Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase

Mol Cell. 2022 Feb 3;82(3):570-584.e8. doi: 10.1016/j.molcel.2021.11.033. Epub 2021 Dec 23.


The hexameric Cdc48 ATPase (p97 or VCP in mammals) cooperates with its cofactor Ufd1/Npl4 to extract polyubiquitinated proteins from membranes or macromolecular complexes for degradation by the proteasome. Here, we clarify how the Cdc48 complex unfolds its substrates and translocates polypeptides with branchpoints. The Cdc48 complex recognizes primarily polyubiquitin chains rather than the attached substrate. Cdc48 and Ufd1/Npl4 cooperatively bind the polyubiquitin chain, resulting in the unfolding of one ubiquitin molecule (initiator). Next, the ATPase pulls on the initiator ubiquitin and moves all ubiquitin molecules linked to its C terminus through the central pore of the hexameric double ring, causing transient ubiquitin unfolding. When the ATPase reaches the isopeptide bond of the substrate, it can translocate and unfold both N- and C-terminal segments. Ubiquitins linked to the branchpoint of the initiator dissociate from Ufd1/Npl4 and move outside the central pore, resulting in the release of unfolded, polyubiquitinated substrate from Cdc48.

Keywords: AAA ATPase; Npl4; Ufd1; VCP; p97; translocation; ubiquitin; unfolding.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Nucleocytoplasmic Transport Proteins / genetics
  • Nucleocytoplasmic Transport Proteins / metabolism
  • Polyubiquitin / metabolism*
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Binding
  • Protein Transport
  • Protein Unfolding
  • Proteolysis
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Ubiquitinated Proteins / genetics
  • Ubiquitinated Proteins / metabolism*
  • Ubiquitination
  • Valosin Containing Protein / genetics
  • Valosin Containing Protein / metabolism*
  • Vesicular Transport Proteins / genetics
  • Vesicular Transport Proteins / metabolism


  • NPL4 protein, S cerevisiae
  • Nucleocytoplasmic Transport Proteins
  • Saccharomyces cerevisiae Proteins
  • UFD1 protein, S cerevisiae
  • Ubiquitinated Proteins
  • Vesicular Transport Proteins
  • Polyubiquitin
  • Proteasome Endopeptidase Complex
  • CDC48 protein, S cerevisiae
  • Valosin Containing Protein