PDBsum entry 2fge

Hydrolase, plant protein

PDB id: 2fge

Contents

Protein chains

979 a.a. *

Ligands

ALA-ALA-LEU-THR-ARG-ALA ×2

Metals

_MG ×4

_ZN ×2

_CL ×2

Waters ×948

* Residue conservation analysis

PDB id:

2fge

Name:

Hydrolase, plant protein

Title:

Crystal structure of presequence protease prep from arabidopsis thaliana

Structure:

Zinc metalloprotease (insulinase family). Chain: a, b. Synonym: presequence protease prep. Atprep2. Metalloendopeptidase. Atprep1/atznmp. Engineered: yes. Mutation: yes. Nonspecific peptide aaltra. Chain: d, e. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.209 R-free: 0.256

Authors:

T.Eneqvist,K.A.Johnson

Key ref:

K.A.Johnson et al. (2006). The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis. EMBO J, 25, 1977-1986. PubMed id: 16601675 DOI: 10.1038/sj.emboj.7601080

Date:

21-Dec-05 Release date: 16-May-06

Protein chains

Q9LJL3  (PREP1_ARATH) -  Presequence protease 1, chloroplastic/mitochondrial from Arabidopsis thaliana

Seq: 1080 a.a.

Struc: 979 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.24.- - ?????

DOI no: 10.1038/sj.emboj.7601080

EMBO J 25:1977-1986 (2006)

PubMed id: 16601675

The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis.

K.A.Johnson, S.Bhushan, A.Ståhl, B.M.Hallberg, A.Frohn, E.Glaser, T.Eneqvist.

ABSTRACT

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 Angstroms resolution shows how the 995-residue polypeptide forms a unique proteolytic chamber of more than 10,000 Angstroms(3) 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.

Selected figure(s)

Figure 5.
Figure 5 Proposed mechanism for the PreP peptidasome substrate binding and release.

Figure 6.
Figure 6 AtPreP1 is inactive if locked in a closed conformation. (A) Schematic representation of the AtPreP1 cysteine double mutants K171C-G852C (C1), K179C-Q810C (C2), E345C-S682C (C3) and A331C-N615C (C4) under reducing and oxidizing conditions. Proteolytic activity of native (wt) AtPreP1 and the cysteine double mutants measured as the degradation of N[5.7]pF[1] (2–54) under reducing (B) and oxidizing conditions (C) and degradation of the P1 peptide under reducing (D) and oxidizing conditions (E).

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 1977-1986) copyright 2006.

Figures were selected by an automated process.