2wvt

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[[Image:2wvt.png|left|200px]]
 
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==Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor==
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The line below this paragraph, containing "STRUCTURE_2wvt", creates the "Structure Box" on the page.
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<StructureSection load='2wvt' size='340' side='right'caption='[[2wvt]], [[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'>[[2wvt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WVT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WVT FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.8&#8491;</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=FHN:(2S,3R,5R,6S)-3,4,5-TRIHYDROXY-2,6-BIS(HYDROXYMETHYL)PIPERIDINIUM'>FHN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
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{{STRUCTURE_2wvt| PDB=2wvt | SCENE= }}
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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=2wvt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wvt OCA], [https://pdbe.org/2wvt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wvt RCSB], [https://www.ebi.ac.uk/pdbsum/2wvt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wvt ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8A3I4_BACTN Q8A3I4_BACTN]
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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/wv/2wvt_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=2wvt 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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The enzymatic hydrolysis of alpha-l-fucosides is of importance in cancer, bacterial infections, and fucosidosis, a neurodegenerative lysosomal storage disorder. Here we show a series of snapshots along the reaction coordinate of a glycoside hydrolase family GH29 alpha-l-fucosidase unveiling a Michaelis (ES) complex in a (1)C(4) (chair) conformation and a covalent glycosyl-enzyme intermediate in (3)S(1) (skew-boat). First principles metadynamics simulations on isolated alpha-l-fucose strongly support a (1)C(4)&lt;--&gt;(3)H(4)&lt;--&gt;(3)S(1) conformational itinerary for the glycosylation step of the reaction mechanism and indicate a strong "preactivation" of the (1)C(4) complex to nucleophilic attack as reflected by free energy, C1-O1/O5-C1 bond length elongation/reduction, C1-O1 bond orientation, and positive charge development around the anomeric carbon. Analysis of an imino sugar inhibitor is consistent with tight binding of a chair-conformed charged species.
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===CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH A NOVEL IMINOSUGAR FUCOSIDASE INHIBITOR===
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Analysis of the Reaction Coordinate of alpha-l-Fucosidases: A Combined Structural and Quantum Mechanical Approach.,Lammerts van Bueren A, Fayers-Kerr J, Luo B, Zhang Y, Sollogoub M, Bleriot Y, Rovira C, Davies GJ J Am Chem Soc. 2010 Jan 21. PMID:20092273<ref>PMID:20092273</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_20092273}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2wvt" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20092273 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20092273}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Bacteroides thetaiotaomicron VPI-5482]]
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[[2wvt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WVT OCA].
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[[Category: Large Structures]]
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[[Category: Ardevol A]]
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==Reference==
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[[Category: Bleriot Y]]
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<ref group="xtra">PMID:020092273</ref><references group="xtra"/>
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[[Category: Davies GJ]]
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[[Category: Bacteroides thetaiotaomicron]]
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[[Category: Fayers-Kerr J]]
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[[Category: Ardevol, A.]]
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[[Category: Lammerts van Bueren A]]
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[[Category: Bleriot, Y.]]
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[[Category: Luo B]]
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[[Category: Bueren, A Lammerts Van.]]
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[[Category: Rovira C]]
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[[Category: Davies, G J.]]
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[[Category: Sollogoub M]]
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[[Category: Fayers-Kerr, J.]]
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[[Category: Zhang Y]]
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[[Category: Luo, B.]]
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[[Category: Rovira, C.]]
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[[Category: Sollogoub, M.]]
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[[Category: Zhang, Y.]]
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[[Category: Alpha-l-fucose]]
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[[Category: Glycoside hydrolase family 29]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor

PDB ID 2wvt

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