6HWM

Structure of Thermus thermophilus ClpP in complex with bortezomib


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E, F, G
A, B, C, D, E, F, G
204Thermus thermophilusMutation(s): 0 
Gene Names: clpPTT_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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72L15
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BO2
Query on BO2

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B],
J [auth C],
L [auth D],
M [auth E],
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
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth C],
N [auth E],
Q [auth G]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
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 = 135.139α = 90
b = 168.74β = 90
c = 166.083γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grenoble Instruct-ERIC CenterFrance301
Grenoble Alliance for Integrated Structural Cell BiologyFranceANR-10-LABX-49-01
French Infrastructure for Integrated Structural BiologyFranceANR-10-INSB-05-02

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