FC0019
Splicing factor 1 (SF1)  -  U2 small nuclear RNA auxiliary factor (U2AF⁶⁵)

Biological function
The interaction of splicing factor 1 (SF1) with the large subunit of the U2 small nuclear RNA auxiliary factor (U2AF⁶⁵) is an initial step in splice site selection in pre-mRNA splicing.

Structural evidence
The C and C secondary chemical shifts of free and bound U2AF⁶⁵-RRM3 are very similar, indicating that the secondary structure of U2AF⁶⁵-RRM3 remains unchanged upon complex formation. NMR spectra of free SF1(1-25) display characteristics of a random coil conformation. Upon addition of unlabeled U2AF⁶⁵-RRM3 to ¹⁵N-labeled SF1(1-25), tight binding is observed (based on large chemical shift changes with slow exchange on the NMR time scale). According to secondary chemical shifts, SF1(1-25) binds to U2AF⁶⁵ in an extended conformation. No significant chemical shift changes are only found for residues C-terminal to Ser14. Negative heteronuclear {¹H}-¹⁵N nuclear Overhauser enhancement (NOE) values for the amides of residues 1–14 of SF1(1-25) when bound to U2AF⁶⁵-RRM3 indicate high backbone flexibility.

Biochemical evidence
In the solved complex, the SF1 construct binds by a motif that is ten residues in length, with an affinity of 23.8 nM, whereas the full-length SF1 has a K_d of 11.8 nM, indicating that flanking regions also contribute to binding. Furthermore, removal of those residues which do not physically contact the partner decreases the binding strength to 55.6 nM.

Mechanism category
flexibility/entropy modulation

Posttranslational modification
Phosphorylation on S20 inhibits spliceosome assembly.

Significance
Fuzzy flanking regions tune the entropy of binding and thus improve binding affinity. Transient interactions also affect specificity for different U2AF RRMs.

Further reading
11551507