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3tvk

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Current revision (13:40, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3tvk' size='340' side='right'caption='[[3tvk]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3tvk' size='340' side='right'caption='[[3tvk]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<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>
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<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>
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<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>
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<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>
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<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 ==
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[[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>
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3tvk" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Diguanylate cyclase]]
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[[Category: Escherichia coli K-12]]
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[[Category: Ecoli]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Schirmer, T]]
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[[Category: Schirmer T]]
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[[Category: Zaehringer, F]]
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[[Category: Zaehringer F]]
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[[Category: C-di-gmp]]
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[[Category: Putative zinc sensor]]
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[[Category: Transferase]]
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Current revision

Diguanylate cyclase domain of DgcZ

PDB ID 3tvk

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