4KA7

Structure of Organellar OligoPeptidase (E572Q) in complex with an endogenous substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts.

Kmiec, B.Teixeira, P.F.Berntsson, R.P.Murcha, M.W.Branca, R.M.Radomiljac, J.D.Regberg, J.Svensson, L.M.Bakali, A.Langel, U.Lehtio, J.Whelan, J.Stenmark, P.Glaser, E.

(2013) Proc. Natl. Acad. Sci. U.S.A. 110: E3761-E3769

  • DOI: 10.1073/pnas.1307637110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Both mitochondria and chloroplasts contain distinct proteolytic systems for precursor protein processing catalyzed by the mitochondrial and stromal processing peptidases and for the degradation of targeting peptides catalyzed by presequence protease. ...

    Both mitochondria and chloroplasts contain distinct proteolytic systems for precursor protein processing catalyzed by the mitochondrial and stromal processing peptidases and for the degradation of targeting peptides catalyzed by presequence protease. Here, we have identified and characterized a component of the organellar proteolytic systems in Arabidopsis thaliana, the organellar oligopeptidase, OOP (At5g65620). OOP belongs to the M3A family of peptide-degrading metalloproteases. Using two independent in vivo methods, we show that the protease is dually localized to mitochondria and chloroplasts. Furthermore, we localized the OPP homolog At5g10540 to the cytosol. Analysis of peptide degradation by OOP revealed substrate size restriction from 8 to 23 aa residues. Short mitochondrial targeting peptides (presequence of the ribosomal protein L29 and presequence of 1-aminocyclopropane-1-carboxylic acid deaminase 1) and N- and C-terminal fragments derived from the presequence of the ATPase beta subunit ranging in size from 11 to 20 aa could be degraded. MS analysis showed that OOP does not exhibit a strict cleavage pattern but shows a weak preference for hydrophobic residues (F/L) at the P1 position. The crystal structures of OOP, at 1.8-1.9 Å, exhibit an ellipsoidal shape consisting of two major domains enclosing the catalytic cavity of 3,000 Å(3). The structural and biochemical data suggest that the protein undergoes conformational changes to allow peptide binding and proteolysis. Our results demonstrate the complementary role of OOP in targeting-peptide degradation in mitochondria and chloroplasts.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA. Michael.Acker@novartis.com.,State Key Laboratory of Membrane Biology, Beijing, 100084 China.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K.,Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,3Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,5Present Address: Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.,Departments of Biochemistry and Biophysics and Neurochemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.,Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia. Electronic address: M.Maher@latrobe.edu.au.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands. b.j.c.janssen@uu.nl.,Department of Pathology, St. Olavs Hospital, Trondheim, Norway.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.,Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K.,Laboratoire des biomolécules, LBM, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.,Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.,School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,4Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Beijing Advanced Innovation Center for Structural Biology, Beijing, 100084 China.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. Stephen_Blacklow@hms.harvard.edu.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3083, Australia.,LCM, CNRS, Ecole Polytechnique , Université Paris-Saclay , 91128 Palaiseau Cedex , France.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. Stephen_Blacklow@hms.harvard.edu.,Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea. Electronic address: jsunkim@chonnam.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligopeptidase A
A
714Arabidopsis thalianaMutation(s): 1 
Gene Names: OOP (TOP1)
EC: 3.4.24.70
Find proteins for Q94AM1 (Arabidopsis thaliana)
Go to UniProtKB:  Q94AM1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
short endogenous peptide substrate
C
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.466α = 90.00
b = 100.771β = 90.00
c = 132.484γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Refinement description, Source and taxonomy
  • Version 1.2: 2018-10-17
    Type: Data collection, Database references