1UM8

Crystal structure of helicobacter pylori ClpX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of ClpX Molecular Chaperone from Helicobacter pylori

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

(2003) J.Biol.Chem. 278: 50664-50670

  • DOI: 10.1074/jbc.M305882200

  • PubMed Abstract: 
  • ClpX, a heat shock protein 100 chaperone, which acts as the regulatory subunit of the ATP-dependent ClpXP protease, is responsible for intracellular protein remodeling and degradation. To provide a structural basis for a better understanding of the f ...

    ClpX, a heat shock protein 100 chaperone, which acts as the regulatory subunit of the ATP-dependent ClpXP protease, is responsible for intracellular protein remodeling and degradation. To provide a structural basis for a better understanding of the function of the Clp ATPase family, the crystal structures of Helicobacter pylori ClpX, lacking an N-terminal Cys cluster region complexed with ADP, was determined. The overall structure of ClpX is similar to that of heat shock locus U (HslU), consisting of two subdomains, with ADP bound at the subdomain interface. The crystal structure of ClpX reveals that a conserved tripeptide (LGF) is located on the tip of ClpP binding loop extending from the N-terminal subdomain. A hexameric model of ClpX suggests that six tripeptides make hydrophobic contacts with the hydrophobic clefts of the ClpP heptmer asymmetrically. In addition, the nucleotide binding environment provides the structural explanation for the hexameric assembly and the modulation of ATPase activity.


    Organizational Affiliation

    Department of Molecular Cell Biology, Center for Molecular Medicine, SBRI, 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 ATP-binding subunit clpX
A
376Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: clpX
Find proteins for O25926 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25926
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.219 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 78.515α = 90.00
b = 78.515β = 90.00
c = 131.514γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-09-25 
  • Released Date: 2003-12-23 
  • Deposition Author(s): Kim, D.Y., Kim, K.K.

Revision History 

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance