3tvk - Revision history

OCA at 13:40, 14 March 2024

2024-03-14T13:40:44Z

←Older revision		Revision as of 13:40, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3tvk' size='340' side='right'caption='[[3tvk]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3tvk' size='340' side='right'caption='[[3tvk]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tvk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tvk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVK 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=TAR:D(-)-TARTARIC+ACID'>TAR</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]] 1.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3t9o\|3t9o]]</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=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1535, JW1528, ydeG, ydeH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diguanylate_cyclase Diguanylate cyclase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.65 2.7.7.65] </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=3tvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvk OCA], [https://pdbe.org/3tvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tvk RCSB], [https://www.ebi.ac.uk/pdbsum/3tvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvk 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=3tvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvk OCA], [https://pdbe.org/3tvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tvk RCSB], [https://www.ebi.ac.uk/pdbsum/3tvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~YDEH_ECOLI YDEH_ECOLI~~]~~] A diguanylate cyclase~~, ~~overexpression~~ leads to a strong repression of swimming; swimming returnes to normal when residues 206-207 are both mutated to Ala. Overexpression also leads to a reduction in flagellar abundance and a 20-fold increase in c-di-GMP levels in vivo. Required for aminoglycoside-mediated induction of biofilm formation, it also plays a lesser role in biofilm production in response to other classes of translation inhibitors. The c-di-GMP produced by this enzyme up-regulates poly-GlcNAc production as well as the biofilm synthesis protein PgaD, although c-di-GMP is probably not the main inducing principle. ~~Cyclic~~-di-GMP is a second messenger which controls cell surface-associated traits in bacteria.<ref>PMID:19460094</ref>	+	[https://www.uniprot.org/uniprot/DGCZ_ECOLI DGCZ_ECOLI] Catalyzes the synthesis of cyclic-di-GMP (c-di-GMP) via the condensation of 2 GTP molecules (PubMed:18713317, PubMed:19460094, PubMed:20582742). May act as a zinc sensor that controls, via c-di-GMP, post-translational events (PubMed:23769666). Overexpression leads to a strong repression of swimming; swimming returnes to normal when residues 206-207 are both mutated to Ala. Overexpression also leads to a reduction in flagellar abundance and a 20-fold increase in c-di-GMP levels in vivo. Required for aminoglycoside-mediated induction of biofilm formation, it also plays a lesser role in biofilm production in response to other classes of translation inhibitors. The c-di-GMP produced by this enzyme up-regulates poly-GlcNAc production as well as the biofilm synthesis protein PgaD, although c-di-GMP is probably not the main inducing principle. C-di-GMP is a second messenger which controls cell surface-associated traits in bacteria (PubMed:19460094).<ref>PMID:19460094</ref> <ref>PMID:20582742</ref> <ref>PMID:23769666</ref> <ref>PMID:18713317</ref>
-	<~~div style="background-color:#fffaf0;"~~>	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Diguanylate cyclases synthesize the second messenger c-di-GMP, which in turn governs a plethora of physiological processes in bacteria. Although most diguanylate cyclases harbor sensory domains, their input signals are largely unknown. Here, we demonstrate that diguanylate cyclase DgcZ (YdeH) from Escherichia coli is regulated allosterically by zinc. Crystal structures show that the zinc ion is bound to the 3His/1Cys motif of the regulatory chemoreceptor zinc-binding domain, which mediates subunit contact within the dimeric enzyme. In vitro, zinc reversibly inhibits DgcZ with a subfemtomolar Ki constant. In vivo, bacterial biofilm formation is modulated by externally applied zinc in a DgcZ- and c-di-GMP-dependent fashion. The study outlines the structural principles of this zinc sensor. Zinc binding seems to regulate the activity of the catalytic GGDEF domains by impeding their mobility and thus preventing productive encounter of the two GTP substrates.	+
-		+
-	Structure and Signaling Mechanism of a Zinc-Sensory Diguanylate Cyclase.,Zahringer F, Lacanna E, Jenal U, Schirmer T, Boehm A Structure. 2013 Jun 11. pii: S0969-2126(13)00156-1. doi:, 10.1016/j.str.2013.04.026. PMID:~~23769666~~<ref>PMID:23769666</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3tvk" style="background-color~~:~~#fffaf0;">~~</~~div~~>	+

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Diguanylate cyclase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Schirmer, T]]	+	[[Category: Schirmer T]]
-	[[Category: Zaehringer, F]]	+	[[Category: Zaehringer F]]
-	~~[[Category: C-di-gmp]]~~	+
-	~~[[Category: Putative zinc sensor]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:47, 13 July 2022

2022-07-13T05:47:14Z

←Older revision		Revision as of 05:47, 13 July 2022
Line 1:		Line 1:

	==Diguanylate cyclase domain of DgcZ==		==Diguanylate cyclase domain of DgcZ==
-	<StructureSection load='3tvk' size='340' side='right' caption='[[3tvk]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3tvk' size='340' side='right'caption='[[3tvk]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tvk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tvk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TVK 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=TAR:D(-)-TARTARIC+ACID'>TAR</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=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t9o\|3t9o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3t9o\|3t9o]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1535, JW1528, ydeG, ydeH ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1535, JW1528, ydeG, ydeH ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Diguanylate_cyclase Diguanylate cyclase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.65 2.7.7.65] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diguanylate_cyclase Diguanylate cyclase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.65 2.7.7.65] </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=3tvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvk OCA], [~~http~~://pdbe.org/3tvk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tvk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tvk PDBsum]</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=3tvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvk OCA], [https://pdbe.org/3tvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tvk RCSB], [https://www.ebi.ac.uk/pdbsum/3tvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tvk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/YDEH_ECOLI YDEH_ECOLI]] A diguanylate cyclase, overexpression leads to a strong repression of swimming; swimming returnes to normal when residues 206-207 are both mutated to Ala. Overexpression also leads to a reduction in flagellar abundance and a 20-fold increase in c-di-GMP levels in vivo. Required for aminoglycoside-mediated induction of biofilm formation, it also plays a lesser role in biofilm production in response to other classes of translation inhibitors. The c-di-GMP produced by this enzyme up-regulates poly-GlcNAc production as well as the biofilm synthesis protein PgaD, although c-di-GMP is probably not the main inducing principle. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria.<ref>PMID:19460094</ref>	+	[[https://www.uniprot.org/uniprot/YDEH_ECOLI YDEH_ECOLI]] A diguanylate cyclase, overexpression leads to a strong repression of swimming; swimming returnes to normal when residues 206-207 are both mutated to Ala. Overexpression also leads to a reduction in flagellar abundance and a 20-fold increase in c-di-GMP levels in vivo. Required for aminoglycoside-mediated induction of biofilm formation, it also plays a lesser role in biofilm production in response to other classes of translation inhibitors. The c-di-GMP produced by this enzyme up-regulates poly-GlcNAc production as well as the biofilm synthesis protein PgaD, although c-di-GMP is probably not the main inducing principle. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria.<ref>PMID:19460094</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 30:		Line 30:
	[[Category: Diguanylate cyclase]]		[[Category: Diguanylate cyclase]]
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Schirmer, T]]		[[Category: Schirmer, T]]
	[[Category: Zaehringer, F]]		[[Category: Zaehringer, F]]

OCA at 19:48, 10 May 2016

2016-05-10T19:48:26Z

←Older revision		Revision as of 19:48, 10 May 2016
Line 1:		Line 1:
-	==Diguanylate cyclase domain of ~~YdeH~~==	+
		+	==Diguanylate cyclase domain of DgcZ==
	<StructureSection load='3tvk' size='340' side='right' caption='[[3tvk]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3tvk' size='340' side='right' caption='[[3tvk]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TVK 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=TAR:D(-)-TARTARIC+ACID'>TAR</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=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t9o\|3t9o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t9o\|3t9o]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1535, JW1528, ydeG, ydeH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1535, JW1528, ydeG, ydeH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Diguanylate_kinase~~ Diguanylate ~~kinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.65 2.7.7.65] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diguanylate_cyclase Diguanylate cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.65 2.7.7.65] </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=3tvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tvk RCSB], [http://www.ebi.ac.uk/pdbsum/3tvk 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=3tvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvk OCA], [http://pdbe.org/3tvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tvk RCSB], [http://www.ebi.ac.uk/pdbsum/3tvk PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YDEH_ECOLI YDEH_ECOLI]] A diguanylate cyclase, overexpression leads to a strong repression of swimming; swimming returnes to normal when residues 206-207 are both mutated to Ala. Overexpression also leads to a reduction in flagellar abundance and a 20-fold increase in c-di-GMP levels in vivo. Required for aminoglycoside-mediated induction of biofilm formation, it also plays a lesser role in biofilm production in response to other classes of translation inhibitors. The c-di-GMP produced by this enzyme up-regulates poly-GlcNAc production as well as the biofilm synthesis protein PgaD, although c-di-GMP is probably not the main inducing principle. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria.<ref>PMID:19460094</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Diguanylate cyclases synthesize the second messenger c-di-GMP, which in turn governs a plethora of physiological processes in bacteria. Although most diguanylate cyclases harbor sensory domains, their input signals are largely unknown. Here, we demonstrate that diguanylate cyclase DgcZ (YdeH) from Escherichia coli is regulated allosterically by zinc. Crystal structures show that the zinc ion is bound to the 3His/1Cys motif of the regulatory chemoreceptor zinc-binding domain, which mediates subunit contact within the dimeric enzyme. In vitro, zinc reversibly inhibits DgcZ with a subfemtomolar Ki constant. In vivo, bacterial biofilm formation is modulated by externally applied zinc in a DgcZ- and c-di-GMP-dependent fashion. The study outlines the structural principles of this zinc sensor. Zinc binding seems to regulate the activity of the catalytic GGDEF domains by impeding their mobility and thus preventing productive encounter of the two GTP substrates.
		+
		+	Structure and Signaling Mechanism of a Zinc-Sensory Diguanylate Cyclase.,Zahringer F, Lacanna E, Jenal U, Schirmer T, Boehm A Structure. 2013 Jun 11. pii: S0969-2126(13)00156-1. doi:, 10.1016/j.str.2013.04.026. PMID:23769666<ref>PMID:23769666</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3tvk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Diguanylate cyclase\|Diguanylate cyclase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Diguanylate ~~kinase~~]]	+	[[Category: Diguanylate cyclase]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Schirmer, T]]		[[Category: Schirmer, T]]
	[[Category: Zaehringer, F]]		[[Category: Zaehringer, F]]
	[[Category: C-di-gmp]]		[[Category: C-di-gmp]]
-	[[Category: Diguanylate cyclase]]
	[[Category: Putative zinc sensor]]		[[Category: Putative zinc sensor]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 11:09, 4 January 2015

2015-01-04T11:09:17Z

←Older revision		Revision as of 11:09, 4 January 2015
Line 1:		Line 1:
-	~~[[Image:3tvk.jpg\|left\|200px]]~~	+	==Diguanylate cyclase domain of YdeH==
-		+	<StructureSection load='3tvk' size='340' side='right' caption='[[3tvk]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~{{STRUCTURE_3tvk\| PDB=3tvk \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3tvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TVK FirstGlance]. <br>
-	===Diguanylate cyclase domain of YdeH===	+	</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=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t9o\|3t9o]]</td></tr>
-		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b1535, JW1528, ydeG, ydeH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	==~~About this Structure~~==	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diguanylate_kinase Diguanylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.65 2.7.7.65] </span></td></tr>
-	[[3tvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA].	+	<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=3tvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tvk RCSB], [http://www.ebi.ac.uk/pdbsum/3tvk PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Diguanylate kinase]]		[[Category: Diguanylate kinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Schirmer, T.]]	+	[[Category: Schirmer, T]]
-	[[Category: Zaehringer, F.]]	+	[[Category: Zaehringer, F]]
	[[Category: C-di-gmp]]		[[Category: C-di-gmp]]
	[[Category: Diguanylate cyclase]]		[[Category: Diguanylate cyclase]]
	[[Category: Putative zinc sensor]]		[[Category: Putative zinc sensor]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:19, 3 October 2012

2012-10-03T06:19:42Z

←Older revision		Revision as of 06:19, 3 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tvk.jpg\|left\|200px]]

-	~~The entry~~ 3tvk ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3tvk\| PDB=3tvk \| SCENE= }}

-	~~Authors: Zaehringer, F., Schirmer, T.~~	+	===Diguanylate cyclase domain of YdeH===

-	~~Description~~: Diguanylate cyclase ~~domain of YdeH~~	+
		+	==About this Structure==
		+	[[3tvk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TVK OCA].
		+	[[Category: Diguanylate kinase]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Schirmer, T.]]
		+	[[Category: Zaehringer, F.]]
		+	[[Category: C-di-gmp]]
		+	[[Category: Diguanylate cyclase]]
		+	[[Category: Putative zinc sensor]]
		+	[[Category: Transferase]]

OCA at 08:44, 30 October 2011

2011-10-30T08:44:25Z

←Older revision		Revision as of 08:44, 30 October 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3tvk is ON HOLD	+	The entry 3tvk is ON HOLD until Paper Publication

	Authors: Zaehringer, F., Schirmer, T.		Authors: Zaehringer, F., Schirmer, T.

	Description: Diguanylate cyclase domain of YdeH		Description: Diguanylate cyclase domain of YdeH

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

2011-09-28T05:18:17Z

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

←Older revision

Revision as of 05:18, 28 September 2011

OCA: New page: '''Unreleased structure''' The entry 3tvk is ON HOLD Authors: Zaehringer, F., Schirmer, T. Description: Diguanylate cyclase domain of YdeH

2011-09-28T05:18:16Z

New page: '''Unreleased structure''' The entry 3tvk is ON HOLD Authors: Zaehringer, F., Schirmer, T. Description: Diguanylate cyclase domain of YdeH

New page

'''Unreleased structure'''

The entry 3tvk is ON HOLD

Authors: Zaehringer, F., Schirmer, T.

Description: Diguanylate cyclase domain of YdeH