Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome.

Autor: Aupič J; National Research Council of Italy (CNR)-Materials Foundry (IOM) c/o International School for Advanced Studies (SISSA), Trieste, Italy., Borišek J; Theory department, National Institute of Chemistry, Ljubljana, Slovenia., Fica SM; Department of Biochemistry, University of Oxford, Oxford, UK., Galej WP; European Molecular Biology Laboratory, Grenoble, France., Magistrato A; National Research Council of Italy (CNR)-Materials Foundry (IOM) c/o International School for Advanced Studies (SISSA), Trieste, Italy. alessandra.magistrato@sissa.it.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2023 Dec 20; Vol. 14 (1), pp. 8482. Date of Electronic Publication: 2023 Dec 20.
DOI: 10.1038/s41467-023-44174-2
Abstrakt: Cleavage and formation of phosphodiester bonds in nucleic acids is accomplished by large cellular machineries composed of both protein and RNA. Long thought to rely on a two-metal-ion mechanism for catalysis, structure comparisons revealed many contain highly spatially conserved second-shell monovalent cations, whose precise function remains elusive. A recent high-resolution structure of the spliceosome, essential for pre-mRNA splicing in eukaryotes, revealed a potassium ion in the active site. Here, we employ biased quantum mechanics/ molecular mechanics molecular dynamics to elucidate the function of this monovalent ion in splicing. We discover that the K + ion regulates the kinetics and thermodynamics of the first splicing step by rigidifying the active site and stabilizing the substrate in the pre- and post-catalytic state via formation of key hydrogen bonds. Our work supports a direct role for the K + ion during catalysis and provides a mechanistic hypothesis likely shared by other nucleic acid processing enzymes.
(© 2023. The Author(s).)
Databáze: MEDLINE
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