4HSE

Crystal structure of ClpB NBD1 in complex with guanidinium chloride and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The molecular mechanism of hsp100 chaperone inhibition by the prion curing agent guanidinium chloride.

Zeymer, C.Werbeck, N.D.Schlichting, I.Reinstein, J.

(2013) J.Biol.Chem. 288: 7065-7076

  • DOI: 10.1074/jbc.M112.432583

  • PubMed Abstract: 
  • The Hsp100 chaperones ClpB and Hsp104 utilize the energy from ATP hydrolysis to reactivate aggregated proteins in concert with the DnaK/Hsp70 chaperone system, thereby playing an important role in protein quality control. They belong to the family of ...

    The Hsp100 chaperones ClpB and Hsp104 utilize the energy from ATP hydrolysis to reactivate aggregated proteins in concert with the DnaK/Hsp70 chaperone system, thereby playing an important role in protein quality control. They belong to the family of AAA+ proteins (ATPases associated with various cellular activities), possess two nucleotide binding domains per monomer (NBD1 and NBD2), and oligomerize into hexameric ring complexes. Furthermore, Hsp104 is involved in yeast prion propagation and inheritance. It is well established that low concentrations of guanidinium chloride (GdmCl) inhibit the ATPase activity of Hsp104, leading to so called "prion curing," the loss of prion-related phenotypes. Here, we present mechanistic details about the Hsp100 chaperone inhibition by GdmCl using the Hsp104 homolog ClpB from Thermus thermophilus. Initially, we demonstrate that NBD1 of ClpB, which was previously considered inactive as a separately expressed construct, is a fully active ATPase on its own. Next, we show that only NBD1, but not NBD2, is affected by GdmCl. We present a crystal structure of ClpB NBD1 in complex with GdmCl and ADP, showing that the Gdm(+) ion binds specifically to the active site of NBD1. A conserved essential glutamate residue is involved in this interaction. Additionally, Gdm(+) interacts directly with the nucleotide, thereby increasing the nucleotide binding affinity of NBD1. We propose that both the interference with the essential glutamate and the modulation of nucleotide binding properties in NBD1 is responsible for the GdmCl-specific inhibition of Hsp100 chaperones.


    Organizational Affiliation

    Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chaperone protein ClpB
A
397Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: clpB
Find proteins for Q9RA63 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9RA63
Small Molecules
Ligands 3 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
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GAI
Query on GAI

Download SDF File 
Download CCD File 
A
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADPKd: 13700 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.225 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.990α = 90.00
b = 60.990β = 90.00
c = 213.870γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Database references
  • Version 1.2: 2013-04-03
    Type: Database references