5i3d: Difference between revisions

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'''Unreleased structure'''


The entry 5i3d is ON HOLD
==Sulfolobus solfataricus beta-glycosidase - E387Y mutant==
<StructureSection load='5i3d' size='340' side='right'caption='[[5i3d]], [[Resolution|resolution]] 2.16&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5i3d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I3D 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]] 2.16&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</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=5i3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i3d OCA], [https://pdbe.org/5i3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i3d RCSB], [https://www.ebi.ac.uk/pdbsum/5i3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i3d ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/BGAL_SACS2 BGAL_SACS2]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
SNi-like mechanisms, which involve front-face leaving group departure and nucleophile approach, have been observed experimentally and computationally in chemical and enzymatic substitution at alpha-glycosyl electrophiles. Since SNi-like, SN1 and SN2 substitution pathways can be energetically comparable, engineered switching could be feasible. Here, engineering of Sulfolobus solfataricus beta-glycosidase, which originally catalyzed double SN2 substitution, changed its mode to SNi-like. Destruction of the first SN2 nucleophile through E387Y mutation created a beta-stereoselective catalyst for glycoside synthesis from activated substrates, despite lacking a nucleophile. The pH profile, kinetic and mutational analyses, mechanism-based inactivators, X-ray structure and subsequent metadynamics simulations together suggest recruitment of substrates by pi-sugar interaction and reveal a quantum mechanics-molecular mechanics (QM/MM) free-energy landscape for the substitution reaction that is similar to those of natural, SNi-like glycosyltransferases. This observation of a front-face mechanism in a beta-glycosyltransfer enzyme highlights that SNi-like pathways may be engineered in catalysts with suitable environments and suggests that 'beta-SNi' mechanisms may be feasible for natural glycosyltransfer enzymes.


Authors: Iglesias-Fernandez, J., Hancock, S.M., Lee, S.S., McAuley, K.E., Fordham-Skelton, A., Rovira, C., Davis, B.D.
A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase.,Iglesias-Fernandez J, Hancock SM, Lee SS, Khan M, Kirkpatrick J, Oldham NJ, McAuley K, Fordham-Skelton A, Rovira C, Davis BG Nat Chem Biol. 2017 Jun 12. doi: 10.1038/nchembio.2394. PMID:28604696<ref>PMID:28604696</ref>


Description: Sulfolobus solfataricus beta-glycosidase -E387Y mutant
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Davis, B.D]]
<div class="pdbe-citations 5i3d" style="background-color:#fffaf0;"></div>
[[Category: Fordham-Skelton, A]]
 
[[Category: Mcauley, K.E]]
==See Also==
[[Category: Rovira, C]]
*[[Galactosidase 3D structures|Galactosidase 3D structures]]
[[Category: Iglesias-Fernandez, J]]
== References ==
[[Category: Lee, S.S]]
<references/>
[[Category: Hancock, S.M]]
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharolobus solfataricus P2]]
[[Category: Davis BD]]
[[Category: Fordham-Skelton A]]
[[Category: Hancock SM]]
[[Category: Iglesias-Fernandez J]]
[[Category: Lee SS]]
[[Category: McAuley KE]]
[[Category: Rovira C]]
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