The APC/C subunit Cdc16/Cut9 is a contiguous tetratricopeptide repeat superhelix with a homo‐dimer interface similar to Cdc27

The anaphase‐promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase responsible for controlling cell cycle transitions, is a multisubunit complex assembled from 13 different proteins. Numerous APC/C subunits incorporate multiple copies of the tetratricopeptide repeat (TPR). Here, we report the crystal structure of Schizosaccharomyces pombe Cut9 (Cdc16/Apc6) in complex with Hcn1 (Cdc26), showing that Cdc16/Cut9 is a contiguous TPR superhelix of 14 TPR units. A C‐terminal block of TPR motifs interacts with Hcn1, whereas an N‐terminal TPR block mediates Cdc16/Cut9 self‐association through a homotypic interface. This dimer interface is structurally related to the N‐terminal dimerization domain of Cdc27, demonstrating that both Cdc16/Cut9 and Cdc27 form homo‐dimers through a conserved mechanism. The acetylated N‐terminal Met residue of Hcn1 is enclosed within a chamber created from the Cut9 TPR superhelix. Thus, in complex with Cdc16/Cut9, the N ‐acetyl‐Met residue of Hcn1, a putative degron for the Doa10 E3 ubiquitin ligase, is inaccessible for Doa10 recognition, protecting Hcn1/Cdc26 from ubiquitin‐dependent degradation. This finding may provide a structural explanation for a mechanism to control the stoichiometry of proteins participating in multisubunit complexes.