3i5b - Revision history

OCA at 10:03, 21 February 2024

OCA — Wed, 21 Feb 2024 10:03:49 GMT

←Older revision		Revision as of 10:03, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3i5b' size='340' side='right'caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='3i5b' size='340' side='right'caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I5B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I5B FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=TLA:L(+)~~-~~TARTARIC+ACID'>TLA</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]] 2.043Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3i5a\|3i5a]], [[3i5c\|3i5c]]~~</~~div~~>~~</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~</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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [https://pdbe.org/3i5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [https://www.ebi.ac.uk/pdbsum/3i5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5b 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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [https://pdbe.org/3i5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [https://www.ebi.ac.uk/pdbsum/3i5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5b ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9HXT9_PSEAE Q9HXT9_PSEAE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3i5b 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=3i5b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The bacterial second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) controls secretion, cell adhesion, and motility, leading to biofilm formation and increased cytotoxicity. Diguanylate cyclases containing GGDEF and phosphodiesterases containing EAL or HD-GYP domains have been identified as the enzymes controlling cellular c-di-GMP levels, yet less is known regarding the molecular mechanisms governing regulation and signaling specificity. We recently determined a product-inhibition pathway for the diguanylate cyclase response regulator WspR from Pseudomonas, a potent molecular switch that controls biofilm formation. In WspR, catalytic activity is modulated by a helical stalk motif that connects its phospho-receiver and GGDEF domains. The stalks facilitate the formation of distinct oligomeric states that contribute to both activation and autoinhibition. Here, we provide novel insights into the regulation of diguanylate cyclase activity in WspR based on the crystal structures of full-length WspR, the isolated GGDEF domain, and an artificially dimerized catalytic domain. The structures highlight that inhibition is achieved by restricting the mobility of rigid GGDEF domains, mediated by c-di-GMP binding to an inhibitory site at the GGDEF domain. Kinetic measurements and biochemical characterization corroborate a model in which the activation of WspR requires the formation of a tetrameric species. Tetramerization occurs spontaneously at high protein concentration or upon addition of the phosphomimetic compound beryllium fluoride. Our analyses elucidate common and WspR-specific mechanisms for the fine-tuning of diguanylate cyclase activity.
-
-	Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR.,De N, Navarro MV, Raghavan RV, Sondermann H J Mol Biol. 2009 Oct 30;393(3):619-33. Epub 2009 Aug 18. PMID:19695263<ref>PMID:19695263</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3i5b" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Response regulator 3D structure\|Response regulator 3D structure]]		*[[Response regulator 3D structure\|Response regulator 3D structure]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: De, N]]	+	[[Category: De N]]
-	[[Category: Navarro~~, M V.A S~~]]	+	[[Category: Navarro MVAS]]
-	[[Category: Sondermann, H]]	+	[[Category: Sondermann H]]
-	~~[[Category: C-di-gmp]]~~	+
-	~~[[Category: Ggdef]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 10:58, 13 April 2022

OCA — Wed, 13 Apr 2022 10:58:04 GMT

←Older revision		Revision as of 10:58, 13 April 2022
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	==Crystal structure of the isolated GGDEF domain of WpsR from Pseudomonas aeruginosa==		==Crystal structure of the isolated GGDEF domain of WpsR from Pseudomonas aeruginosa==
-	<StructureSection load='3i5b' size='340' side='right' caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='3i5b' size='340' side='right'caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3I5B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I5B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5a\|3i5a]], [[3i5c\|3i5c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i5a\|3i5a]], [[3i5c\|3i5c]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [~~http~~://pdbe.org/3i5b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3i5b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5b 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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [https://pdbe.org/3i5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [https://www.ebi.ac.uk/pdbsum/3i5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5b ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Response regulator\|Response regulator]]	+	*[[Response regulator 3D structure\|Response regulator 3D structure]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pseae]]		[[Category: Pseae]]
	[[Category: De, N]]		[[Category: De, N]]

OCA at 09:38, 19 December 2018

OCA — Wed, 19 Dec 2018 09:38:54 GMT

←Older revision		Revision as of 09:38, 19 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of the isolated GGDEF domain of WpsR from Pseudomonas aeruginosa==		==Crystal structure of the isolated GGDEF domain of WpsR from Pseudomonas aeruginosa==
	<StructureSection load='3i5b' size='340' side='right' caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='3i5b' size='340' side='right' caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5a\|3i5a]], [[3i5c\|3i5c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5a\|3i5a]], [[3i5c\|3i5c]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [http://pdbe.org/3i5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [http://www.ebi.ac.uk/pdbsum/3i5b 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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [http://pdbe.org/3i5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [http://www.ebi.ac.uk/pdbsum/3i5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i5b ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/i5/3i5b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i5/3i5b_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 16:52, 9 February 2016

OCA — Tue, 09 Feb 2016 16:52:36 GMT

←Older revision		Revision as of 16:52, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3i5b' size='340' side='right' caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='3i5b' size='340' side='right' caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa Pseudomonas aeruginosa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5a\|3i5a]], [[3i5c\|3i5c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5a\|3i5a]], [[3i5c\|3i5c]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~287 Pseudomonas aeruginosa~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [http://www.ebi.ac.uk/pdbsum/3i5b 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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [http://pdbe.org/3i5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [http://www.ebi.ac.uk/pdbsum/3i5b PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=3i5b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3i5b" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseudomonas aeruginosa~~]]	+	[[Category: Pseae]]
	[[Category: De, N]]		[[Category: De, N]]
	[[Category: Navarro, M V.A S]]		[[Category: Navarro, M V.A S]]

OCA at 10:20, 20 January 2015

OCA — Tue, 20 Jan 2015 10:20:13 GMT

←Older revision		Revision as of 10:20, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5B FirstGlance]. <br>		<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5B FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5a\|3i5a]], [[3i5c\|3i5c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5a\|3i5a]], [[3i5c\|3i5c]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [http://www.ebi.ac.uk/pdbsum/3i5b 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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [http://www.ebi.ac.uk/pdbsum/3i5b PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
-	[[Category: De, N.]]	+	[[Category: De, N]]
-	[[Category: Navarro, M V.A S.]]	+	[[Category: Navarro, M V.A S]]
-	[[Category: Sondermann, H.]]	+	[[Category: Sondermann, H]]
	[[Category: C-di-gmp]]		[[Category: C-di-gmp]]
	[[Category: Ggdef]]		[[Category: Ggdef]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

OCA at 12:22, 29 September 2014

OCA — Mon, 29 Sep 2014 12:22:20 GMT

←Older revision		Revision as of 12:22, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3i5b.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the isolated GGDEF domain of WpsR from Pseudomonas aeruginosa==
		+	<StructureSection load='3i5b' size='340' side='right' caption='[[3i5b]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3i5b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I5B FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i5a\|3i5a]], [[3i5c\|3i5c]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA3702, wspR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])</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=3i5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i5b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i5b RCSB], [http://www.ebi.ac.uk/pdbsum/3i5b 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/i5/3i5b_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 ==
		+	The bacterial second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) controls secretion, cell adhesion, and motility, leading to biofilm formation and increased cytotoxicity. Diguanylate cyclases containing GGDEF and phosphodiesterases containing EAL or HD-GYP domains have been identified as the enzymes controlling cellular c-di-GMP levels, yet less is known regarding the molecular mechanisms governing regulation and signaling specificity. We recently determined a product-inhibition pathway for the diguanylate cyclase response regulator WspR from Pseudomonas, a potent molecular switch that controls biofilm formation. In WspR, catalytic activity is modulated by a helical stalk motif that connects its phospho-receiver and GGDEF domains. The stalks facilitate the formation of distinct oligomeric states that contribute to both activation and autoinhibition. Here, we provide novel insights into the regulation of diguanylate cyclase activity in WspR based on the crystal structures of full-length WspR, the isolated GGDEF domain, and an artificially dimerized catalytic domain. The structures highlight that inhibition is achieved by restricting the mobility of rigid GGDEF domains, mediated by c-di-GMP binding to an inhibitory site at the GGDEF domain. Kinetic measurements and biochemical characterization corroborate a model in which the activation of WspR requires the formation of a tetrameric species. Tetramerization occurs spontaneously at high protein concentration or upon addition of the phosphomimetic compound beryllium fluoride. Our analyses elucidate common and WspR-specific mechanisms for the fine-tuning of diguanylate cyclase activity.

-	~~{{STRUCTURE_3i5b\| PDB=3i5b \| SCENE= }}~~	+	Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR.,De N, Navarro MV, Raghavan RV, Sondermann H J Mol Biol. 2009 Oct 30;393(3):619-33. Epub 2009 Aug 18. PMID:19695263<ref>PMID:19695263</ref>

-	~~===Crystal structure~~ of the ~~isolated GGDEF domain of WpsR from Pseudomonas aeruginosa===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19695263}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3i5b]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA].~~	+

	==See Also==		==See Also==
	*[[Response regulator\|Response regulator]]		*[[Response regulator\|Response regulator]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019695263<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Pseudomonas aeruginosa]]		[[Category: Pseudomonas aeruginosa]]
	[[Category: De, N.]]		[[Category: De, N.]]

OCA at 14:31, 20 October 2012

OCA — Sat, 20 Oct 2012 14:31:09 GMT

←Older revision		Revision as of 14:31, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3i5b]] is a 2 chain structure ~~of [[Response regulator]]~~ with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA].	+	[[3i5b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA].

	==See Also==		==See Also==

OCA: Protected "3i5b" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 15:24:14 GMT

Protected "3i5b" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:24, 26 July 2012

OCA at 15:24, 26 July 2012

OCA — Thu, 26 Jul 2012 15:24:12 GMT

←Older revision		Revision as of 15:24, 26 July 2012
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-	{{Seed}}
	[[Image:3i5b.png\|left\|200px]]		[[Image:3i5b.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3i5b", 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_3i5b\| PDB=3i5b \| SCENE= }}		{{STRUCTURE_3i5b\| PDB=3i5b \| SCENE= }}

	===Crystal structure of the isolated GGDEF domain of WpsR from Pseudomonas aeruginosa===		===Crystal structure of the isolated GGDEF domain of WpsR from Pseudomonas aeruginosa===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19695263}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19695263 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19695263}}		{{ABSTRACT_PUBMED_19695263}}

	==About this Structure==		==About this Structure==
-	~~3I5B~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/~~Pseudomonas_aeruginosa_pao1~~ Pseudomonas aeruginosa ~~pao1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA].	+	[[3i5b]] is a 2 chain structure of [[Response regulator]] with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA].
		+
		+	==See Also==
		+	*[[Response regulator\|Response regulator]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19695263~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019695263</ref><references group="xtra"/>
-	[[Category: Pseudomonas aeruginosa ~~pao1~~]]	+	[[Category: Pseudomonas aeruginosa]]
	[[Category: De, N.]]		[[Category: De, N.]]
	[[Category: Navarro, M V.A S.]]		[[Category: Navarro, M V.A S.]]
Line 31:		Line 22:
	[[Category: Ggdef]]		[[Category: Ggdef]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Aug 12 00:06:21 2010''

OCA at 19:59, 11 August 2010

OCA — Wed, 11 Aug 2010 19:59:04 GMT

←Older revision		Revision as of 19:59, 11 August 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3I5B is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_pao1 Pseudomonas aeruginosa pao1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA].	+	3I5B is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_pao1 Pseudomonas aeruginosa pao1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I5B OCA].

	==Reference==		==Reference==
Line 32:		Line 32:
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Sep 3 15~~:57:~~55 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Aug 12 00:06:21 2010''