3TT7

Structure of ClpP from Bacillus subtilis in complex with DFP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.558 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the conformational diversity of ClpP from Bacillus subtilis

Lee, B.-G.Kim, M.K.Song, H.K.

(2011) Mol.Cells 32: 589-595

  • DOI: 10.1007/s10059-011-0197-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ClpP is a cylindrical protease that is tightly regulated by Clp-ATPases. The activation mechanism of ClpP using acyldepsipeptide antibiotics as mimics of natural activators showed enlargement of the axial entrance pore for easier processing of incomi ...

    ClpP is a cylindrical protease that is tightly regulated by Clp-ATPases. The activation mechanism of ClpP using acyldepsipeptide antibiotics as mimics of natural activators showed enlargement of the axial entrance pore for easier processing of incoming substrates. However, the elimination of degradation products from inside the ClpP chamber remains unclear since there is no exit pore for releasing these products in all determined ClpP structures. Here we report a new crystal structure of ClpP from Bacillus subtilis, which shows a significantly compressed shape along the axial direction. A portion of the handle regions comprising the heptameric ring-ring contacts shows structural transition from an ordered to a disordered state, which triggers the large conformational change from an extended to an overall compressed structure. Along with this structural change, 14 side pores are generated for product release and the catalytic triad adopts an inactive orientation. We have also determined B. subtilis ClpP inhibited by diisopropylfluoro-phosphate and analyzed the active site in detail. Structural information pertaining to several different conformational steps such as those related to extended, ADEP-activated, DFP-inhibited and compressed forms of ClpP from B. subtilis is available. Structural comparisons suggest that functionally important regions in the ClpP-family such as N-terminal segments for the axial pore, catalytic triads, and handle domains for the product releasing pore exhibit intrinsically dynamic and unique structural features. This study provides valuable insights for understanding the enigmatic cylindrical degradation machinery of ClpP as well as other related proteases such as HslV and the 20S proteasome.


    Organizational Affiliation

    School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E, F, G
197Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: clpP (yvdN)
EC: 3.4.21.92
Find proteins for P80244 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P80244
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DFP
Query on DFP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
DIISOPROPYL PHOSPHONATE
C6 H15 O3 P
BLKXLEPPVDUHBY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.558 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.337α = 90.00
b = 152.000β = 113.21
c = 110.067γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description