4EMM

Crystal structure of Staphylococcus aureus ClpP in compact conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Helix unfolding/refolding characterizes the functional dynamics of Staphylococcus aureus Clp protease

Ye, F.Zhang, J.Liu, H.Hilgenfeld, R.Zhang, R.Kong, X.Li, L.Lu, J.Zhang, X.Li, D.Jiang, H.Yang, C.-G.Luo, C.

(2013) J.Biol.Chem. 288: 17643-17653

  • DOI: 10.1074/jbc.M113.452714
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ATP-dependent Clp protease (ClpP) plays an essential role not only in the control of protein quality but also in the regulation of bacterial pathogen virulence, making it an attractive target for antibacterial treatment. We have previously determ ...

    The ATP-dependent Clp protease (ClpP) plays an essential role not only in the control of protein quality but also in the regulation of bacterial pathogen virulence, making it an attractive target for antibacterial treatment. We have previously determined the crystal structures of Staphylococcus aureus ClpP (SaClpP) in two different states, extended and compressed. To investigate the dynamic switching of ClpP between these states, we performed a series of molecular dynamics simulations. During the structural transition, the long and straight helix E in the extended SaClpP monomer underwent an unfolding/refolding process, resulting in a kinked helix very similar to that in the compressed monomer. As a stable intermediate in the molecular dynamics simulation, the compact state was suggested and subsequently identified in x-ray crystallographic experiment. Our combined studies also determined that Ala(140) acted as a "hinge" during the transition between the extended and compressed states, and Glu(137) was essential for stabilizing the compressed state. Overall, this study provides molecular insights into the dynamics and mechanism of the functional conformation changes of SaClpP. Given the highly conserved sequences of ClpP proteins among different species, these findings potentially reflect a switching mechanism for the dynamic process shared in the whole ClpP family in general and thus aid in better understand the principles of Clp protease assembly and function.


    Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit
V, A, B, C, D, E, F, G, H, I, J, K, L, M
203Staphylococcus aureus (strain MW2)Mutation(s): 0 
Gene Names: clpP
EC: 3.4.21.92
Find proteins for P63786 (Staphylococcus aureus (strain MW2))
Go to UniProtKB:  P63786
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 96.384α = 90.00
b = 170.046β = 102.87
c = 96.332γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
HKL-2000data reduction
ADSCdata collection
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2014-01-01
    Type: Database references