2bas: Difference between revisions

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 <StructureSection load='2bas' size='340' side='right'caption='[[2bas]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2bas]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BAS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2bas]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BAS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</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]] 2.61&#8491;</td></tr>
-<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>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ykuI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2bas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bas OCA], [https://pdbe.org/2bas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bas RCSB], [https://www.ebi.ac.uk/pdbsum/2bas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bas ProSAT], [https://www.topsan.org/Proteins/MCSG/2bas TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/YKUI_BACSU YKUI_BACSU]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=2bas ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that is involved in the regulation of cell surface-associated traits and the persistence of infections. Omnipresent GGDEF and EAL domains, which occur in various combinations with regulatory domains, catalyze c-di-GMP synthesis and degradation, respectively. The crystal structure of full-length YkuI from Bacillus subtilis, composed of an EAL domain and a C-terminal PAS-like domain, has been determined in its native form and in complex with c-di-GMP and Ca(2+). The EAL domain exhibits a triose-phosphate isomerase-barrel fold with one antiparallel beta-strand. The complex with c-di-GMP-Ca(2+) defines the active site of the putative phosphodiesterase located at the C-terminal end of the beta-barrel. The EAL motif is part of the active site with Glu-33 of the motif being involved in cation coordination. The structure of the complex allows the proposal of a phosphodiesterase mechanism, in which the divalent cation and the general base Glu-209 activate a catalytic water molecule for nucleophilic in-line attack on the phosphorus. The C-terminal domain closely resembles the PAS-fold. Its pocket-like structure could accommodate a yet unknown ligand. YkuI forms a tight dimer via EAL-EAL and trans EAL-PAS-like domain association. The possible regulatory significance of the EAL-EAL interface and a mechanism for signal transduction between sensory and catalytic domains of c-di-GMP-specific phosphodiesterases are discussed.
-Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains.,Minasov G, Padavattan S, Shuvalova L, Brunzelle JS, Miller DJ, Basle A, Massa C, Collart FR, Schirmer T, Anderson WF J Biol Chem. 2009 May 8;284(19):13174-84. Epub 2009 Feb 24. PMID:19244251<ref>PMID:19244251</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2bas" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus globigii migula 1900]]
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: Anderson, W F]]
+[[Category: Anderson WF]]
-[[Category: Brunzelle, J S]]
+[[Category: Brunzelle JS]]
-[[Category: Collart, F R]]
+[[Category: Collart FR]]
-[[Category: Joachimiak, A]]
+[[Category: Joachimiak A]]
-[[Category: Structural genomic]]
+[[Category: Miller DJ]]
-[[Category: Miller, D J]]
+[[Category: Minasov G]]
-[[Category: Minasov, G]]
+[[Category: Shuvalova L]]
-[[Category: Shuvalova, L]]
-[[Category: Eal domain]]
-[[Category: Mcsg]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Signaling protein]]
-[[Category: Ykui protein]]