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Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.

Publication Date
  • Archaea
  • Crystallography
  • X-Ray
  • Peptide Hydrolases/Chemistry
  • Peptides/Chemistry
  • Protein Conformation
  • Pyrococcus Abyssi/Enzymology
  • Substrate Specificity
  • Life Sciences :: Biochemistry
  • Biophysics & Molecular Biology [F05]
  • Sciences Du Vivant :: Biochimie
  • Biophysique & Biologie Moléculaire [F05]
  • Biology
  • Ecology
  • Geography


Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D(4) symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 A resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.

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