title: Identifying the catalytic acid/base in GH29 α-L-fucosidase subfamilies.
abstract: While the catalytic nucleophile in the configuration-retaining α-L-fucosidases from family GH29 is fully conserved with respect to sequence, there is no fully sequence-conserved acid/base residue candidate across the family. X-ray crystallographic studies and kinetic characterizations have allowed the identification of this residue in a few cases, and a recent combination of phylogenetic tree analyses with substrate specificity data has allowed the division of GH29 enzymes into two subfamilies, A and B, allowing the probable assignment of these residues. Here, we perform detailed kinetic and mechanistic characterizations of the corresponding alanine mutants and other candidates. Through comparison of kinetic parameters obtained for the hydrolysis of fucosyl substrates with activated leaving groups by these mutants with those of the corresponding wild-type enzymes, in conjunction with the demonstration of azide rescue, we largely confirm the acid/base residue predictions for the GH29 fucosidases from the two subfamilies.
authors.affiliation: Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1.
authors.forename: F Aidha
authors.initials: FA
authors.lastname: Shaikh
authors.forename: Alicia
authors.initials: A
authors.lastname: Lammerts van Bueren
authors.forename: Gideon J
authors.initials: GJ
authors.lastname: Davies
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Withers
mesh_terms: D001224:Aspartic Acid / Q000737:chemistry; D001439:Bacteroides / Q000201:enzymology; D002384:Catalysis; D018698:Glutamic Acid / Q000737:chemistry; D007700:Kinetics; D010802:Phylogeny; D013379:Substrate Specificity; D020124:Thermotoga maritima / Q000201:enzymology; D005644:alpha-L-Fucosidase / Q000737:chemistry* / Q000235:genetics
chemical_list: D001224:Aspartic Acid; D018698:Glutamic Acid; D005644:alpha-L-Fucosidase