Hierarchical binding of cofactors to the AAA ATPase p97

Structure. 2011 Jun 8;19(6):833-43. doi: 10.1016/j.str.2011.03.018.


The hexameric AAA ATPase p97 is involved in several human proteinopathies and mediates ubiquitin-dependent protein degradation among other essential cellular processes. Via its N-terminal domain (N domain), p97 interacts with multiple regulatory cofactors including the UFD1/NPL4 heterodimer and members of the "ubiquitin regulatory X" (UBX) domain protein family; however, the principles governing cofactor selectivity remain to be deciphered. Our crystal structure of the FAS-associated factor 1 (FAF1)UBX domain in complex with the p97N domain reveals that the signature Phe-Pro-Arg motif known to be crucial for interactions of UBX domains with p97 adopts a cis-proline configuration, in contrast to a cis-trans mixture we derive for the isolated FAF1UBX domain. Biochemical studies confirm that binding critically depends on a proline at this position. Furthermore, we observe that the UBX proteins FAF1 and UBXD7 only bind to p97-UFD1/NPL4, but not free p97, thus demonstrating for the first time a hierarchy in p97-cofactor interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / chemistry*
  • Adaptor Proteins, Vesicular Transport
  • Adenosine Triphosphatases / chemistry*
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Apoptosis Regulatory Proteins
  • Calorimetry
  • Carrier Proteins / chemistry
  • Chromatography, Gel
  • Coenzymes / chemistry*
  • Conserved Sequence
  • Crystallography, X-Ray
  • Humans
  • Intracellular Signaling Peptides and Proteins
  • Molecular Sequence Data
  • Nuclear Proteins / chemistry*
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Proteins / chemistry
  • Surface Properties
  • Titrimetry
  • Ubiquitin / chemistry
  • Ubiquitinated Proteins / chemistry


  • Adaptor Proteins, Signal Transducing
  • Adaptor Proteins, Vesicular Transport
  • Apoptosis Regulatory Proteins
  • Carrier Proteins
  • Coenzymes
  • FAF1 protein, human
  • Intracellular Signaling Peptides and Proteins
  • NPLOC4 protein, human
  • Nuclear Proteins
  • Proteins
  • UBXN7 protein, human
  • UFD1 protein, human
  • Ubiquitin
  • Ubiquitinated Proteins
  • Adenosine Triphosphatases
  • p97 ATPase

Associated data

  • PDB/3QQ7
  • PDB/3QQ8
  • PDB/3R3M