Background: The FF domain is conserved across all eukaryotes and usually acts as an adaptor module in RNA metabolism and transcription. Saccharomyces cerevisiae encodes two FF domain proteins, Prp40, a component of the U1 snRNP, and Ypr152c, a protein of unknown function. The structure of Prp40, its relationship to other proteins within the U1 snRNP, and its precise function remain little understood.
Results: Here we have investigated the essentiality and interaction properties of the FF domains of yeast Prp40. We show that the C-terminal two FF domains of Prp40 are dispensable. Deletion of additional FF domains is lethal. The first FF domain of Prp40 binds to U1 protein Luc7 in yeast two-hybrid and GST pulldown experiments. FF domains 2 and 3 bind to Snu71, another known U1 protein. Peptide array screens identified binding sites for FF1-2 within Snu71 (NDVHY) and for FF1 within Luc7 (phi[FHL] x [KR] x [GHL] with phi being a hydrophobic amino acid).
Conclusion: Prp40, Luc7, and Snu71 appear to form a subcomplex within the yeast U1snRNP. Our data suggests that the N-terminal FF domains are critical for these interactions. Crystallization of Prp40, Luc7, and Snu71 have failed so far but co-crystallization of pairs or the whole tri-complex may facilitate crystallographic and further functional analysis.