title: A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing.
abstract: 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.
authors.affiliation: Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
authors.forename: Sunbin
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
authors.forename: Sina
authors.initials: S
authors.lastname: Mozaffari-Jovin
authors.affiliation: Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Wollenhaupt
authors.affiliation: Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
authors.forename: Karine F
authors.initials: KF
authors.lastname: Santos
authors.affiliation: Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Theuser
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland.
authors.forename: Stanislaw
authors.initials: S
authors.lastname: Dunin-Horkawicz
authors.affiliation: Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
authors.forename: Patrizia
authors.initials: P
authors.lastname: Fabrizio
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland.
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
authors.affiliation: Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Lührmann
authors.affiliation: Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.
authors.forename: Markus C
authors.initials: MC
authors.lastname: Wahl
mesh_terms: D018360:Crystallography, X-Ray; D004252:DNA Mutational Analysis; D006801:Humans; D008954:Models, Biological; D008958:Models, Molecular; D009154:Mutation; D009687:Nuclear Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D012313:RNA / Q000378:metabolism*; D012326:RNA Splicing; D017414:Ribonucleoprotein, U4-U6 Small Nuclear / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017411:Ribonucleoproteins, Small Nuclear / Q000737:chemistry / Q000378:metabolism*
chemical_list: D009687:Nuclear Proteins; C108507:PRPF3 protein, human; D017414:Ribonucleoprotein, U4-U6 Small Nuclear; D017411:Ribonucleoproteins, Small Nuclear; D012313:RNA
keywords: S. cerevisiae; X-ray crystallography; biochemistry; biophysics; human; pre-mRNA splicing; protein–RNA interaction; small nuclear ribonucleoprotein particle; structural biology