Structural basis of UGUA recognition by the Nudix protein CFIm25 and implications for a regulatory role in mRNA 3‧ processing

Human Cleavage Factor Im (CFI_m) is an essential component of the pre-mRNA 3' processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI_m25) of the CFI_m complex possesses a characteristic α/β/α Nudix fold, CFI_m25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI_m25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI_m25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap₄A (diadenosine tetraphosphate) by CFI_m25 suggests a potential role for small molecules in the regulation of mRNA 3' processing.