Mechanistic insight into substrate processing and allosteric inhibition of human p97

Nat Struct Mol Biol. 2021 Jul;28(7):614-625. doi: 10.1038/s41594-021-00617-2. Epub 2021 Jul 14.

Abstract

p97 processes ubiquitinated substrates and plays a central role in cellular protein homeostasis. Here, we report a series of cryo-EM structures of the substrate-engaged human p97 complex with resolutions ranging from 2.9 to 3.8 Å that captured 'power-stroke'-like motions of both the D1 and D2 ATPase rings of p97. A key feature of these structures is the critical conformational changes of the intersubunit signaling (ISS) motifs, which tighten the binding of nucleotides and neighboring subunits and contribute to the spiral staircase conformation of the D1 and D2 rings. In addition, we determined the cryo-EM structure of human p97 in complex with NMS-873, a potent p97 inhibitor, at a resolution of 2.4 Å. The structures showed that NMS-873 binds at a cryptic groove in the D2 domain and interacts with the ISS motif, preventing its conformational change and thus blocking substrate translocation allosterically.

Publication types

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

MeSH terms

  • Acetanilides / pharmacology
  • Adenosine Triphosphate / chemistry*
  • Animals
  • Benzothiazoles / pharmacology
  • Cryoelectron Microscopy
  • Endoplasmic Reticulum / metabolism
  • Endoplasmic Reticulum-Associated Degradation / physiology
  • Humans
  • Intracellular Signaling Peptides and Proteins / metabolism
  • Nuclear Proteins / metabolism
  • Proteasome Endopeptidase Complex / metabolism
  • Protein Conformation
  • Protein Folding*
  • Proteostasis / physiology*
  • Signal Transduction / physiology*
  • Ubiquitinated Proteins / metabolism
  • Valosin Containing Protein / antagonists & inhibitors
  • Valosin Containing Protein / metabolism*

Substances

  • Acetanilides
  • Benzothiazoles
  • Intracellular Signaling Peptides and Proteins
  • NMS-873
  • NPLOC4 protein, human
  • Nuclear Proteins
  • UFD1 protein, human
  • Ubiquitinated Proteins
  • Adenosine Triphosphate
  • Proteasome Endopeptidase Complex
  • VCP protein, human
  • Valosin Containing Protein