Non-coding RNA polymerase II transcripts are processed by the poly(A)-independent termination pathway that requires the Nrd1 complex. The Nrd1 complex includes two RNA-binding proteins, the nuclear polyadenylated RNA-binding (Nab) 3 and the nuclear pre-mRNA down-regulation (Nrd) 1 that bind their specific termination elements. Here we report the solution structure of the RNA-recognition motif (RRM) of Nab3 in complex with a UCUU oligonucleotide, representing the Nab3 termination element. The structure shows that the first three nucleotides of UCUU are accommodated on the β-sheet surface of Nab3 RRM, but reveals a sequence-specific recognition only for the central cytidine and uridine. The specific contacts we identified are important for binding affinity in vitro as well as for yeast viability. Furthermore, we show that both RNA-binding motifs of Nab3 and Nrd1 alone bind their termination elements with a weak affinity. Interestingly, when Nab3 and Nrd1 form a heterodimer, the affinity to RNA is significantly increased due to the cooperative binding. These findings are in accordance with the model of their function in the poly(A) independent termination, in which binding to the combined and/or repetitive termination elements elicits efficient termination.

• MeSH
• Transcription, Genetic * MeSH
• Nuclear Proteins chemistry   genetics   metabolism   MeSH
• Protein Conformation MeSH
• Magnetic Resonance Spectroscopy MeSH
• Protein Multimerization MeSH
• Oligonucleotides chemistry   metabolism   MeSH
• RNA-Binding Proteins chemistry   genetics   metabolism   MeSH
• Solutions MeSH
• Saccharomyces cerevisiae Proteins chemistry   genetics   metabolism   MeSH
• Saccharomyces cerevisiae genetics   MeSH
• Base Sequence MeSH
• Protein Binding MeSH
• Binding Sites MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Nuclear Proteins MeSH
• NAB3 protein, S cerevisiae MeSH Browser
• NRD1 protein, S cerevisiae MeSH Browser
• Oligonucleotides MeSH
• RNA-Binding Proteins MeSH
• Solutions MeSH
• Saccharomyces cerevisiae Proteins MeSH