylation state, while maintaining its hexameric ring structure. This transition triggered by ATP hydrolysis in the C1 ring in specific phosphorylation states is a necessary event for recruitment of KaiB, limiting the overall rate of slow complex formation. Our results provide structural and kinetic insights into the C1-ring rearrangements governing the slow dynamics of the cyanobacterial circadian clock.
		+
		+	Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB.,Mukaiyama A, Furuike Y, Abe J, Yamashita E, Kondo T, Akiyama S Sci Rep. 2018 Jun 11;8(1):8803. doi: 10.1038/s41598-018-27131-8. PMID:29892030<ref>PMID:29892030</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yz8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Circadian clock protein 3D structures\|Circadian clock protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Anacystis nidulans r2]]
		+	[[Category: Large Structures]]
	[[Category: Non-specific serine/threonine protein kinase]]		[[Category: Non-specific serine/threonine protein kinase]]
	[[Category: Abe, J]]		[[Category: Abe, J]]

OCA at 08:09, 30 January 2019

OCA — Wed, 30 Jan 2019 08:09:51 GMT

←Older revision		Revision as of 08:09, 30 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yz8 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal Structure of N-terminal C1 domain of KaiC==
-		+	<StructureSection load='5yz8' size='340' side='right' caption='[[5yz8]], [[Resolution\|resolution]] 2.81Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yz8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZ8 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=5yz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz8 OCA], [http://pdbe.org/5yz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz8 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KAIC_SYNE7 KAIC_SYNE7]] 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.<ref>PMID:9727980</ref> <ref>PMID:14709675</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Non-specific serine/threonine protein kinase]]
		+	[[Category: Abe, J]]
		+	[[Category: Akiyama, S]]
		+	[[Category: Furuike, Y]]
		+	[[Category: Mukaiyama, A]]
		+	[[Category: Clock protein]]
		+	[[Category: Transferase]]

OCA at 04:50, 3 January 2018

OCA — Wed, 03 Jan 2018 04:50:44 GMT

←Older revision		Revision as of 04:50, 3 January 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yz8 is ON HOLD	+	The entry 5yz8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5yz8" [edit=sysop:move=sysop]

OCA — Wed, 20 Dec 2017 04:52:55 GMT

Protected "5yz8" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yz8 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Dec 2017 04:52:54 GMT

New page: '''Unreleased structure''' The entry 5yz8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yz8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]