New water-assisted catalytic mechanism of the glycoside hydrolase family demonstrated on the Staphylococcus Aureus Autolysin E

Glycoside hydrolases (GH) are widespread enzymes with different roles in nature from degradation of biomass, anti-bacterial defense, pathogenetic mechanisms to physiological cellular functions. From mechanistic point of view they are commonly classified as inverting or retaining ones, the latter are further subdivided into several different catalytic mechanisms, which are in many cases for specific GH families and their members still hypothesized. It remains a challenge to elucidate their catalytic mechanism, and diverse structural features of these enzymes open up possibilities of novel mechanisms, not yet described in the literature. Studying their catalytic mechanism is of importance to either inhibit or engineer them for new functions. Autolysin E (AtlE), from Staphylococcus aureus, is a cell wall degrading enzyme from the GH73 family, which is a potential drug target. 

In our work we addressed the catalytic mechanism of AtlE. Site directed mutagenesis studies identified Glu138 as the only plausible catalytic residue. Quantum mechanics/molecular mechanics (QM/MM) simulations of the possible reaction pathways suggest that hydrolysis proceeds via a retaining, water-assisted mechanism and an oxocarbenium ion-like transition state. These results, on the basis of structural data from a member of the hydrolase GH73 family, support the hypothesis of the presence of a new catalytic mechanism in the glycoside hydrolases, which can be considered in the design of future AtlE inhibitors.

The work is a result of the cooperation between the Theory Department at the National Institute of Chemistry, the Structural Biology Group at the Jožef Stefan Institute and the Center for Excellence CIPKeBiP. We have shown that there is enough domestic knowledge in Slovenia that can lead to important new discoveries in the field of life sciences by effectively integrating and using domestic research equipment and computational recourses.

This article was published in ACS Catalysis, the authors of the research are: dr. Jure Borišek, dr. Mitja Ogrizek, doc. dr. Andrej Perdih and prof. dr. Marjana Novič from the National Institute of Chemistry Slovenia, Ljubljana, and Sara Pintar and prof. dr. Dušan Turk from the Jožef Stefan Institute/ Center for Excellence CIPKeBiP, Ljubljana.

New water-assisted catalytic mechanism of the glycoside hydrolase family demonstrated on the Staphylococcus Aureus Autolysin E

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