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ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213.

Juraj Ahel1, Arda Balci2, Victoria Faas1,3

  • 1Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.

Nature Communications
|May 13, 2025
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Summary

The giant E3 ubiquitin ligase RNF213

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Area of Science:

  • Cellular and Molecular Immunology
  • Biochemistry
  • Structural Biology

Background:

  • RNF213 is a crucial E3 ubiquitin ligase in mammalian cell-autonomous immunity.
  • It restricts the replication of diverse intracellular pathogens like bacteria, viruses, and parasites.

Purpose of the Study:

  • To elucidate the activation mechanism of RNF213 in response to pathogens.
  • To understand how RNF213's E3 ligase activity is regulated within the cell.

Main Methods:

  • Chemical and structural biology approaches were used to study RNF213.
  • Proteome-wide E3 activity profiling in living cells was developed.
  • Quantitative labeling and cryo-electron microscopy (cryo-EM) were employed.

Main Results:

  • ATP binding to RNF213's AAA core activates its E3 ligase function.
  • RNF213 activity reversibly switches based on cellular ATP levels, influenced by interferon and glycolysis.
  • A catalytic cysteine and a novel E2 docking site were identified; a cryo-EM structure of the conjugation intermediate was obtained.

Conclusions:

  • RNF213 is a novel class of ATP-dependent E3 enzyme.
  • ATP acts as a danger/pathogen-associated molecular pattern, coordinating cell-autonomous defense.
  • RNF213 utilizes unique catalytic and regulatory mechanisms for broad pathogen defense.