Fig. 5: Structural basis of AlfC α(1,6)-specificity. | Nature Communications

Fig. 5: Structural basis of AlfC α(1,6)-specificity.

From: Structure and dynamics of an α-fucosidase reveal a mechanism for highly efficient IgG transfucosylation

Fig. 5

a Crystal structure of AlfCD200A with Fucα(1,6)GlcNAc. The gray mesh represents a composite omit map of electron density surrounding the ligand, contoured to 1.5 σ, and carved to 2.2 Å. An aromatic pocket that accommodates the GlcNAc +1 moiety is colored blue. b Superposition of Fucα(1,6)GlcNAc crystal structure over the closed state from molecular dynamic simulation (Fig. 3e) depicts a well-accommodated substrate. c–e Molecular docking of AlfC ligands (yellow) compared to crystal structures (magenta). Accuracy of docking shown by structural comparisons of c fucose; d 4NP-Fuc; e Fucα(1,6)GlcNAc. f–h Molecular docking results for inefficient substrates show +1 moiety outside the aromatic pocket, near the D242 loop. f Result for Fucα(1,2)Gal; g Fucα(1,3)GlcNAc; and h Fucα(1,4)GlcNAc.

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