6DKF

Caseinolytic protease (ClpP) from Staphylococcus aureus mutant - V7A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reversible inhibition of the ClpP protease via an N-terminal conformational switch.

Vahidi, S.Ripstein, Z.A.Bonomi, M.Yuwen, T.Mabanglo, M.F.Juravsky, J.B.Rizzolo, K.Velyvis, A.Houry, W.A.Vendruscolo, M.Rubinstein, J.L.Kay, L.E.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E6447-E6456

  • DOI: 10.1073/pnas.1805125115

  • PubMed Abstract: 
  • Protein homeostasis is critically important for cell viability. Key to this process is the refolding of misfolded or aggregated proteins by molecular chaperones or, alternatively, their degradation by proteases. In most prokaryotes and in chloroplast ...

    Protein homeostasis is critically important for cell viability. Key to this process is the refolding of misfolded or aggregated proteins by molecular chaperones or, alternatively, their degradation by proteases. In most prokaryotes and in chloroplasts and mitochondria, protein degradation is performed by the caseinolytic protease ClpP, a tetradecamer barrel-like proteolytic complex. Dysregulating ClpP function has shown promise in fighting antibiotic resistance and as a potential therapy for acute myeloid leukemia. Here we use methyl-transverse relaxation-optimized spectroscopy (TROSY)-based NMR, cryo-EM, biochemical assays, and molecular dynamics simulations to characterize the structural dynamics of ClpP from Staphylococcus aureus (SaClpP) in wild-type and mutant forms in an effort to discover conformational hotspots that regulate its function. Wild-type SaClpP was found exclusively in the active extended form, with the N-terminal domains of its component protomers in predominantly β-hairpin conformations that are less well-defined than other regions of the protein. A hydrophobic site was identified that, upon mutation, leads to unfolding of the N-terminal domains, loss of SaClpP activity, and formation of a previously unobserved split-ring conformation with a pair of 20-Å-wide pores in the side of the complex. The extended form of the structure and partial activity can be restored via binding of ADEP small-molecule activators. The observed structural plasticity of the N-terminal gates is shown to be a conserved feature through studies of Escherichia coli and Neisseria meningitidis ClpP, suggesting a potential avenue for the development of molecules to allosterically modulate the function of ClpP.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; john.rubinstein@utoronto.ca kay@pound.med.utoronto.ca.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; john.rubinstein@utoronto.ca kay@pound.med.utoronto.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit
B, D, C, A, E, F, G, I, K, J, H, L, M, N
195Staphylococcus aureus (strain Newman)Mutation(s): 1 
Gene Names: clpP
EC: 3.4.21.92
Find proteins for A6QF76 (Staphylococcus aureus (strain Newman))
Go to UniProtKB:  A6QF76
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanada--
Natural Sciences and Engineering Research Council (Canada)Canada--
Canadian Institutes of Health ResearchCanada--
Natural Sciences and Engineering Research Council (Canada)Canada--
Canadian Institutes of Health ResearchCanada--
Natural Sciences and Engineering Research Council (Canada)Canada--

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Data collection, Database references
  • Version 1.2: 2018-07-25
    Type: Data collection, Database references