Structure of ClpP from Bacillus subtilis in monoclinic crystal form

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.212 

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Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism

Lee, B.-G.Park, E.Y.Lee, K.-E.Jeon, H.Sung, K.H.Paulsen, H.Rubsamen-Schaeff, H.Brotz-Oesterhelt, H.Song, H.K.

(2010) Nat Struct Mol Biol 17: 471-478

  • DOI: https://doi.org/10.1038/nsmb.1787
  • Primary Citation of Related Structures:  
    3KTG, 3KTH, 3KTI, 3KTJ, 3KTK

  • PubMed Abstract: 

    Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. Nonetheless, the proteolytic activation mechanism has remained elusive because of the lack of a complex structure. Acyldepsipeptides (ADEPs), a recently discovered class of antibiotics, activate and disregulate ClpP. Here we have elucidated the structural changes underlying the ClpP activation process by ADEPs. We present the structures of Bacillus subtilis ClpP alone and in complex with ADEP1 and ADEP2. The structures show the closed-to-open-gate transition of the ClpP N-terminal segments upon activation as well as conformational changes restricted to the upper portion of ClpP. The direction of the conformational movement and the hydrophobic clustering that stabilizes the closed structure are markedly different from those of other ATP-dependent proteases, providing unprecedented insights into the activation of ClpP.

  • Organizational Affiliation

    School of Life Sciences and Biotechnology, Korea University, Seoul, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E
A, B, C, D, E, F, G
199Bacillus subtilisMutation(s): 4 
Gene Names: clpPyvdNBSU34540
Find proteins for P80244 (Bacillus subtilis (strain 168))
Explore P80244 
Go to UniProtKB:  P80244
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80244
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.5α = 90
b = 150.701β = 121.65
c = 106.543γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection