Download MendeleyCysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.
McGregor, N.G.S., Coines, J., Borlandelli, V., Amaki, S., Artola, M., Nin-Hill, A., Linzel, D., Yamada, C., Arakawa, T., Ishiwata, A., Ito, Y., van der Marel, G.A., Codee, J.D.C., Fushinobu, S., Overkleeft, H.S., Rovira, C., Davies, G.J.(2021) Angew Chem Int Ed Engl 60: 5754-5758
- PubMed: 33528085
- DOI: https://doi.org/10.1002/anie.202013920
- Primary Citation of Related Structures:
6YQH, 7BZL, 7DIF - PubMed Abstract:
The recent discovery of zinc-dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys) 3 (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn-coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial. This is primarily due to the expected stability of the intermediate C-S bond. To facilitate the study of this atypical mechanism, we report the synthesis of a cyclophellitol-derived β-l-arabinofuranosidase inhibitor, hypothesised to react with the catalytic nucleophile to form a non-hydrolysable adduct analogous to the mechanistic covalent intermediate. This β-l-arabinofuranosidase inhibitor reacts exclusively with the proposed cysteine thiol catalytic nucleophiles of representatives of GH families 127 and 146. X-ray crystal structures determined for the resulting adducts enable MD and QM/MM simulations, which provide insight into the mechanism of thioglycosyl enzyme intermediate breakdown. Leveraging the unique chemistry of cyclophellitol derivatives, the structures and simulations presented here support the assignment of a zinc-coordinated cysteine as the catalytic nucleophile and illuminate the finely tuned energetics of this remarkable metalloenzyme clan.
Organizational Affiliation:
York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5DD, UK.
