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Detailed dissection of a new mechanism for glycoside cleavage: alpha-1,4-glucan lyase

TitleDetailed dissection of a new mechanism for glycoside cleavage: alpha-1,4-glucan lyase
Publication TypeJournal Article
Year of Publication2003
AuthorsLee, SS, Yu, S, Withers, SG
Date PublishedNOV 11

The unusual enzyme, Gracilariopsis alpha-1,4-glucan lyase of the sequence-related glycoside hydrolase family 3 1, cleaves the glycosidic bond of alpha-1,4-glucans via a beta-elimination reaction involving a covalent glycosyl-enzyme intermediate (Lee, S. S., Yu, S., and Withers, S. G. (2002) J. Am. Chem. Soc. 124, 4948-4949). The classical bell-shaped pH dependence of k(cat)/K-m indicates two ionizable groups in the active site with apparent pK(a) values of 3.05 and 6.66. Bronsted relationships of log k(cat), versus pKa and log(k(cat)/K-m) versus pK(a) for a series of aryl glucosides both show a linear monotonic dependence on leaving group pK(a) with low beta(1g) values of 0.32 and 0.33, respectively. The combination of these low beta(1g) values with large secondary deuterium kinetic isotope effects (k(H)/k(D) = 1.16similar to1.19) on the first step indicate a glycosylation step with substantial glycosidic bond cleavage and proton donation to the leaving group oxygen at the transition state. Developed oxocarbenium ion character of the transition state is also suggested by the potent inhibition afforded by acarbose and 1-deoxynojirimycin (K-i = 20 and 130 nM, respectively) and by the substantial rate reduction afforded by adjacent fluorine substitution. For only one substrate, 5-fluoro-alpha-D-glucopyranosyl fluoride, was the second elimination step shown to be rate-limiting. The large a-secondary deuterium kinetic isotope effect (k(H)/k(D) = 1.23) at C-1 and the small primary deuterium kinetic isotope effect (k(H)/k(D) = 1.92) at C-2 confirm an E2 mechanism with strong El character for this second step. This considerable structural and mechanistic similarity with retaining alpha-glucosidases is clear evidence for the evolution of an enzyme mechanism within the family.