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

详细信息    查看全文

• 作者：Santiago Alonso-Gil ; Alexandra Males ; Pearl Z. Fernandes ; Spencer J. WilliamsGideon J. Davies ; Carme Rovira
• 刊名：Journal of the American Chemical Society
• 出版年：2017
• 出版时间：January 25, 2017
• 年：2017
• 卷：139
• 期：3
• 页码：1085-1088
• 全文大小：362K
• ISSN：1520-5126

文摘

Conformational analysis of enzyme-catalyzed mannoside hydrolysis has revealed two predominant conformational itineraries through B_2,5 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 B_2,5 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 → B_2,5 → 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.