Structure of the Cdc48 ATPase With Its Ubiquitin-Binding Cofactor Ufd1-Npl4

Nat Struct Mol Biol. 2018 Jul;25(7):616-622. doi: 10.1038/s41594-018-0085-x. Epub 2018 Jul 2.

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.

Publication types

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

MeSH terms

  • Chaetomium / metabolism*
  • Coenzymes / chemistry
  • Coenzymes / metabolism
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Fungal Proteins / chemistry*
  • Fungal Proteins / metabolism*
  • Models, Molecular
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / metabolism
  • Mutagenesis, Site-Directed
  • Nucleocytoplasmic Transport Proteins / chemistry
  • Nucleocytoplasmic Transport Proteins / genetics
  • Nucleocytoplasmic Transport Proteins / metabolism
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Quaternary
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Ubiquitin / metabolism
  • Unfolded Protein Response
  • Valosin Containing Protein / chemistry*
  • Valosin Containing Protein / genetics
  • Valosin Containing Protein / metabolism*
  • Vesicular Transport Proteins / chemistry
  • Vesicular Transport Proteins / genetics
  • Vesicular Transport Proteins / metabolism

Substances

  • Coenzymes
  • Fungal Proteins
  • Multiprotein Complexes
  • NPL4 protein, S cerevisiae
  • Nucleocytoplasmic Transport Proteins
  • Saccharomyces cerevisiae Proteins
  • UFD1 protein, S cerevisiae
  • Ubiquitin
  • Vesicular Transport Proteins
  • CDC48 protein, S cerevisiae
  • Valosin Containing Protein