Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine

Pairing of a consensus sequence of the precursor (pre)-mRNA intron with a short region of the U2 small nuclear (sn)RNA during assembly of the eukaryotic spliceosome results in formation of a complementary helix of seven base pairs with a single unpaired adenosine residue. The 2′ OH of this adenosine, called the branch site, brings about nucleophilic attack at the pre-mRNA 5′ splice site in the first step of splicing. Another feature of this pairing is the phylogenetic conservation of a pseudouridine (ψ) residue in U2 snRNA nearly opposite the branch site. We show that the presence of this ψ in the pre-mRNA branch-site helix of Saccharomyces cerevisiae induces a dramatically altered architectural landscape compared with that of its unmodified counterpart. The ψ-induced structure places the nucleophile in an accessible position for the first step of splicing.