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3qyy

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Current revision (08:35, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3qyy' size='340' side='right'caption='[[3qyy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3qyy' size='340' side='right'caption='[[3qyy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3qyy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xance Xance]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3qyy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QYY 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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.9&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">XCC3486 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=340 XANCE])</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=3qyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyy OCA], [https://pdbe.org/3qyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyy RCSB], [https://www.ebi.ac.uk/pdbsum/3qyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyy 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=3qyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyy OCA], [https://pdbe.org/3qyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qyy RCSB], [https://www.ebi.ac.uk/pdbsum/3qyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyy ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q8P559_XANCP Q8P559_XANCP]
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Cyclic diguanosine monophosphate (c-di-GMP) is a key signalling molecule involved in regulating many important biological functions in bacteria. The synthesis of c-di-GMP is catalyzed by the GGDEF-domain-containing diguanylate cyclase (DGC), the activity of which is regulated by the binding of product at the allosteric inhibitory (I) site. However, a significant number of GGDEF domains lack the RxxD motif characteristic of the allosteric I site. Here, the structure of XCC4471(GGDEF), the GGDEF domain of a DGC from Xanthomonas campestris, in complex with c-di-GMP has been solved. Unexpectedly, the structure of the complex revealed a GGDEF-domain dimer cross-linked by two molecules of c-di-GMP at the strongly conserved active sites. In the complex (c-di-GMP)(2) adopts a novel partially intercalated form, with the peripheral guanine bases bound to the guanine-binding pockets and the two central bases stacked upon each other. Alteration of the residues involved in specific binding to c-di-GMP led to dramatically reduced K(d) values between XCC4471(GGDEF) and c-di-GMP. In addition, these key residues are strongly conserved among the many thousands of GGDEF-domain sequences identified to date. These results indicate a new product-bound form for GGDEF-domain-containing proteins obtained via (c-di-GMP)(2) binding at the active site. This novel XCC4471(GGDEF)-c-di-GMP complex structure may serve as a general model for the design of lead compounds to block the DGC activity of GGDEF-domain-containing proteins in X. campestris or other microorganisms that contain multiple GGDEF-domain proteins.
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The structure and inhibition of a GGDEF diguanylate cyclase complexed with (c-di-GMP)(2) at the active site.,Yang CY, Chin KH, Chuah ML, Liang ZX, Wang AH, Chou SH Acta Crystallogr D Biol Crystallogr. 2011 Dec;67(Pt 12):997-1008. Epub 2011 Nov, 18. PMID:22120736<ref>PMID:22120736</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 3qyy" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Diguanylate cyclase|Diguanylate cyclase]]
*[[Diguanylate cyclase|Diguanylate cyclase]]
*[[Response regulator 3D structure|Response regulator 3D structure]]
*[[Response regulator 3D structure|Response regulator 3D structure]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Xance]]
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[[Category: Xanthomonas campestris pv. campestris]]
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[[Category: Chin, K H]]
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[[Category: Chin K-H]]
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[[Category: Chou, S H]]
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[[Category: Chou S-H]]
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[[Category: Yang, C Y]]
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[[Category: Yang C-Y]]
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[[Category: C-di-gmp]]
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[[Category: Competitive inhibition]]
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[[Category: Dgc]]
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[[Category: Ggdef]]
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[[Category: Signaling protein-inhibitor complex]]
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[[Category: Xanthomonas campestri]]
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Current revision

A Novel Interaction Mode between a Microbial GGDEF Domain and the Bis-(3, 5 )-cyclic di-GMP

PDB ID 3qyy

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