Journal article

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

Santiago Alonso-Gil, Alexandra Males, Pearl Z Fernandes, Spencer J Williams, Gideon J Davies, Carme Rovira

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY | AMER CHEMICAL SOC | Published : 2017

Abstract

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 ene..

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University of Melbourne Researchers

Grants

Awarded by Australian Research Council


Awarded by Spanish Ministry of Economy and Competitiveness


Awarded by GENCAT


Awarded by Biotechnology and Biological Sciences Research Council


Funding Acknowledgements

We are supported by the Royal Society (Ken Murray Research professorship to G.J.D.), the Biotechnology and Biological Sciences Research Council (A.M.), the Australian Research Council (FT130100103) (S.J.W.), the Spanish Ministry of Economy and Competitiveness (CTQ2014-55174-P) (C.R. and S.A.-G.) and GENCAT (2014SGR-987) (C.R). We thank Diamond Light Source for access to beamline 102 and 104 (mx-13587) and BSC-CNS for computer resources and technical support at MareNostrum (RES-QCM-2016-3-0017).