“Amide Resonance” in the Catalysis of
1,2-α‑l‑Fucosidase from Bifidobacterium bifidum
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Abstract
Bifidobacterium is a genus of Gram-positive
bacteria, which is important in the absorption of nourishment from
the human milk oligosaccharides (HMO). We present here the detailed
simulation of the enzymatic hydrolysis of 2′-fucosyllactose
catalyzed by 1,2-α-l-fucosidase from Bifidobacterium bifidum using the combined quantum
mechanical and molecular mechanical approach. Molecular dynamics simulations
and free energy profiles support that the overall reaction is a stepwise
mechanism. The first step is the proton transfer from N423 to D766,
and the second step involves the hydrolysis reaction via the inversion
mechanism catalyzed by the amide group of N423. Assisted by D766,
N423 serves as the general base to activate the water molecule to
attack the anomeric carbon center. E566 is the general acid to facilitate
the cleavage of glycosidic bond between l-fucose and galactose
units. The intrinsic resonance structure for the side chain amide
group of the asparagine residue is shown to be the origin to the catalytic
activity, which is also confirmed by the mutagenesis simulation of
N423G