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6ih1

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Current revision (10:33, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6ih1' size='340' side='right'caption='[[6ih1]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='6ih1' size='340' side='right'caption='[[6ih1]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6ih1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibc3 Vibc3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IH1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IH1 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6ih1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O395 Vibrio cholerae O395]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IH1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IH1 FirstGlance]. <br>
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</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=CA:CALCIUM+ION'>CA</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]] 1.95&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VC0395_A1247 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=345073 VIBC3])</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=CA:CALCIUM+ION'>CA</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyclic-guanylate-specific_phosphodiesterase Cyclic-guanylate-specific phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.52 3.1.4.52] </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=6ih1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ih1 OCA], [https://pdbe.org/6ih1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ih1 RCSB], [https://www.ebi.ac.uk/pdbsum/6ih1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ih1 ProSAT]</span></td></tr>
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<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=6ih1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ih1 OCA], [http://pdbe.org/6ih1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ih1 RCSB], [http://www.ebi.ac.uk/pdbsum/6ih1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ih1 ProSAT]</span></td></tr>
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</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/A0A0H3AJ04_VIBC3 A0A0H3AJ04_VIBC3]
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Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3'3'-cyclic GMP-AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5'-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5'-pGpG-Ca2+ structure, beta5-alpha5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5'-pGpG-Ca2+ structure quite different from other 5'-pGpG bound structures reported earlier.
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Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication.,Yadav M, Pal K, Sen U Biochem J. 2019 Nov 15;476(21):3333-3353. doi: 10.1042/BCJ20190399. PMID:31647518<ref>PMID:31647518</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 6ih1" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Cyclic-guanylate-specific phosphodiesterase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Vibc3]]
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[[Category: Vibrio cholerae O395]]
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[[Category: Pal, K]]
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[[Category: Pal K]]
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[[Category: Sen, U]]
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[[Category: Sen U]]
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[[Category: Yadav, M]]
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[[Category: Yadav M]]
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[[Category: Cyclic dinucleotide phosphodiesterase]]
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[[Category: Hydrolase]]
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[[Category: Nucleotide binding]]
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Current revision

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-GMP bound form

PDB ID 6ih1

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