Affiliation:
1. Department of Physics Engineering Hacettepe University Üniversiteler Mahallesi Beytepe Kampüsü 06800 Ankara Turkey
2. Current Address: Departament de Química Inorgànica i Orgànica (Seccióde Química Orgànica) Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona Carrer de Martí i Franquès, 1 08028 Barcelona Spain
Abstract
AbstractThe catalytic mechanism of a
‐dependent family 92
‐mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α‐mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of
and the
ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of
conformers for the ensuing reaction. This mechanistic insight is well‐aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.
Subject
Physical and Theoretical Chemistry,Atomic and Molecular Physics, and Optics