Structure and RNA binding of Nab3

F. Hóbor¹, K. Kubicek², J. Pasulka¹, R. Stefl¹

¹National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno

²Dept. of Condensed Matter Physics, Faculty of Science, Masaryk University, 61137 Brno

stefl@chemi.muni.cz

Besides mRNA, RNA polymerase II also transcribes a subset of small nuclear and small nucleoar RNAs, and a class of intergenic and anti-sense RNAs. Termination of these transcripts requires the nuclear pre-mRNA down- regulation (Nrd)1 and the nuclear polyadenylated RNA-binding (Nab)3 proteins, and the RNA helicase Sen1. In this so-called nonpoly(A) termination pathway, the RNA-binding proteins, Nrd1 and Nab3, recognize Nrd1- and Nab3-binding sites which is an initial step in the termination and subsequent processing or degradation of these transcripts.

Recent studies identified sequence motives for Nrd1 and Nab3, as the signals that direct termination and exosome-TRAMP trimming/degradation of nonpolyadenylated transcripts. It was shown that the RNA-recognition motif (RRM) of Nrd1 and Nab3 bind to the GUA[A/G] and UCUU sequences, respectively. In addition, it was demonstrated that Nrd1 and Nab3 form a stable heterodimer and bind to snoRNA terminators that contain multiple Nrd1- and Nab3- binding sequences.

To fully understand the structural basis behind the RNA recognition by the Nrd1-Nab3 complex, we use multidimensional NMR spectroscopy to determine the three- dimensional structures of the individual RRMs of Nrd1 and Nab3 and the minimal Nrd1- Nab3 heterodimer alone as well as in complex with their RNA substrates.