title: A novel protein-protein interaction in the RES (REtention and Splicing) complex.
abstract: The retention and splicing (RES) complex is a conserved spliceosome-associated module that was shown to enhance splicing of a subset of transcripts and promote the nuclear retention of unspliced pre-mRNAs in yeast. The heterotrimeric RES complex is organized around the Snu17p protein that binds to both the Bud13p and Pml1p subunits. Snu17p exhibits an RRM domain that resembles a U2AF homology motif (UHM) and Bud13p harbors a Trp residue reminiscent of an UHM-ligand motif (ULM). It has therefore been proposed that the interaction between Snu17p and Bud13p resembles canonical UHM-ULM complexes. Here, we have used biochemical and NMR structural analysis to characterize the structure of the yeast Snu17p-Bud13p complex. Unlike known UHMs that sequester the Trp residue of the ULM ligand in a hydrophobic pocket, Snu17p and Bud13p utilize a large interaction surface formed around the two helices of the Snu17p domain. In total 18 residues of the Bud13p ligand wrap around the Snu17p helical surface in an U-turn-like arrangement. The invariant Trp(232) in Bud13p is located in the center of the turn, and contacts surface residues of Snu17p. The structural data are supported by mutational analysis and indicate that Snu17p provides an extended binding surface with Bud13p that is notably distinct from canonical UHM-ULM interactions. Our data highlight structural diversity in RRM-protein interactions, analogous to the one seen for nucleic acid interactions.
authors.affiliation: From the Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, kostas.tripsianes@ceitec.muni.cz.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Tripsianes
authors.affiliation: the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, the Center for Integrated Protein Science Munich and Chair of Biomolecular NMR, TU München, Lichtenbergstr. 4, 85747 Garching, Germany.
authors.forename: Anders
authors.initials: A
authors.lastname: Friberg
authors.affiliation: the Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Barrandon
authors.affiliation: the University Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, F-91405 Orsay, France, and.
authors.forename: Mark
authors.initials: M
authors.lastname: Brooks
authors.affiliation: the University Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, F-91405 Orsay, France, and.
authors.forename: Herman
authors.initials: H
authors.lastname: van Tilbeurgh
authors.affiliation: the Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91198 Gif sur Yvette, France, the Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de Recherche Scientifique (CNRS) UMR 7104, Institut National de Santé et de Recherche Médicale (INSERM) U964, Université de Strasbourg, 67404 Illkirch, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Seraphin
authors.affiliation: the Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, the Center for Integrated Protein Science Munich and Chair of Biomolecular NMR, TU München, Lichtenbergstr. 4, 85747 Garching, Germany, sattler@helmholtz-muenchen.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Sattler
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010766:Phosphorylation; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D012322:RNA Precursors / Q000096:biosynthesis* / Q000235:genetics; D012326:RNA Splicing; D012331:RNA, Fungal / Q000096:biosynthesis* / Q000235:genetics; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017413:Ribonucleoprotein, U2 Small Nuclear / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017381:Spliceosomes / Q000737:chemistry* / Q000378:metabolism; D014364:Tryptophan / Q000737:chemistry / Q000378:metabolism
chemical_list: C534389:Bud13 protein, S cerevisiae; D002352:Carrier Proteins; C425663:IST3 protein, S cerevisiae; D012322:RNA Precursors; D012331:RNA, Fungal; D011994:Recombinant Proteins; D017413:Ribonucleoprotein, U2 Small Nuclear; D029701:Saccharomyces cerevisiae Proteins; D014364:Tryptophan
keywords: Gene Regulation; Protein Complex; Protein Structure; Protein-protein Interaction; RNA-binding Protein; Spliceosome; U2AF Homology Motif