Mechanism and regulation of the Lys6-selective deubiquitinase USP30

Nat Struct Mol Biol. 2017 Nov;24(11):920-930. doi: 10.1038/nsmb.3475. Epub 2017 Sep 25.


Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein kinase PINK1 and the ubiquitin E3 ligase Parkin. Ubiquitin-specific protease USP30 antagonizes Parkin-mediated ubiquitination events on mitochondria and is a key negative regulator of mitophagy. Parkin and USP30 both show a preference for assembly or disassembly, respectively, of Lys6-linked polyubiquitin, a chain type that has not been well studied. Here we report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces. We assess the interplay between USP30, PINK1 and Parkin and show that distally phosphorylated ubiquitin chains impair USP30 activity. Lys6-linkage-specific affimers identify numerous mitochondrial substrates for this modification, and we show that USP30 regulates Lys6-polyubiquitinated TOM20. Our work provides insights into the architecture, activity and regulation of USP30, which will aid drug design against this and related enzymes.

MeSH terms

  • Deubiquitinating Enzymes / chemistry*
  • Deubiquitinating Enzymes / metabolism*
  • Humans
  • Mitochondrial Proteins / chemistry*
  • Mitochondrial Proteins / metabolism*
  • Protein Binding
  • Protein Kinases / metabolism
  • Substrate Specificity
  • Thiolester Hydrolases / chemistry*
  • Thiolester Hydrolases / metabolism*
  • Ubiquitin / chemistry*
  • Ubiquitin / metabolism*
  • Ubiquitin-Protein Ligases / metabolism


  • Mitochondrial Proteins
  • Ubiquitin
  • Usp30 protein, human
  • Ubiquitin-Protein Ligases
  • parkin protein
  • Protein Kinases
  • PTEN-induced putative kinase
  • Thiolester Hydrolases
  • Deubiquitinating Enzymes