3STA

Crystal structure of ClpP in tetradecameric form from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural switching of Staphylococcus aureus Clp protease: a key to understanding protease dynamics

Zhang, J.Ye, F.Lan, L.Jiang, H.Luo, C.Yang, C.-G.

(2011) J.Biol.Chem. 286: 37590-37601

  • DOI: 10.1074/jbc.M111.277848
  • Primary Citation of Related Structures:  
  • Also Cited By: 6CFD, 5W18, 5VZ2

  • PubMed Abstract: 
  • ATP-dependent Clp protease (ClpP) is an attractive new target for the development of anti-infective agents. The ClpP protease consists of two heptameric rings that enclose a large chamber containing 14 proteolytic active sites. Recent studies indicat ...

    ATP-dependent Clp protease (ClpP) is an attractive new target for the development of anti-infective agents. The ClpP protease consists of two heptameric rings that enclose a large chamber containing 14 proteolytic active sites. Recent studies indicate that ClpP likely undergoes conformational switching between an extended and degraded active state required for substrate proteolysis and a compacted and catalytically inactive state allowing product release. Here, we present the wild-type ClpP structures in two distinct states from Staphylococcus aureus. One structure is very similar to those solved ClpP structures in the extended states. The other is strikingly different from both the extended and the compacted state as observed in ClpP from other species; the handle domain of this structure kinks to take on a compressed conformation. Structural analysis and molecular dynamic simulations show that the handle domain predominantly controls the way in which degradation products exit the chamber through dynamic conformational switching from the extended state to the compressed state. Given the highly conserved sequences among ClpP from different species, this compressed conformation is unexpected and novel, which is potentially valuable for understanding the enzymatic dynamics and the acting mechanisms of ClpP.


    Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, 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, E, F, G, I, K, L, M, N, S, T
197Staphylococcus 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: 2.28 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 168.572α = 90.00
b = 96.292β = 91.40
c = 192.614γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PHASESphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2012-01-25
    Type: Database references