Mechanism of the glycosylation step catalyzed by human α- galactosidase: A QM/MM metadynamics study

Abstract

The enzyme α-galactosidase (α-GAL), a member of glycoside hydrolase family 27, catalyzes the removal of a nonreducing terminal α-galactose residue from polysaccharides, glycolipids, and glycopeptides. α-GAL is believed to have the double displacement retaining reaction mechanism. In this work, the glycosylation step catalyzed by human α-GAL was computationally simulated with quantum mechanics/molecular mechanics metadynamics. Our simulations show that the overall catalytic mechanism follows a DN*AN-like mechanism, and the transition state has a oxocarbenium ion like character with a partially formed double bond between the ring oxygen and C5′ carbon atoms. In addition, the galactosyl ring of the substrate follows a conformational itinerary of 4C1 → [E3/4H3]§ → 1S3 along the reaction coordinate. © 2012 American Chemical Society.