Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1–Npl4

Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains. Cdc48 binds various cofactors, including the Ufd1–Npl4 heterodimer. Here, we report structures of the Cdc48–Ufd1–Npl4 complex from Chaetomium thermophilum . Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and it uses two Zn 2+ -finger domains to anchor the enzymatically inactive Mpr1–Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48’s central pore, a position similar to the MPN domain from deubiquitinase Rpn11 in the proteasome. Our results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase.