2FGE

Crystal structure of presequence protease PreP from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The closed structure of presequence protease PreP forms a unique 10 000 A(3) chamber for proteolysis

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

(2006) Embo J. 25: 1977-1986

  • DOI: 10.1038/sj.emboj.7601080

  • PubMed 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 sho ...

    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.


    Related Citations: 
    • Characterization of a novel zinc metalloprotease involved in degrading targeting peptides in mitochondria and chloroplasts
      Moberg, P.,Stahl, A.,Bhushan, S.,Wright, S.J.,Eriksson, A.,Bruce, B.D.,Glaser, E.
      (2003) Plant J. 36: 616


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
zinc metalloprotease (insulinase family)
A, B
995Arabidopsis thalianaMutation(s): 1 
Gene Names: PREP1 (ZNMP1)
EC: 3.4.24.-
Find proteins for Q9LJL3 (Arabidopsis thaliana)
Go to UniProtKB:  Q9LJL3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
nonspecific peptide AALTRA
D, E
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 110.834α = 90.00
b = 114.332β = 90.00
c = 162.984γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance