1w25 - Revision history

OCA at 09:09, 9 May 2024

OCA — Thu, 09 May 2024 09:09:29 GMT

←Older revision		Revision as of 09:09, 9 May 2024
Line 3:		Line 3:
	<StructureSection load='1w25' size='340' side='right'caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1w25' size='340' side='right'caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Cauvc Cauvc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_CB15 Caulobacter vibrioides CB15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W25 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wb4\|2wb4]], [[2v0n\|2v0n]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [https://pdbe.org/1w25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [https://www.ebi.ac.uk/pdbsum/1w25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w25 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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [https://pdbe.org/1w25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [https://www.ebi.ac.uk/pdbsum/1w25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w25 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~PLED_CAUCR PLED_CAUCR]~~] Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition ~~(By similarity)~~. Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger ~~(By similarity)~~.	+	[https://www.uniprot.org/uniprot/PLED_CAUVN PLED_CAUVN] Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition.<ref>PMID:12622822</ref> Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger.<ref>PMID:15075296</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cauvc~~]]	+	[[Category: Caulobacter vibrioides CB15]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chan, C]]	+	[[Category: Chan C]]
-	[[Category: Jenal, U]]	+	[[Category: Jenal U]]
-	[[Category: Schirmer, T]]	+	[[Category: Schirmer T]]
-	~~[[Category: Allosteric product inhibition]]~~	+
-	~~[[Category: Cyclic dinucleotide]]~~	+
-	~~[[Category: Cyclic-digmp]]~~	+
-	~~[[Category: Ggdef domain]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Two-component system~~]]	+

OCA at 15:24, 3 March 2021

OCA — Wed, 03 Mar 2021 15:24:49 GMT

←Older revision		Revision as of 15:24, 3 March 2021
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	<StructureSection load='1w25' size='340' side='right'caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1w25' size='340' side='right'caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1W25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W25 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wb4\|2wb4]], [[2v0n\|2v0n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wb4\|2wb4]], [[2v0n\|2v0n]]</div></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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [~~http~~://pdbe.org/1w25 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1w25 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1w25 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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [https://pdbe.org/1w25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [https://www.ebi.ac.uk/pdbsum/1w25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w25 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PLED_CAUCR PLED_CAUCR]] Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition (By similarity). Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger (By similarity).	+	[[https://www.uniprot.org/uniprot/PLED_CAUCR PLED_CAUCR]] Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition (By similarity). Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	==See Also==		==See Also==
	*[[Diguanylate cyclase\|Diguanylate cyclase]]		*[[Diguanylate cyclase\|Diguanylate cyclase]]
-	*[[PleD activation\|PleD activation]]	+	*[[Response regulator 3D structure\|Response regulator 3D structure]]
-	*[[PleD catalysis\|PleD catalysis]]	+
-	*[[Response regulator\|Response regulator]]	+
-	*[[Response regulator ~~PLED in complex with C-di-GMP~~\|Response regulator ~~PLED in complex with C-di-GMP~~]]	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:46, 10 May 2019

OCA — Fri, 10 May 2019 11:46:25 GMT

←Older revision		Revision as of 11:46, 10 May 2019
Line 1:		Line 1:

	==Response regulator PleD in complex with c-diGMP==		==Response regulator PleD in complex with c-diGMP==
-	<StructureSection load='1w25' size='340' side='right' caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='1w25' size='340' side='right'caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>
Line 41:		Line 41:
	</StructureSection>		</StructureSection>
	[[Category: Cauvc]]		[[Category: Cauvc]]
		+	[[Category: Large Structures]]
	[[Category: Chan, C]]		[[Category: Chan, C]]
	[[Category: Jenal, U]]		[[Category: Jenal, U]]

OCA at 07:36, 4 April 2018

OCA — Wed, 04 Apr 2018 07:36:06 GMT

←Older revision		Revision as of 07:36, 4 April 2018
Line 1:		Line 1:
-	==~~RESPONSE REGULATOR PLED IN COMPLEX WITH C~~-~~DIGMP~~==	+
		+	==Response regulator PleD in complex with c-diGMP==
	<StructureSection load='1w25' size='340' side='right' caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1w25' size='340' side='right' caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Caucr Caucr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,~~3AS~~,5S,~~7AR~~,9R,10R,~~10AS~~,12S,~~14AR~~)-3,5,10,12-~~TETRAHYDROXY~~-5,12-~~DIOXIDOOCTAHYDRO~~-2H,7H-~~DIFURO~~[3,2-D 3,2-J][1,3,7,9,2,8]~~TETRAOXADIPHOSPHACYCLODODECINE~~-2,9-~~DIYL~~]~~BIS~~(2-~~AMINO~~-1,9-~~DIHYDRO~~-6H-~~PURIN~~-6-~~ONE~~)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wb4\|2wb4]], [[2v0n\|2v0n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wb4\|2wb4]], [[2v0n\|2v0n]]</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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [http://pdbe.org/1w25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [http://www.ebi.ac.uk/pdbsum/1w25 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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [http://pdbe.org/1w25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [http://www.ebi.ac.uk/pdbsum/1w25 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1w25 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w2/1w25_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w2/1w25_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>
Line 39:		Line 40:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caucr~~]]	+	[[Category: Cauvc]]
	[[Category: Chan, C]]		[[Category: Chan, C]]
	[[Category: Jenal, U]]		[[Category: Jenal, U]]

OCA at 21:10, 7 February 2016

OCA — Sun, 07 Feb 2016 21:10:15 GMT

←Older revision		Revision as of 21:10, 7 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=1w25 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:00, 10 September 2015

OCA — Thu, 10 Sep 2015 05:00:59 GMT

←Older revision		Revision as of 05:00, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1w25' size='340' side='right' caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='1w25' size='340' side='right' caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Caulobacter_vibrioides Caulobacter vibrioides~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caucr Caucr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wb4\|2wb4]], [[2v0n\|2v0n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wb4\|2wb4]], [[2v0n\|2v0n]]</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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [http://www.ebi.ac.uk/pdbsum/1w25 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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [http://pdbe.org/1w25 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [http://www.ebi.ac.uk/pdbsum/1w25 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1w25" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
		+	*[[Diguanylate cyclase\|Diguanylate cyclase]]
	*[[PleD activation\|PleD activation]]		*[[PleD activation\|PleD activation]]
	*[[PleD catalysis\|PleD catalysis]]		*[[PleD catalysis\|PleD catalysis]]
Line 37:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caulobacter vibrioides~~]]	+	[[Category: Caucr]]
	[[Category: Chan, C]]		[[Category: Chan, C]]
	[[Category: Jenal, U]]		[[Category: Jenal, U]]

OCA at 18:16, 24 December 2014

OCA — Wed, 24 Dec 2014 18:16:34 GMT

←Older revision		Revision as of 18:16, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wb4\|2wb4]], [[2v0n\|2v0n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wb4\|2wb4]], [[2v0n\|2v0n]]</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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [http://www.ebi.ac.uk/pdbsum/1w25 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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [http://www.ebi.ac.uk/pdbsum/1w25 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PLED_CAUCR PLED_CAUCR]] Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition (By similarity). Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
-	[[Category: Chan, C.]]	+	[[Category: Chan, C]]
-	[[Category: Jenal, U.]]	+	[[Category: Jenal, U]]
-	[[Category: Schirmer, T.]]	+	[[Category: Schirmer, T]]
	[[Category: Allosteric product inhibition]]		[[Category: Allosteric product inhibition]]
	[[Category: Cyclic dinucleotide]]		[[Category: Cyclic dinucleotide]]

OCA at 19:08, 29 September 2014

OCA — Mon, 29 Sep 2014 19:08:09 GMT

←Older revision		Revision as of 19:08, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1w25\| PDB=1w25 \| SCENE= }}~~	+	==RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP==
-	===RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP===	+	<StructureSection load='1w25' size='340' side='right' caption='[[1w25]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_15569936}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W25 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)'>C2E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wb4\|2wb4]], [[2v0n\|2v0n]]</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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [http://www.ebi.ac.uk/pdbsum/1w25 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/w2/1w25_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 ==
		+	Recent discoveries suggest that a novel second messenger, bis-(3'-->5')-cyclic di-GMP (c-diGMP), is extensively used by bacteria to control multicellular behavior. Condensation of two GTP to the dinucleotide is catalyzed by the widely distributed diguanylate cyclase (DGC or GGDEF) domain that occurs in various combinations with sensory and/or regulatory modules. The crystal structure of the unorthodox response regulator PleD from Caulobacter crescentus, which consists of two CheY-like receiver domains and a DGC domain, has been solved in complex with the product c-diGMP. PleD forms a dimer with the CheY-like domains (the stem) mediating weak monomer-monomer interactions. The fold of the DGC domain is similar to adenylate cyclase, but the nucleotide-binding mode is substantially different. The guanine base is H-bonded to Asn-335 and Asp-344, whereas the ribosyl and alpha-phosphate moieties extend over the beta2-beta3-hairpin that carries the GGEEF signature motif. In the crystal, c-diGMP molecules are crosslinking active sites of adjacent dimers. It is inferred that, in solution, the two DGC domains of a dimer align in a two-fold symmetric way to catalyze c-diGMP synthesis. Two mutually intercalated c-diGMP molecules are found tightly bound at the stem-DGC interface. This allosteric site explains the observed noncompetitive product inhibition. We propose that product inhibition is due to domain immobilization and sets an upper limit for the concentration of this second messenger in the cell.

-	~~==About this Structure==~~	+	Structural basis of activity and allosteric control of diguanylate cyclase.,Chan C, Paul R, Samoray D, Amiot NC, Giese B, Jenal U, Schirmer T Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17084-9. Epub 2004 Nov 29. PMID:15569936<ref>PMID:15569936</ref>
-	~~[[1w25]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1W25 OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
Line 11:		Line 31:
	*[[Response regulator\|Response regulator]]		*[[Response regulator\|Response regulator]]
	*[[Response regulator PLED in complex with C-di-GMP\|Response regulator PLED in complex with C-di-GMP]]		*[[Response regulator PLED in complex with C-di-GMP\|Response regulator PLED in complex with C-di-GMP]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015569936<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
	[[Category: Chan, C.]]		[[Category: Chan, C.]]

OCA at 10:00, 11 March 2013

OCA — Mon, 11 Mar 2013 10:00:11 GMT

←Older revision		Revision as of 10:00, 11 March 2013
Line 1:		Line 1:
-	[[Image:1w25.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1w25", 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_1w25\| PDB=1w25 \| SCENE= }}		{{STRUCTURE_1w25\| PDB=1w25 \| SCENE= }}
-
	===RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP===		===RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15569936}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15569936 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15569936}}		{{ABSTRACT_PUBMED_15569936}}

Line 24:		Line 9:
	*[[PleD activation\|PleD activation]]		*[[PleD activation\|PleD activation]]
	*[[PleD catalysis\|PleD catalysis]]		*[[PleD catalysis\|PleD catalysis]]
		+	*[[Response regulator\|Response regulator]]
	*[[Response regulator PLED in complex with C-di-GMP\|Response regulator PLED in complex with C-di-GMP]]		*[[Response regulator PLED in complex with C-di-GMP\|Response regulator PLED in complex with C-di-GMP]]

OCA at 07:17, 13 June 2012

OCA — Wed, 13 Jun 2012 07:17:10 GMT

←Older revision		Revision as of 07:17, 13 June 2012
Line 24:		Line 24:
	*[[PleD activation\|PleD activation]]		*[[PleD activation\|PleD activation]]
	*[[PleD catalysis\|PleD catalysis]]		*[[PleD catalysis\|PleD catalysis]]
		+	*[[Response regulator PLED in complex with C-di-GMP\|Response regulator PLED in complex with C-di-GMP]]

	==Reference==		==Reference==