UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex

• Published in: Acta crystallographica. Section D, Structural biology Vol. 72; no. Pt 4; p. 497
• Main Authors: Stepanyuk, Galina A, Serrano, Pedro, Peralta, Eigen, Farr, Carol L, Axelrod, Herbert L, Geralt, Michael, Das, Debanu, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Deacon, Ashley M, Lesley, Scott A, Elsliger, Marc-André, Godzik, Adam, Wilson, Ian A, Wüthrich, Kurt, Salomon, Daniel R, Williamson, James R
• Format: Journal Article
• Language: English
• Published: United States 01.04.2016
• Subjects: Crystallography, X-Ray; Humans; Jurkat Cells; Multiprotein Complexes - chemistry; Nuclear Magnetic Resonance, Biomolecular; Nuclear Proteins - chemistry; Protein Domains; Protein Structure, Quaternary; RNA-Binding Proteins - chemistry; Splicing Factor U2AF - chemistry; RBM39; U2AF homology motif; alternative splicing; U2AF5; ULM; HCC1; RNA-binding proteins; UHM; CAPERα; RNA-binding protein 39
• ISSN: 2059-7983
• DOI: 10.1107/S2059798316001248

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.