Structure of the Yeast SR Protein Npl3 and Interaction with mRNA 3′-End Processing Signals

Yeast Npl3 is homologous to SR proteins in higher eukaryotes, a family of RNA-binding proteins that have multiple essential roles in RNA metabolism. This protein competes with 3′-end processing factors for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. The NMR structure of its RNA-binding domain shows two unusually compact RNA recognition motifs (RRMs), and identifies the RNA recognition surface in Npl3. Biochemical and NMR studies identify a class of G+U-rich RNA sequences with high specificity for this protein. The protein binds to RNA and forms a single globular structure, but the two RRMs of Npl3 are not equivalent, with the second domain forming much stronger interactions with G+U-rich RNA sequences that occur independently of the interaction of the first RRM. The specific binding to G+U-rich RNAs observed for the two RRMs of Npl3 is masked in the full-length protein by a much stronger but non-sequence-specific RNA-binding activity residing outside of its RRMs. The preference of Npl3 for G+U-rich sequences supports the model for its function in regulating recognition of 3′-end processing sites through competition with the Rna15 (yeast analog of human CstF-64 protein) subunit of the processing complex.