2r2d: Difference between revisions

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 <StructureSection load='2r2d' size='340' side='right'caption='[[2r2d]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2r2d]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrt5 Agrt5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R2D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2r2d]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R2D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.75&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aiiB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRT5])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2r2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r2d OCA], [https://pdbe.org/2r2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r2d RCSB], [https://www.ebi.ac.uk/pdbsum/2r2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r2d ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AHLLB_AGRFC AHLLB_AGRFC]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 18: / Line 20: @@
 </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=2r2d ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-N-Acyl-l-homoserine lactone (AHL) mediated quorum-sensing regulates virulence factor production in a variety of Gram-negative bacteria. Proteins capable of degrading these autoinducers have been called "quorum-quenching" enzymes, can block many quorum-sensing dependent phenotypes, and represent potentially useful reagents for clinical, agricultural, and industrial applications. The most characterized quorum-quenching enzymes to date are the AHL lactonases, which are metalloproteins that belong to the metallo-beta-lactamase superfamily. Here, we report the cloning, heterologous expression, purification, metal content, substrate specificity, and three-dimensional structure of AiiB, an AHL lactonase from Agrobacterium tumefaciens. Much like a homologous AHL lactonase from Bacillus thuringiensis, AiiB appears to be a metal-dependent AHL lactonase with broad specificity. A phosphate dianion is bound to the dinuclear zinc site and the active-site structure suggests specific mechanistic roles for an active site tyrosine and aspartate. To our knowledge, this is the second representative structure of an AHL lactonase and the first of an AHL lactonase from a microorganism that also produces AHL autoinducers. This work should help elucidate the hydrolytic ring-opening mechanism of this family of enzymes and also facilitate the design of more effective quorum-quenching catalysts.
-Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens.,Liu D, Thomas PW, Momb J, Hoang QQ, Petsko GA, Ringe D, Fast W Biochemistry. 2007 Oct 23;46(42):11789-99. Epub 2007 Sep 28. PMID:17900178<ref>PMID:17900178</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2r2d" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Agrt5]]
+[[Category: Agrobacterium fabrum str. C58]]
 [[Category: Large Structures]]
-[[Category: Fast, W]]
+[[Category: Fast W]]
-[[Category: Hoang, Q]]
+[[Category: Hoang Q]]
-[[Category: Liu, D]]
+[[Category: Liu D]]
-[[Category: Momb, J]]
+[[Category: Momb J]]
-[[Category: Petsko, G A]]
+[[Category: Petsko GA]]
-[[Category: Ringe, D]]
+[[Category: Ringe D]]
-[[Category: Thomas, P W]]
+[[Category: Thomas PW]]
-[[Category: Agrobacterium tumefacien]]
-[[Category: Aiib]]
-[[Category: Di-nuclear zinc center]]
-[[Category: Hydrolase]]
-[[Category: Lactonase]]
-[[Category: N-acyl hompserine lactone]]
-[[Category: Phosphate]]
-[[Category: Quorum quenching]]