2r6o

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[[Image:2r6o.png|left|200px]]
 
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==Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans==
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The line below this paragraph, containing "STRUCTURE_2r6o", creates the "Structure Box" on the page.
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<StructureSection load='2r6o' size='340' side='right'caption='[[2r6o]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2r6o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thida Thida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R6O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R6O FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_2r6o| PDB=2r6o | SCENE= }}
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tbd_1265 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=292415 THIDA])</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=2r6o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r6o OCA], [https://pdbe.org/2r6o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r6o RCSB], [https://www.ebi.ac.uk/pdbsum/2r6o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r6o ProSAT], [https://www.topsan.org/Proteins/MCSG/2r6o TOPSAN]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r6/2r6o_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2r6o ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Cyclic diguanylate (or bis-(3'-5') cyclic dimeric guanosine monophosphate; c-di-GMP) is a ubiquitous second messenger that regulates diverse cellular functions, including motility, biofilm formation, cell cycle progression, and virulence in bacteria. In the cell, degradation of c-di-GMP is catalyzed by highly specific EAL domain phosphodiesterases whose catalytic mechanism is still unclear. Here, we purified 13 EAL domain proteins from various organisms and demonstrated that their catalytic activity is associated with the presence of 10 conserved EAL domain residues. The crystal structure of the TBD1265 EAL domain was determined in free state (1.8 A) and in complex with c-di-GMP (2.35 A), and unveiled the role of conserved residues in substrate binding and catalysis. The structure revealed the presence of two metal ions directly coordinated by six conserved residues, two oxygens of c-di-GMP phosphate, and potential catalytic water molecule. Our results support a two-metal-ion catalytic mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.
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===Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans===
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Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.,Tchigvintsev A, Xu X, Singer A, Chang C, Brown G, Proudfoot M, Cui H, Flick R, Anderson WF, Joachimiak A, Galperin MY, Savchenko A, Yakunin AF J Mol Biol. 2010 Sep 24;402(3):524-38. Epub 2010 Aug 4. PMID:20691189<ref>PMID:20691189</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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The line below this paragraph, {{ABSTRACT_PUBMED_020691189}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2r6o" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 020691189 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_020691189}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[2r6o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thiobacillus_denitrificans Thiobacillus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R6O OCA].
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[[Category: Thida]]
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[[Category: Chang, C]]
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==Reference==
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[[Category: Edwards, A M]]
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<ref group="xtra">PMID:020691189</ref><references group="xtra"/>
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[[Category: Joachimiak, A]]
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[[Category: Thiobacillus denitrificans]]
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[[Category: Structural genomic]]
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[[Category: Chang, C.]]
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[[Category: Savchenko, A]]
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[[Category: Edwards, A M.]]
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[[Category: Xu, X]]
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[[Category: Joachimiak, A.]]
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[[Category: Zheng, H]]
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[[Category: MCSG, Midwest Center for Structural Genomics.]]
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[[Category: Savchenko, A.]]
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[[Category: Xu, X.]]
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[[Category: Zheng, H.]]
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[[Category: Diguanylate cyclase]]
[[Category: Diguanylate cyclase]]
[[Category: Ggdef and eal domain]]
[[Category: Ggdef and eal domain]]
[[Category: Mcsg]]
[[Category: Mcsg]]
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[[Category: Midwest center for structural genomic]]
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[[Category: PSI, Protein structure initiative]]
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[[Category: Protein structure initiative]]
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[[Category: Psi-2]]
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[[Category: Structural genomic]]
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[[Category: Thiobacillus denitrifican]]
[[Category: Thiobacillus denitrifican]]
[[Category: Transferase]]
[[Category: Transferase]]
[[Category: Unknown function]]
[[Category: Unknown function]]

Current revision

Crystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans

PDB ID 2r6o

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