The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase

The exosome is a conserved multi‐subunit ribonuclease complex that functions in 3′ end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10‐subunit core complex of the exosome (Exo‐10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo‐10 in vitro is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N‐terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N‐terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C‐terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6–Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome. Synopsis Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47. The N‐terminal domains of S. cerevisiae Rrp6 and Rrp47 form a highly intertwined structural unit. The Rrp6–Rrp47 complex creates a composite and conserved surface groove that binds the N‐terminus of Mtr4 and recruits Mtr4 to the nuclear exosome. Structure‐based mutations of conserved residues within Rrp6 and Mtr4 disrupt their interaction, result in 5.8S RNA processing defects in vivo and inhibit growth of strains expressing a C‐terminal GFP fusion of Mtr4. Graphical Abstract Mtr4 is an RNA helicase involved in targeting nuclear RNAs for degradation. A new crystal structure reveals the basis for Mtr4 recruitment on the nuclear exosome through a direct interaction with Rrp6 and Rrp47.