Related Experiment Video
Updated: Feb 8, 2026

Detection of Protein Ubiquitination
Published on: August 19, 2009
Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4
Nicholas O Bodnar1, Kelly H Kim2, Zhejian Ji1
1Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
Abstract:
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 Zn2+-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.
Related Concept Videos
Cofactors and Coenzymes
Cofactors and Coenzymes
Cofactors can be metallic ions or organic molecules called coenzymes. These types of helper...
The Equilibrium Binding Constant and Binding Strength
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Ligand Binding and Linkage
Cooperative Binding of Transcription Regulators

