Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4

Nat Commun. 2019 Dec 13;10(1):5708. doi: 10.1038/s41467-019-13697-y.


Npl4 is likely to be the most upstream factor recognizing Lys48-linked polyubiquitylated substrates in the proteasomal degradation pathway in yeast. Along with Ufd1, Npl4 forms a heterodimer (UN), and functions as a cofactor for the Cdc48 ATPase. Here, we report the crystal structures of yeast Npl4 in complex with Lys48-linked diubiquitin and with the Npl4-binding motif of Ufd1. The distal and proximal ubiquitin moieties of Lys48-linked diubiquitin primarily interact with the C-terminal helix and N-terminal loop of the Npl4 C-terminal domain (CTD), respectively. Mutational analysis suggests that the CTD contributes to linkage selectivity and initial binding of ubiquitin chains. Ufd1 occupies a hydrophobic groove of the Mpr1/Pad1 N-terminal (MPN) domain of Npl4, which corresponds to the catalytic groove of the MPN domain of JAB1/MPN/Mov34 metalloenzyme (JAMM)-family deubiquitylating enzyme. This study provides important structural insights into the polyubiquitin chain recognition by the Cdc48-UN complex and its assembly.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • Nucleocytoplasmic Transport Proteins / isolation & purification
  • Nucleocytoplasmic Transport Proteins / metabolism
  • Nucleocytoplasmic Transport Proteins / ultrastructure*
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Recombinant Proteins / isolation & purification
  • Recombinant Proteins / metabolism
  • Recombinant Proteins / ultrastructure
  • Saccharomyces cerevisiae Proteins / isolation & purification
  • Saccharomyces cerevisiae Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / ultrastructure*
  • Ubiquitin / metabolism
  • Ubiquitin / ultrastructure*
  • Ubiquitination
  • Valosin Containing Protein / metabolism
  • Vesicular Transport Proteins / isolation & purification
  • Vesicular Transport Proteins / metabolism
  • Vesicular Transport Proteins / ultrastructure*


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