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Area of Science:

  • Biochemistry
  • Structural Biology
  • Archaea Biology

Background:

  • Protein ubiquitination was historically considered exclusive to eukaryotes.
  • Recent discoveries show ubiquitin modification operons in archaea.

Purpose of the Study:

  • Characterize the archaeal Rpn11 deubiquitinase (CsRpn11) from Caldiarchaeum subterraneum.
  • Investigate its role in processing ubiquitin (Ub) precursors and ubiquitinated proteins.
  • Explore the evolutionary origins of protein ubiquitination.

Main Methods:

  • Structural and mechanistic characterization of CsRpn11.
  • Analysis of CsRpn11 activity based on metal ion type, inhibitors, cleavage site, and substrate folding.
  • Comparison of CsRpn11 and CsRpn11-CsUb crystal structures.

Main Results:

  • CsRpn11 activity is modulated by metal ions, inhibitors, cleavage site sequence, and Ub-conjugated protein folding.
  • A key conformational switch in the CsRpn11 Ins-1 site facilitates CsUb binding for catalysis.
  • This switch is present in a primitive soluble Rpn11, predating eukaryotic proteasomal Rpn11.

Conclusions:

  • Experimental evidence supports an archaeal origin for protein ubiquitination.
  • The findings suggest that the ubiquitination machinery evolved before the emergence of eukaryotes.
  • CsRpn11 and CsUb are functional homologs of their eukaryotic counterparts.