Crystal structure of H.pylori ClpP S99A

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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The structural basis for the activation and peptide recognition of bacterial ClpP

Kim, D.Y.Kim, K.K.

(2008) J Mol Biol 379: 760-771

  • DOI: https://doi.org/10.1016/j.jmb.2008.04.036
  • Primary Citation of Related Structures:  
    2ZL0, 2ZL2, 2ZL3, 2ZL4

  • PubMed Abstract: 

    ClpP and its ATPase compartment, ClpX or ClpA, remove misfolded proteins in cells and are of utmost importance in protein quality control. The ring hexamers of ClpA or ClpX recognize, unfold, and translocate target substrates into the degradation chamber of the double-ring tetradecamer of ClpP. The overall reaction scheme catalyzed by ClpXP or ClpAP has been proposed; however, the molecular mechanisms associated with substrate recognition and degradation have not yet been clarified in detail. To investigate these mechanisms, we determined the crystal structures of ClpP from Helicobacter pylori in complex with product peptides bound to the active site as well as in the apo state. In the complex structure, the peptides are zipped with two antiparallel strands of ClpP and point to the adjacent active site, thus providing structural explanations for the broad substrate specificity, the product inhibition and the processive degradation of substrates in the chamber. The structures also suggest that substrate binding causes local conformational changes around the active site that ultimately induce the active conformation of ClpP.

  • Organizational Affiliation

    The Department of Molecular Cell Biology, Institute of Basic Science, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, 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, H, I, J, K, L, M, N
196Helicobacter pyloriMutation(s): 1 
Gene Names: clpP
Find proteins for P56156 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56156 
Go to UniProtKB:  P56156
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56156
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.739α = 90
b = 166.411β = 90
c = 186.78γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    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: 2023-11-01
    Changes: Data collection, Refinement description