Bipartite determinants mediate an evolutionarily conserved interaction between Cdc48 and the 20S peptidase

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3327-32. doi: 10.1073/pnas.1300408110. Epub 2013 Feb 11.

Abstract

Proteasomes are essential and ubiquitous ATP-dependent proteases that function in eukarya, archaea, and some bacteria. These destructive but critically important proteolytic machines use a 20S core peptidase and a hexameric ATPase associated with a variety of cellular activities (AAA+) unfolding ring that unfolds and spools substrates into the peptidase chamber. In archaea, 20S can function with the AAA+ Cdc48 or proteasome-activating nucleotidase (PAN) unfoldases. Both interactions are stabilized by C-terminal tripeptides in AAA+ subunits that dock into pockets on the 20S periphery. Here, we provide evidence that archaeal Cdc48 also uses a distinct set of near-axial interactions to bind 20S and propose that similar dual determinants mediate PAN-20S interactions and Rpt(1-6)-20S interactions in the 26S proteasome. Current dogma holds that the Rpt(1-6) unfolding ring of the 19S regulatory particle is the only AAA+ partner of eukaryotic 20S. By contrast, we show that mammalian Cdc48, a key player in cell-cycle regulation, membrane fusion, and endoplasmic-reticulum-associated degradation, activates mammalian 20S and find that a mouse Cdc48 variant supports protein degradation in combination with 20S. Our results suggest that eukaryotic Cdc48 orthologs function directly with 20S to maintain intracellular protein quality control.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenosine Triphosphatases / chemistry
  • Adenosine Triphosphatases / metabolism*
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Archaeal Proteins / chemistry
  • Archaeal Proteins / metabolism
  • Cell Cycle Proteins / chemistry
  • Cell Cycle Proteins / metabolism*
  • Evolution, Molecular*
  • Mice
  • Models, Biological
  • Molecular Sequence Data
  • Mutant Proteins / metabolism
  • Proteasome Endopeptidase Complex / chemistry
  • Proteasome Endopeptidase Complex / metabolism*
  • Protein Binding
  • Protein Structure, Secondary
  • Proteolysis
  • Saccharomyces cerevisiae / enzymology
  • Saccharomyces cerevisiae Proteins
  • Substrate Specificity
  • Thermoplasma / metabolism
  • Valosin Containing Protein

Substances

  • Archaeal Proteins
  • Cell Cycle Proteins
  • Mutant Proteins
  • Saccharomyces cerevisiae Proteins
  • Proteasome Endopeptidase Complex
  • Adenosine Triphosphatases
  • CDC48 protein, S cerevisiae
  • PAN enzyme
  • Valosin Containing Protein