7UVM

Crystal structure of human ClpP protease in complex with TR-27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Potent ClpP agonists with anticancer properties bind with improved structural complementarity and alter the mitochondrial N-terminome.

Mabanglo, M.F.Wong, K.S.Barghash, M.M.Leung, E.Chuang, S.H.W.Ardalan, A.Majaesic, E.M.Wong, C.J.Zhang, S.Lang, H.Karanewsky, D.S.Iwanowicz, A.A.Graves, L.M.Iwanowicz, E.J.Gingras, A.C.Houry, W.A.

(2023) Structure 31: 185

  • DOI: https://doi.org/10.1016/j.str.2022.12.002
  • Primary Citation of Related Structures:  
    7UVM, 7UVN, 7UVR, 7UVU, 7UW0

  • PubMed Abstract: 

    The mitochondrial ClpP protease is responsible for mitochondrial protein quality control through specific degradation of proteins involved in several metabolic processes. ClpP overexpression is also required in many cancer cells to eliminate reactive oxygen species (ROS)-damaged proteins and to sustain oncogenesis. Targeting ClpP to dysregulate its function using small-molecule agonists is a recent strategy in cancer therapy. Here, we synthesized imipridone-derived compounds and related chemicals, which we characterized using biochemical, biophysical, and cellular studies. Using X-ray crystallography, we found that these compounds have enhanced binding affinities due to their greater shape and charge complementarity with the surface hydrophobic pockets of ClpP. N-terminome profiling of cancer cells upon treatment with one of these compounds revealed the global proteomic changes that arise and identified the structural motifs preferred for protein cleavage by compound-activated ClpP. Together, our studies provide the structural and molecular basis by which dysregulated ClpP affects cancer cell viability and proliferation.


  • Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G
221Homo sapiensMutation(s): 0 
Gene Names: CLPP
EC: 3.4.21.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q16740 (Homo sapiens)
Explore Q16740 
Go to UniProtKB:  Q16740
PHAROS:  Q16740
GTEx:  ENSG00000125656 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16740
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.148α = 90
b = 153.722β = 117.76
c = 105.101γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-173345

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description