A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing
Sunbin Liu,
Sina Mozaffari-Jovin,
Jan Wollenhaupt,
Karine F Santos,
Matthias Theuser,
Stanislaw Dunin-Horkawicz,
Patrizia Fabrizio,
Janusz M Bujnicki,
Reinhard Lührmann,
Markus C Wahl
Affiliations
Sunbin Liu
Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
Sina Mozaffari-Jovin
Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
Jan Wollenhaupt
Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
Karine F Santos
Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
Matthias Theuser
Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
Stanislaw Dunin-Horkawicz
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
Patrizia Fabrizio
Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
Janusz M Bujnicki
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
Reinhard Lührmann
Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
Markus C Wahl
Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany
Prp3 is an essential U4/U6 di-snRNP-associated protein whose functions and molecular mechanisms in pre-mRNA splicing are presently poorly understood. We show by structural and biochemical analyses that Prp3 contains a bipartite U4/U6 di-snRNA-binding region comprising an expanded ferredoxin-like fold, which recognizes a 3′-overhang of U6 snRNA, and a preceding peptide, which binds U4/U6 stem II. Phylogenetic analyses revealed that the single-stranded RNA-binding domain is exclusively found in Prp3 orthologs, thus qualifying as a spliceosome-specific RNA interaction module. The composite double-stranded/single-stranded RNA-binding region assembles cooperatively with Snu13 and Prp31 on U4/U6 di-snRNAs and inhibits Brr2-mediated U4/U6 di-snRNA unwinding in vitro. RNP-disrupting mutations in Prp3 lead to U4/U6•U5 tri-snRNP assembly and splicing defects in vivo. Our results reveal how Prp3 acts as an important bridge between U4/U6 and U5 in the tri-snRNP and comparison with a Prp24-U6 snRNA recycling complex suggests how Prp3 may be involved in U4/U6 reassembly after splicing.
