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

Nat Struct Biol. 2002 Dec;9(12):958-65. doi: 10.1038/nsb873.


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 (psi) residue in U2 snRNA nearly opposite the branch site. We show that the presence of this psi in the pre-mRNA branch-site helix of Saccharomyces cerevisiae induces a dramatically altered architectural landscape compared with that of its unmodified counterpart. The psi-induced structure places the nucleophile in an accessible position for the first step of splicing.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine / chemistry
  • Base Sequence
  • Binding Sites
  • Introns
  • Models, Molecular*
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation
  • Phylogeny
  • Pseudouridine / chemistry*
  • Pseudouridine / genetics
  • RNA Precursors / chemistry
  • RNA Splicing*
  • RNA, Fungal / chemistry
  • Saccharomyces cerevisiae / genetics
  • Spliceosomes / chemistry*
  • Uridine / chemistry


  • RNA Precursors
  • RNA, Fungal
  • Pseudouridine
  • Adenosine
  • Uridine

Associated data

  • PDB/1LMV
  • PDB/1LPW