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

ABSTRACT: 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.

SUBMITTER: Aupic J 

PROVIDER: S-EPMC10733407 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature