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  • The EMBO Journal (2006) 25, 1977 - 1986
  • doi:10.1038/sj.emboj.7601080

Published online: 6 April 2006

The closed structure of presequence protease PreP forms a unique 10 000 Å3 chamber for proteolysis

Kenneth A Johnson1,2,a, Shashi Bhushan1,a, Annelie Ståhl1,b, B Martin Hallberg2, Anne Frohn1, Elzbieta Glaser1 and Therese Eneqvist1,2

  1. Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
  2. Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden

Correspondence to:

Elzbieta Glaser, Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm 106 91, Sweden. Tel.: +46 8 16 24 57; Fax: +46 8 15 36 79; E-mail: e_glaser@dbb.su.se

Therese Eneqvist, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden. Tel.: +46 8 52 486 882; Fax: +46 8 52 48 6850; E-mail: eneqvist@dbb.su.se

aThese authors contributed equally to this work

bPresent address: Ludwig Institute for Cancer Research, Karolinska Institute, SE-171 77 Stockholm, Sweden

Received 1 September 2005; Accepted 14 March 2006

Presequence protease PreP is a novel protease that degrades targeting peptides as well as other unstructured peptides in both mitochondria and chloroplasts. The first structure of PreP from Arabidopsis thaliana refined at 2.1 Å resolution shows how the 995-residue polypeptide forms a unique proteolytic chamber of more than 10 000 Å3 in which the active site resides. Although there is no visible opening to the chamber, a peptide is bound to the active site. The closed conformation places previously unidentified residues from the C-terminal domain at the active site, separated by almost 800 residues in sequence to active site residues located in the N-terminal domain. Based on the structure, a novel mechanism for proteolysis is proposed involving hinge-bending motions that cause the protease to open and close in response to substrate binding. In support of this model, cysteine double mutants designed to keep the chamber covalently locked show no activity under oxidizing conditions. The manner in which substrates are processed inside the chamber is reminiscent of the proteasome; therefore, we refer to this protein as a peptidasome.

  • Keywords:

    • peptidase,
    • peptide degradation,
    • PreP protease,
    • protein import,
    • targeting peptide