title: Shape-specific recognition in the structure of the Vts1p SAM domain with RNA.
abstract: Although the abundant sterile alpha motif (SAM) domain was originally classified as a protein-protein interaction domain, it has recently been shown that certain SAM domains have the ability to bind RNA, defining a new type of post-transcriptional gene regulator. To further understand the function of SAM-RNA recognition, we determined the solution structures of the SAM domain of the Saccharomyces cerevisiae Vts1p (Vts1p-SAM) and the Smaug response element (SRE) stem-loop RNA as a complex and in isolation. The structures show that Vts1p-SAM recognizes predominantly the shape of the SRE rather than its sequence, with the exception of a G located at the tip of the pentaloop. Using microarray gene profiling, we identified several genes in S. cerevisiae that seem to be regulated by Vts1p and contain one or more copies of the SRE.
authors.affiliation: Institute for Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zurich, Switzerland.
authors.forename: Florian C
authors.initials: FC
authors.lastname: Oberstrass
authors.forename: Albert
authors.initials: A
authors.lastname: Lee
authors.forename: Richard
authors.initials: R
authors.lastname: Stefl
authors.forename: Michael
authors.initials: M
authors.lastname: Janis
authors.forename: Guillaume
authors.initials: G
authors.lastname: Chanfreau
authors.forename: Frédéric H-T
authors.initials: FH
authors.lastname: Allain
mesh_terms: D000595:Amino Acid Sequence; D017353:Gene Deletion; D016681:Genome, Fungal / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012331:RNA, Fungal / Q000737:chemistry* / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020218:Response Elements / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D012331:RNA, Fungal; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; C508663:Vts1 protein, S cerevisiae