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2wvs
From Proteopedia
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| - | {{STRUCTURE_2wvs| PDB=2wvs | SCENE= }} | ||
| - | ===CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 TRAPPED COVALENT INTERMEDIATE FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH 2-FLUORO-FUCOSYL FLUORIDE USING AN E288Q MUTANT=== | ||
| - | {{ABSTRACT_PUBMED_20092273}} | ||
| - | == | + | ==Crystal structure of an alpha-L-fucosidase GH29 trapped covalent intermediate from Bacteroides thetaiotaomicron in complex with 2- fluoro-fucosyl fluoride using an E288Q mutant== |
| - | [[2wvs]] is a 4 chain structure with sequence from [ | + | <StructureSection load='2wvs' size='340' side='right'caption='[[2wvs]], [[Resolution|resolution]] 2.19Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2wvs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WVS FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUF:2-DEOXY-2-FLUORO-BETA-L-FUCOPYRANOSE'>FUF</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2wvt|2wvt]], [[2wvv|2wvv]], [[2wvu|2wvu]]</div></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=2wvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wvs OCA], [https://pdbe.org/2wvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wvs RCSB], [https://www.ebi.ac.uk/pdbsum/2wvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wvs ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wv/2wvs_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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=2wvs ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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)<-->(3)H(4)<-->(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. | ||
| - | + | 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> | |
| - | <ref | + | |
| - | [[Category: | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | [[Category: Ardevol, A | + | </div> |
| - | [[Category: Bleriot, Y | + | <div class="pdbe-citations 2wvs" style="background-color:#fffaf0;"></div> |
| - | [[Category: Bueren, A Lammerts | + | == References == |
| - | [[Category: Davies, G J | + | <references/> |
| - | [[Category: Fayers-Kerr, J | + | __TOC__ |
| - | [[Category: Luo, B | + | </StructureSection> |
| - | [[Category: Rovira, C | + | [[Category: Bactn]] |
| - | [[Category: Sollogoub, M | + | [[Category: Large Structures]] |
| - | [[Category: Zhang, Y | + | [[Category: Ardevol, A]] |
| + | [[Category: Bleriot, Y]] | ||
| + | [[Category: Bueren, A Lammerts van]] | ||
| + | [[Category: Davies, G J]] | ||
| + | [[Category: Fayers-Kerr, J]] | ||
| + | [[Category: Luo, B]] | ||
| + | [[Category: Rovira, C]] | ||
| + | [[Category: Sollogoub, M]] | ||
| + | [[Category: Zhang, Y]] | ||
[[Category: Alpha-l-fucose]] | [[Category: Alpha-l-fucose]] | ||
[[Category: Glycoside hydrolase family 29]] | [[Category: Glycoside hydrolase family 29]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
Current revision
Crystal structure of an alpha-L-fucosidase GH29 trapped covalent intermediate from Bacteroides thetaiotaomicron in complex with 2- fluoro-fucosyl fluoride using an E288Q mutant
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