Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D7  (3D View)
Global Stoichiometry: Homo 14-mer - A14 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 162.35 kDa 
• Atom Count: 10130 
• Modelled Residue Count: 1311 
• Deposited Residue Count: 1428 
• Unique protein chains: 1

6HWM

Structure of Thermus thermophilus ClpP in complex with bortezomib

• PDB DOI: 10.2210/pdb6HWM/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-12 Released: 2019-09-18 
• Deposition Author(s): Felix, J., Schanda, P., Fraga, H., Morlot, C.
• Funding Organization(s): Grenoble Instruct-ERIC Center, Grenoble Alliance for Integrated Structural Cell Biology, French Infrastructure for Integrated Structural Biology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

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

• PubMed: 31517045 
• DOI: 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.

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Organizational Affiliation: 

i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A, B, C, D, E, F, G	204	Thermus thermophilus	Mutation(s): 0  Gene Names: clpP, TT_C0250 EC: 3.4.21.92
UniProt
Find proteins for Q72L15 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72L15  Go to UniProtKB:  Q72L15

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BO2	H [auth A], I [auth B], J [auth C], L [auth D], M [auth E], O [auth F], P [auth G]	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE C19 H25 B N4 O4 GXJABQQUPOEUTA-RDJZCZTQSA-N
PEG	K [auth C], N [auth E], Q [auth G]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.139	α = 90
b = 168.74	β = 90
c = 166.083	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-10-12 
• Released Date: 2019-09-18 
Deposition Author(s): Felix, J., Schanda, P., Fraga, H., Morlot, C.

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Funding Organization	Location	Grant Number
Grenoble Instruct-ERIC Center	France	301
Grenoble Alliance for Integrated Structural Cell Biology	France	ANR-10-LABX-49-01
French Infrastructure for Integrated Structural Biology	France	ANR-10-INSB-05-02

Revision History  

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