title: UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex.
abstract: RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein-protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39-U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35-U2AF65 and RBM39-SF3b155, the RBM39-UHM-U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM-ULM binding interface, providing a rationale for the known specificity of UHM-ULM interactions. This study therefore establishes a structural basis for specific UHM-ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Galina A
authors.initials: GA
authors.lastname: Stepanyuk
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Pedro
authors.initials: P
authors.lastname: Serrano
authors.affiliation: Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Eigen
authors.initials: E
authors.lastname: Peralta
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Carol L
authors.initials: CL
authors.lastname: Farr
authors.affiliation: Joint Center for Structural Genomics, http://www.jcsg.org.
authors.forename: Herbert L
authors.initials: HL
authors.lastname: Axelrod
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Geralt
authors.affiliation: Joint Center for Structural Genomics, http://www.jcsg.org.
authors.forename: Debanu
authors.initials: D
authors.lastname: Das
authors.affiliation: Joint Center for Structural Genomics, http://www.jcsg.org.
authors.forename: Hsiu-Ju
authors.initials: HJ
authors.lastname: Chiu
authors.affiliation: Joint Center for Structural Genomics, http://www.jcsg.org.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Jaroszewski
authors.affiliation: Joint Center for Structural Genomics, http://www.jcsg.org.
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Deacon
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Lesley
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Elsliger
authors.affiliation: Joint Center for Structural Genomics, http://www.jcsg.org.
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Kurt
authors.initials: K
authors.lastname: Wüthrich
authors.affiliation: Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Salomon
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Williamson
mesh_terms: D018360:Crystallography, X-Ray; D006801:Humans; D019169:Jurkat Cells; D046912:Multiprotein Complexes / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009687:Nuclear Proteins / Q000737:chemistry*; D000072417:Protein Domains; D020836:Protein Structure, Quaternary; D016601:RNA-Binding Proteins / Q000737:chemistry*; D000072668:Splicing Factor U2AF / Q000737:chemistry*
chemical_list: C084105:HCC1 autoantigen; D046912:Multiprotein Complexes; D009687:Nuclear Proteins; D016601:RNA-Binding Proteins; D000072668:Splicing Factor U2AF
keywords: CAPERα; HCC1; RBM39; RNA-binding protein 39; RNA-binding proteins; U2AF homology motif; U2AF5; UHM; ULM; alternative splicing