Structural insights into cis element recognition of non-polyadenylated RNAs by the Nab3-RRM

Termination of non-polyadenylated transcripts in Saccharomyces cerevisiae occurs through the action of the Nrd1-Nab3-Sen1 complex. Key signals for termination by the Nrd1-Nab3-Sen1 complex are RNA sequences which are recognized by RNA recognition motifs (RRMs) within Nrd1 and Nab3. In order to understand how these signals are recognized we determined the crystal structure of Nab3-RRM bound to its UCUU recognition sequence. Nab3-RRM establishes a clear preference for the central cytidine of the UCUU motif, which forms pseudo-base pairing interactions primarily through hydrogen bonds to main chain atoms and one serine hydroxyl group. Specificity for the flanking uridines is less defined; however, binding experiments confirm that these residues are also important for high affinity binding. Comparison of the Nab3-RRM structure with other RRMs bound to polypyrimidine RNAs showed that Nab3-RRM’s mode of recognition is very similar to what is observed for the polypyrimidine tract binding (PTB) RRMs, and may suggest a possible mechanism for discriminating between C and U in polypyrimidine binding RRMs.