Architecture of the Nuclease Module of the Yeast Ccr4-Not Complex: the Not1-Caf1-Ccr4 Interaction

Shortening eukaryotic poly(A) tails represses mRNA translation and induces mRNA turnover. The major cytoplasmic deadenylase, the Ccr4-Not complex, is a conserved multisubunit assembly. Ccr4-Not is organized around Not1, a large scaffold protein that recruits two 3′-5′ exoribonucleases, Caf1 and Ccr4. We report structural studies showing that the N-terminal arm of yeast Not1 has a HEAT-repeat structure with domains related to the MIF4G fold. A MIF4G domain positioned centrally within the Not1 protein recognizes Caf1, which in turn binds the LRR domain of Ccr4 and tethers the Ccr4 nuclease domain. The interactions that form the nuclease core of the Ccr4-Not complex are evolutionarily conserved. Their specific disruption affects cell growth and mRNA deadenylation and decay in vivo in yeast. Thus, the N-terminal arm of Not1 forms an extended platform reminiscent of scaffolding proteins like eIF4G and CBP80, and places the two nucleases in a pivotal position within the Ccr4-Not complex. ► HEAT repeats and MIF4G-like domains form the scaffold of the Not1 N-terminal arm ► Caf1 is sandwiched between the conserved Not1 MIF4G fold and Ccr4 LRR ► The nuclease active sites are in a central position and accessible in the complex ► Connecting Caf1 and Ccr4 to Not1 is essential for normal growth and deadenylation