title: Analysis of the reaction coordinate of alpha-L-fucosidases: a combined structural and quantum mechanical approach.
abstract: 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.
authors.affiliation: York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, UK.
authors.forename: Alicia
authors.initials: A
authors.lastname: Lammerts van Bueren
authors.forename: Albert
authors.initials: A
authors.lastname: Ardèvol
authors.forename: Jennifer
authors.initials: J
authors.lastname: Fayers-Kerr
authors.forename: Bo
authors.initials: B
authors.lastname: Luo
authors.forename: Yongmin
authors.initials: Y
authors.lastname: Zhang
authors.forename: Matthieu
authors.initials: M
authors.lastname: Sollogoub
authors.forename: Yves
authors.initials: Y
authors.lastname: Blériot
authors.forename: Carme
authors.initials: C
authors.lastname: Rovira
authors.forename: Gideon J
authors.initials: GJ
authors.lastname: Davies
mesh_terms: D001439:Bacteroides / Q000201:enzymology; D005643:Fucose / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D011789:Quantum Theory; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics; D005644:alpha-L-Fucosidase / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D005643:Fucose; D005644:alpha-L-Fucosidase