5idj - Revision history

OCA at 07:47, 7 February 2024

OCA — Wed, 07 Feb 2024 07:47:51 GMT

←Older revision		Revision as of 07:47, 7 February 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q9X688_CAUVI Q9X688_CAUVI]		[https://www.uniprot.org/uniprot/Q9X688_CAUVI Q9X688_CAUVI]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Histidine kinases are key components of regulatory networks in bacteria. Although many of these enzymes are bifunctional, mediating both phosphorylation and dephosphorylation of downstream targets, the molecular details of this central regulatory switch are unclear. We showed recently that the universal second messenger cyclic di-guanosine monophosphate (c-di-GMP) drives Caulobacter crescentus cell cycle progression by forcing the cell cycle kinase CckA from its default kinase into phosphatase mode. We use a combination of structure determination, modeling, and functional analysis to demonstrate that c-di-GMP reciprocally regulates the two antagonistic CckA activities through noncovalent cross-linking of the catalytic domain with the dimerization histidine phosphotransfer (DHp) domain. We demonstrate that both c-di-GMP and ADP (adenosine diphosphate) promote phosphatase activity and propose that c-di-GMP stabilizes the ADP-bound quaternary structure, which allows the receiver domain to access the dimeric DHp stem for dephosphorylation. In silico analyses predict that c-di-GMP control is widespread among bacterial histidine kinases, arguing that it can replace or modulate canonical transmembrane signaling.
-
-	Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.,Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T Sci Adv. 2016 Sep 16;2(9):e1600823. doi: 10.1126/sciadv.1600823. eCollection 2016, Sep. PMID:27652341<ref>PMID:27652341</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5idj" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:22, 28 June 2023

OCA — Wed, 28 Jun 2023 21:22:42 GMT

←Older revision		Revision as of 21:22, 28 June 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5idj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IDJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5idj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IDJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 3.02Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5idj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5idj OCA], [https://pdbe.org/5idj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5idj RCSB], [https://www.ebi.ac.uk/pdbsum/5idj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5idj 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=5idj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5idj OCA], [https://pdbe.org/5idj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5idj RCSB], [https://www.ebi.ac.uk/pdbsum/5idj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5idj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q9X688_CAUVI Q9X688_CAUVI]]	+	[https://www.uniprot.org/uniprot/Q9X688_CAUVI Q9X688_CAUVI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:49, 7 September 2022

OCA — Wed, 07 Sep 2022 18:49:37 GMT

←Older revision		Revision as of 18:49, 7 September 2022
Line 9:		Line 9:
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/Q9X688_CAUVI Q9X688_CAUVI]]		[[https://www.uniprot.org/uniprot/Q9X688_CAUVI Q9X688_CAUVI]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Histidine kinases are key components of regulatory networks in bacteria. Although many of these enzymes are bifunctional, mediating both phosphorylation and dephosphorylation of downstream targets, the molecular details of this central regulatory switch are unclear. We showed recently that the universal second messenger cyclic di-guanosine monophosphate (c-di-GMP) drives Caulobacter crescentus cell cycle progression by forcing the cell cycle kinase CckA from its default kinase into phosphatase mode. We use a combination of structure determination, modeling, and functional analysis to demonstrate that c-di-GMP reciprocally regulates the two antagonistic CckA activities through noncovalent cross-linking of the catalytic domain with the dimerization histidine phosphotransfer (DHp) domain. We demonstrate that both c-di-GMP and ADP (adenosine diphosphate) promote phosphatase activity and propose that c-di-GMP stabilizes the ADP-bound quaternary structure, which allows the receiver domain to access the dimeric DHp stem for dephosphorylation. In silico analyses predict that c-di-GMP control is widespread among bacterial histidine kinases, arguing that it can replace or modulate canonical transmembrane signaling.
		+
		+	Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.,Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T Sci Adv. 2016 Sep 16;2(9):e1600823. doi: 10.1126/sciadv.1600823. eCollection 2016, Sep. PMID:27652341<ref>PMID:27652341</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5idj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:43, 7 September 2022

OCA — Wed, 07 Sep 2022 16:43:20 GMT

←Older revision		Revision as of 16:43, 7 September 2022
Line 1:		Line 1:

	==Bifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP/Mg2+==		==Bifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP/Mg2+==
-	<StructureSection load='5idj' size='340' side='right' caption='[[5idj]], [[Resolution\|resolution]] 3.01Å' scene=''>	+	<StructureSection load='5idj' size='340' side='right'caption='[[5idj]], [[Resolution\|resolution]] 3.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5idj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cauvi Cauvi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IDJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5idj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IDJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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">cckA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155892 CAUVI])~~</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=5idj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5idj OCA], [https://pdbe.org/5idj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5idj RCSB], [https://www.ebi.ac.uk/pdbsum/5idj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5idj 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=5idj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5idj OCA], [~~http~~://pdbe.org/5idj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5idj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5idj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5idj ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/Q9X688_CAUVI Q9X688_CAUVI]]
-	Histidine kinases are key components of regulatory networks in bacteria. Although many of these enzymes are bifunctional, mediating both phosphorylation and dephosphorylation of downstream targets, the molecular details of this central regulatory switch are unclear. We showed recently that the universal second messenger cyclic di-guanosine monophosphate (c-di-GMP) drives Caulobacter crescentus cell cycle progression by forcing the cell cycle kinase CckA from its default kinase into phosphatase mode. We use a combination of structure determination, modeling, and functional analysis to demonstrate that c-di-GMP reciprocally regulates the two antagonistic CckA activities through noncovalent cross-linking of the catalytic domain with the dimerization histidine phosphotransfer (DHp) domain. We demonstrate that both c-di-GMP and ADP (adenosine diphosphate) promote phosphatase activity and propose that c-di-GMP stabilizes the ADP-bound quaternary structure, which allows the receiver domain to access the dimeric DHp stem for dephosphorylation. In silico analyses predict that c-di-GMP control is widespread among bacterial histidine kinases, arguing that it can replace or modulate canonical transmembrane signaling.	+
-		+
-	~~Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.,Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T Sci Adv. 2016 Sep 16;2(9)~~:~~e1600823. doi: 10.1126~~/~~sciadv.1600823. eCollection 2016, Sep. PMID:27652341<ref>PMID:27652341<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5idj" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cauvi~~]]	+	[[Category: Caulobacter vibrioides]]
-	[[Category: ~~Dubey, B N~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Schirmer, T~~]]	+	[[Category: Dubey BN]]
-	[[Category: ~~Bifunctional]]~~	+	[[Category: Schirmer T]]
-	~~[[Category: Histidine kinase]]~~	+
-	~~[[Category: Phosphatase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:22, 24 October 2018

OCA — Wed, 24 Oct 2018 06:22:59 GMT

←Older revision		Revision as of 06:22, 24 October 2018
Line 3:		Line 3:
	<StructureSection load='5idj' size='340' side='right' caption='[[5idj]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='5idj' size='340' side='right' caption='[[5idj]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5idj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IDJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5idj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvi Cauvi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IDJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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">cckA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=155892 CAUVI])</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=5idj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5idj OCA], [http://pdbe.org/5idj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5idj RCSB], [http://www.ebi.ac.uk/pdbsum/5idj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5idj 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=5idj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5idj OCA], [http://pdbe.org/5idj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5idj RCSB], [http://www.ebi.ac.uk/pdbsum/5idj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5idj ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cauvi]]
	[[Category: Dubey, B N]]		[[Category: Dubey, B N]]
	[[Category: Schirmer, T]]		[[Category: Schirmer, T]]

OCA at 21:27, 5 October 2016

OCA — Wed, 05 Oct 2016 21:27:27 GMT

←Older revision		Revision as of 21:27, 5 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5idj is ~~ON HOLD~~	+	==Bifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP/Mg2+==
		+	<StructureSection load='5idj' size='340' side='right' caption='[[5idj]], [[Resolution\|resolution]] 3.01Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5idj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IDJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IDJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5idj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5idj OCA], [http://pdbe.org/5idj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5idj RCSB], [http://www.ebi.ac.uk/pdbsum/5idj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5idj ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Histidine kinases are key components of regulatory networks in bacteria. Although many of these enzymes are bifunctional, mediating both phosphorylation and dephosphorylation of downstream targets, the molecular details of this central regulatory switch are unclear. We showed recently that the universal second messenger cyclic di-guanosine monophosphate (c-di-GMP) drives Caulobacter crescentus cell cycle progression by forcing the cell cycle kinase CckA from its default kinase into phosphatase mode. We use a combination of structure determination, modeling, and functional analysis to demonstrate that c-di-GMP reciprocally regulates the two antagonistic CckA activities through noncovalent cross-linking of the catalytic domain with the dimerization histidine phosphotransfer (DHp) domain. We demonstrate that both c-di-GMP and ADP (adenosine diphosphate) promote phosphatase activity and propose that c-di-GMP stabilizes the ADP-bound quaternary structure, which allows the receiver domain to access the dimeric DHp stem for dephosphorylation. In silico analyses predict that c-di-GMP control is widespread among bacterial histidine kinases, arguing that it can replace or modulate canonical transmembrane signaling.

-	~~Authors:~~ Dubey, ~~B.N.~~, ~~Schirmer~~, T.	+	Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.,Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T Sci Adv. 2016 Sep 16;2(9):e1600823. doi: 10.1126/sciadv.1600823. eCollection 2016, Sep. PMID:27652341<ref>PMID:27652341</ref>

-	~~Description: Bifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP~~/~~Mg2+~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Dubey, B.N]]	+	<div class="pdbe-citations 5idj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dubey, B N]]
	[[Category: Schirmer, T]]		[[Category: Schirmer, T]]
		+	[[Category: Bifunctional]]
		+	[[Category: Histidine kinase]]
		+	[[Category: Phosphatase]]
		+	[[Category: Transferase]]

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

OCA — Wed, 02 Mar 2016 13:47:35 GMT

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

←Older revision

Revision as of 13:47, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5idj is ON HOLD Authors: Dubey, B.N., Schirmer, T. Description: Bifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP/Mg2+ [[Cate...

OCA — Wed, 02 Mar 2016 13:47:33 GMT

New page: '''Unreleased structure''' The entry 5idj is ON HOLD Authors: Dubey, B.N., Schirmer, T. Description: Bifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP/Mg2+ [[Cate...

New page

'''Unreleased structure'''

The entry 5idj is ON HOLD

Authors: Dubey, B.N., Schirmer, T.

Description: Bifunctional histidine kinase CckA (domains DHp-CA) in complex with ADP/Mg2+
[[Category: Unreleased Structures]]
[[Category: Dubey, B.N]]
[[Category: Schirmer, T]]