Structure of a Eukaryotic RNase III Postcleavage Complex Reveals a Double-Ruler Mechanism for Substrate Selection

• Published in: Molecular cell Vol. 54; no. 3; pp. 431 - 444
• Main Authors: Liang, Yu-He, Lavoie, Mathieu, Comeau, Marc-Andre, Abou Elela, Sherif, Ji, Xinhua
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 08.05.2014
• Subjects: Amino Acid Sequence; Catalytic Domain; Crystallography, X-Ray; Hydrogen Bonding; Models, Molecular; Protein Binding; Ribonuclease III - chemistry; RNA Cleavage; RNA, Fungal - chemistry; Saccharomyces cerevisiae; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae Proteins - chemistry; Substrate Specificity
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2014.03.006

Ribonuclease III (RNase III) enzymes are a family of double-stranded RNA (dsRNA)-specific endoribonucleases required for RNA maturation and gene regulation. Prokaryotic RNase III enzymes have been well characterized, but how eukaryotic RNase IIIs work is less clear. Here, we describe the structure of the Saccharomyces cerevisiae RNase III (Rnt1p) postcleavage complex and explain why Rnt1p binds to RNA stems capped with an NGNN tetraloop. The structure shows specific interactions between a structural motif located at the end of the Rnt1p dsRNA-binding domain (dsRBD) and the guanine nucleotide in the second position of the loop. Strikingly, structural and biochemical analyses indicate that the dsRBD and N-terminal domains (NTDs) of Rnt1p function as two rulers that measure the distance between the tetraloop and the cleavage site. These findings provide a framework for understanding eukaryotic RNase IIIs. [Display omitted] •The structure of yeast RNase III (Rnt1p) postcleavage complex is determined•The substrate-binding mode of Rnt1p is distinct from that of bacterial RNase III•An RNA-binding motif of Rnt1p functions as a guanine-specific clamp•Rnt1p uses an unusual double-ruler mechanism for substrate selection RNase IIIs are dsRNA-specific endoribonucleases. How eukaryotic RNase IIIs work is not clear. Here, Liang et al. describe the structure of the yeast RNase III, Rnt1p, in complex with RNA product, explaining how the enzyme recognizes substrates and specifies the cleavage sites.