Structure of Thermus thermophilus ClpP in complex with a tripeptide.

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

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Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors.

Felix, J.Weinhaupl, K.Chipot, C.Dehez, F.Hessel, A.Gauto, D.F.Morlot, C.Abian, O.Gutsche, I.Velazquez-Campoy, A.Schanda, P.Fraga, H.

(2019) Sci Adv 5: eaaw3818-eaaw3818

  • DOI: https://doi.org/10.1126/sciadv.aaw3818
  • Primary Citation of Related Structures:  
    6HWM, 6HWN

  • PubMed Abstract: 

    Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation.

  • Organizational Affiliation

    Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy F-54506, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit204Thermus thermophilusMutation(s): 0 
Gene Names: clpPTT_C0250
Find proteins for Q5SKM8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKM8 
Go to UniProtKB:  Q5SKM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKM8
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown tripeptide3Thermus thermophilusMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth E]
CA [auth E]
DA [auth F]
EA [auth G]
AA [auth D],
BA [auth E],
CA [auth E],
DA [auth F],
EA [auth G],
O [auth A],
P [auth A],
Q [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth D],
Y [auth D],
Z [auth D]
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.976α = 90
b = 162.786β = 116.34
c = 107.948γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Grenoble Instruct-ERIC CenterFrance301
FranceFRISBI; ANR-10-INSB-05-02
FranceGRAL; ANR-10-LABX-49-01

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references