2ZL0

Crystal structure of H.pylori ClpP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2008.04.036
  • Primary Citation of Related Structures:  

  • 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 cha ...

    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.




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, H, I, J, K, L, M, N
196Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: clpP
EC: 3.4.21.92
Find proteins for P56156 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56156
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.563α = 90.00
b = 166.225β = 90.00
c = 187.225γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PROTEUM PLUSdata collection
EPMRphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-04-02 
  • Released Date: 2008-04-22 
  • Deposition Author(s): Kim, D.Y., Kim, K.K.

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance