2wvs: Difference between revisions

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[[Image:2wvs.png|left|200px]]


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==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==
The line below this paragraph, containing "STRUCTURE_2wvs", creates the "Structure Box" on the page.
<StructureSection load='2wvs' size='340' side='right'caption='[[2wvs]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2wvs]] 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=2WVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WVS FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.19&#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=FUF:2-DEOXY-2-FLUORO-BETA-L-FUCOPYRANOSE'>FUF</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_2wvs|  PDB=2wvs  |  SCENE=  }}
<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>
== 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/2wvs_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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)&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.


===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===
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2wvs" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 20092273 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_20092273}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Bacteroides thetaiotaomicron VPI-5482]]
[[2wvs]] is a 4 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=2WVS OCA].
[[Category: Large Structures]]
 
[[Category: Ardevol A]]
==Reference==
[[Category: Bleriot Y]]
<ref group="xtra">PMID:020092273</ref><references group="xtra"/>
[[Category: Davies GJ]]
[[Category: Bacteroides thetaiotaomicron]]
[[Category: Fayers-Kerr J]]
[[Category: Ardevol, A.]]
[[Category: Lammerts van Bueren A]]
[[Category: Bleriot, Y.]]
[[Category: Luo B]]
[[Category: Bueren, A Lammerts Van.]]
[[Category: Rovira C]]
[[Category: Davies, G J.]]
[[Category: Sollogoub M]]
[[Category: Fayers-Kerr, J.]]
[[Category: Zhang Y]]
[[Category: Luo, B.]]
[[Category: Rovira, C.]]
[[Category: Sollogoub, M.]]
[[Category: Zhang, Y.]]
[[Category: Alpha-l-fucose]]
[[Category: Glycoside hydrolase family 29]]
[[Category: Hydrolase]]
Retrieved from "https://proteopedia.org/2wvs"