Quantum chemical calculations support pseudouridine synthase reaction through a glycal intermediate and provide details of the mechanism

Pseudouridylation affects almost all types of RNAs and the malfunction of pseudouridine synthases, the enzymes responsible for the uridine–pseudouridine transformation, is linked to severe diseases, like cancer and X-linked dyskeratosis congenita. Stand-alone and guide-dependent pseudouridine synthases share a common active site structure and are assumed to share the catalytic mechanism whose details are not yet elucidated. We performed quantum chemical calculations on model systems to investigate the initial steps of several pathways proposed in the literature or based on biochemical analogy and chemical intuition. Results suggest that the Michael addition scheme is unlikely since no stable adduct is formed between the C6-atom of the uridine and the catalytic aspartate. The nucleophilic substitution scheme is ruled out owing to the unfavorable steric arrangement of the reactants. Our results are in favor of the glycal scheme and provide details for the mechanism that is likely to start with the glycosidic bond cleavage between the ribose and uracil, followed by or coupled to the deprotonation of the C2′-atom of the sugar by the conserved catalytic aspartate. A possible role of the latter step is suggested to be the regulation of the intermediate reactivity: C2′ deprotonation leads to a low-energy intermediate with sufficient lifetime to allow base repositioning before reattachment to ribose by C–C bond formation.