Mapping the conformational itinerary of beta-glycosidases by X-ray crystallography

Biochemical Society Transactions
Gideon J DaviesDavid L Zechel

Abstract

The conformational agenda harnessed by different glycosidases along the reaction pathway has been mapped by X-ray crystallography. The transition state(s) formed during the enzymic hydrolysis of glycosides features strong oxocarbenium-ion-like character involving delocalization across the C-1-O-5 bond. This demands planarity of C-5, O-5, C-1 and C-2 at or near the transition state. It is widely, but incorrectly, assumed that the transition state must be (4)H(3) (half-chair). The transition-state geometry is equally well supported, for pyranosides, by both the (4)H(3) and (3)H(4) half-chair and (2,5)B and B(2,5) boat conformations. A number of retaining beta-glycosidases acting on gluco -configured substrates have been trapped in Michaelis and covalent intermediate complexes in (1)S(3) (skew-boat) and (4)C(1) (chair) conformations, respectively, pointing to a (4)H(3)-conformed transition state. Such a (4)H(3) conformation is consistent with the tight binding of (4)E- (envelope) and (4)H(3)-conformed transition-state mimics to these enzymes and with the solution structures of compounds bearing an sp (2) hybridized anomeric centre. Recent work reveals a (1)S(5) Michaelis complex for beta-mannanases which, together with the (0)S(2)...Continue Reading

Citations

Aug 31, 2007·Organic & Biomolecular Chemistry·Adrian ScaffidiRobert V Stick
Jan 13, 2010·Organic & Biomolecular Chemistry·Tracey M Gloster, Gideon J Davies
Aug 8, 2018·Acta Crystallographica. Section F, Structural Biology Communications·Shinya Fushinobu
Apr 17, 2019·Acta Crystallographica. Section D, Structural Biology·Taisuke NomuraKimihiko Mizutani
Apr 15, 2008·Nature Chemical Biology·Louise E TailfordGideon J Davies
May 22, 2010·Cellular and Molecular Life Sciences : CMLS·James R Ketudat Cairns, Asim Esen
Apr 1, 2006·Canadian Journal of Chemistry·Jorge Gonzalez-OuteiriñoRobert J Woods
Apr 22, 2006·Chembiochem : a European Journal of Chemical Biology·Tracey M GlosterGideon J Davies
Jan 19, 2010·Nature Chemical Biology·Yanping ZhuGideon J Davies
Aug 24, 2010·Journal of Computational Chemistry·Ahmed Mutanabbi AbdulaMutasem O Taha
Mar 15, 2012·Physical Chemistry Chemical Physics : PCCP·Benedict M Sattelle, Andrew Almond
Feb 11, 2016·Biochemical Society Transactions·Gideon J Davies, Spencer J Williams
Oct 6, 2018·Acta Crystallographica. Section D, Structural Biology·Claire A FowlerGideon J Davies
Feb 3, 2012·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Alicia Lammerts van BuerenGideon J Davies
Oct 9, 2013·Acta Crystallographica. Section D, Biological Crystallography·Anupong TankrathokJames R Ketudat Cairns
Dec 19, 2017·Chembiochem : a European Journal of Chemical Biology·Christina RotherBernd Nidetzky
Jan 26, 2007·Organic & Biomolecular Chemistry·Tracey M GlosterGideon J Davies
Sep 20, 2012·Biochemical Society Transactions·Tracey M Gloster
Jan 15, 2014·Acta Crystallographica. Section D, Biological Crystallography·Qun WanAndrey Kovalevsky
Sep 10, 2004·The Journal of Biological Chemistry·Tracey M GlosterGideon J Davies
Apr 11, 2007·The Journal of Biological Chemistry·Thomas R M BarendsBauke W Dijkstra
Jan 7, 2009·The Journal of Biological Chemistry·Masafumi HidakaShinya Fushinobu
Dec 6, 2011·The Journal of Biological Chemistry·Robert J GruningerSteven C Mosimann

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