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

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Abstract

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.

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Acknowledgements

This work was supported by the Hungarian Scientific Research Fund (OTKA) through Grants K111862 and K116305 and by the MedInProt Protein Science Research Synergy Program. J.O. was supported by the Bolyai János Research Scholarship and by NKFIH Grant No. 115503. Part of the computations were performed using the supercomputing service offered by the Hungarian National Information Infrastructure Development Institute. This work is dedicated to the memory of Professor János G. Ángyán.

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Authors and Affiliations

  1. Institute of Chemistry, Eötvös Loránd University, Pázmány s. 1/a, Budapest, 1117, Hungary

    Dóra J. Kiss & Gergely Tóth

  2. Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, Budapest, 1117, Hungary

    Dóra J. Kiss & György G. Ferenczy

  3. Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest, 1111, Hungary

    Julianna Oláh

  4. MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány s. 1/a, Budapest, 1117, Hungary

    Dóra K. Menyhárd

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  1. Dóra J. Kiss
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Correspondence to György G. Ferenczy.

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Published as part of the special collection of articles In Memoriam of János Ángyán.

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Kiss, D.J., Oláh, J., Tóth, G. et al. Quantum chemical calculations support pseudouridine synthase reaction through a glycal intermediate and provide details of the mechanism. Theor Chem Acc 137, 162 (2018). https://doi.org/10.1007/s00214-018-2361-6

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