Structure of Phosphorylated SF1 Bound to U2AF 65 in an Essential Splicing Factor Complex

The essential splicing factors U2AF 65 and SF1 cooperatively bind consensus sequences at the 3′ end of introns. Phosphorylation of SF1 on a highly conserved “SPSP” motif enhances its interaction with U2AF 65 and the pre-mRNA. Here, we reveal that phosphorylation induces essential conformational changes in SF1 and in the SF1/U2AF 65 /3′ splice site complex. Crystal structures of the phosphorylated (P)SF1 domain bound to the C-terminal domain of U2AF 65 at 2.29 Å resolution and of the unphosphorylated SF1 domain at 2.48 Å resolution demonstrate that phosphorylation induces a disorder-to-order transition within a previously unknown SF1/U2AF 65 interface. We find by small-angle X-ray scattering that the local folding of the SPSP motif transduces into global conformational changes in the nearly full-length (P)SF1/U2AF 65 /3′ splice site assembly. We further determine that SPSP phosphorylation and the SF1/U2AF 65 interface are essential in vivo. These results offer a structural prototype for phosphorylation-dependent control of pre-mRNA splicing factors.