new α-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III

Rnt1 endoribonuclease, the yeast homolog of RNAse III, plays an important role in the maturation of a diverse set of RNAs. The enzymatic activity requires a conserved catalytic domain, while RNA binding requires the double‐stranded RNA‐binding domain (dsRBD) at the C‐terminus of the protein. While bacterial RNAse III enzymes cleave double‐stranded RNA, Rnt1p specifically cleaves RNAs that possess short irregular stem‐loops containing 12–14 base pairs interrupted by internal loops and bulges and capped by conserved AGNN tetraloops. Consistent with this substrate specificity, the isolated Rnt1p dsRBD and the 30–40 amino acids that follow bind to AGNN‐containing stem‐loops preferentially in vitro. In order to understand how Rnt1p recognizes its cognate processing sites, we have defined its minimal RNA‐binding domain and determined its structure by solution NMR spectroscopy and X‐ray crystallography. We observe a new carboxy‐terminal helix following a canonical dsRBD structure. Removal of this helix reduces binding to Rnt1p substrates. The results suggest that this helix allows the Rnt1p dsRBD to bind to short RNA stem‐loops by modulating the conformation of helix α1, a key RNA‐recognition element of the dsRBD.