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Computational Design of Experiment Unveils the Conformational Reaction Coordinate of GH125 α-Mannosidases

Alonso-Gil, Santiago, Males, Alexandra, Fernandes, Pearl Z., Williams, Spencer J., Davies, Gideon J., Rovira, Carme
Journal of the American Chemical Society 2017 v.139 no.3 pp. 1085-1088
Clostridium perfringens, Gibbs free energy, X-radiation, active sites, alpha-mannosidase, catalytic activity, glycosidic linkages, hydrolysis, models, molecular conformation, prediction
Conformational analysis of enzyme-catalyzed mannoside hydrolysis has revealed two predominant conformational itineraries through B₂,₅ or ³H₄ transition-state (TS) conformations. A prominent unassigned catalytic itinerary is that of exo-1,6-α-mannosidases belonging to CAZy family 125. A published complex of Clostridium perfringens GH125 enzyme with a nonhydrolyzable 1,6-α-thiomannoside substrate mimic bound across the active site revealed an undistorted ⁴C₁ conformation and provided no insight into the catalytic pathway of this enzyme. We show through a purely computational approach (QM/MM metadynamics) that sulfur-for-oxygen substitution in the glycosidic linkage fundamentally alters the energetically accessible conformational space of a thiomannoside when bound within the GH125 active site. Modeling of the conformational free energy landscape (FEL) of a thioglycoside strongly favors a mechanistically uninformative ⁴C₁ conformation within the GH125 enzyme active site, but the FEL of corresponding O-glycoside substrate reveals a preference for a Michaelis complex in an ᴼS₂ conformation (consistent with catalysis through a B₂,₅ TS). This prediction was tested experimentally by determination of the 3D X-ray structure of the pseudo-Michaelis complex of an inactive (D220N) variant of C. perfringens GH125 enzyme in complex with 1,6-α-mannobiose. This complex revealed unambiguous distortion of the −1 subsite mannoside to an ᴼS₂ conformation, matching that predicted by theory and supporting an ᴼS₂ → B₂,₅ → ¹S₅ conformational itinerary for GH125 α-mannosidases. This work highlights the power of the QM/MM approach and identified shortcomings in the use of nonhydrolyzable substrate analogues for conformational analysis of enzyme-bound species.