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2wvu
From Proteopedia
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| - | [[Image:2wvu.png|left|200px]] | ||
| - | + | ==Crystal structure of a Michaelis complex of alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron with the synthetic substrate 4- nitrophenyl-alpha-L-fucose== | |
| + | <StructureSection load='2wvu' size='340' side='right'caption='[[2wvu]], [[Resolution|resolution]] 1.95Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2wvu]] is a 4 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=2WVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WVU FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JFZ:4-nitrophenyl+6-deoxy-alpha-L-galactopyranoside'>JFZ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2wvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wvu OCA], [https://pdbe.org/2wvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wvu RCSB], [https://www.ebi.ac.uk/pdbsum/2wvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wvu ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q8A3I4_BACTN Q8A3I4_BACTN] | ||
| + | == 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/2wvu_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=2wvu 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> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2wvu" style="background-color:#fffaf0;"></div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | == | + | __TOC__ |
| - | + | </StructureSection> | |
| - | + | [[Category: Bacteroides thetaiotaomicron VPI-5482]] | |
| - | == | + | [[Category: Large Structures]] |
| - | < | + | [[Category: Ardevol A]] |
| - | [[Category: Bacteroides thetaiotaomicron]] | + | [[Category: Bleriot Y]] |
| - | [[Category: | + | [[Category: Davies GJ]] |
| - | [[Category: | + | [[Category: Fayers-Kerr J]] |
| - | [[Category: | + | [[Category: Lammerts van Bueren A]] |
| - | [[Category: Davies | + | [[Category: Luo B]] |
| - | [[Category: Fayers-Kerr | + | [[Category: Rovira C]] |
| - | [[Category: Luo | + | [[Category: Sollogoub M]] |
| - | [[Category: Rovira | + | [[Category: Zhang Y]] |
| - | [[Category: Sollogoub | + | |
| - | [[Category: Zhang | + | |
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Crystal structure of a Michaelis complex of alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron with the synthetic substrate 4- nitrophenyl-alpha-L-fucose
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