1MG9

The structural basis of ClpS-mediated switch in ClpA substrate recognition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA

Zeth, K.Ravelli, R.B.Paal, K.Cusack, S.Bukau, B.Dougan, D.A.

(2002) Nat.Struct.Mol.Biol. 9: 906-911

  • DOI: 10.1038/nsb869
  • Primary Citation of Related Structures:  1LZW

  • PubMed Abstract: 
  • In Escherichia coli, protein degradation is performed by several proteolytic machines, including ClpAP. Generally, the substrate specificity of these machines is determined by chaperone components, such as ClpA. In some cases, however, the specificit ...

    In Escherichia coli, protein degradation is performed by several proteolytic machines, including ClpAP. Generally, the substrate specificity of these machines is determined by chaperone components, such as ClpA. In some cases, however, the specificity is modified by adaptor proteins, such as ClpS. Here we report the 2.5 A resolution crystal structure of ClpS in complex with the N-terminal domain of ClpA. Using mutagenesis, we demonstrate that two contact residues (Glu79 and Lys 84) are essential not only for ClpAS complex formation but also for ClpAPS-mediated substrate degradation. The corresponding residues are absent in the chaperone ClpB, providing a structural rationale for the unique specificity shown by ClpS despite the high overall similarity between ClpA and ClpB. To determine the location of ClpS within the ClpA hexamer, we modeled the N-terminal domain of ClpA onto a structurally defined, homologous AAA+ protein. From this model, we proposed a molecular mechanism to explain the ClpS-mediated switch in ClpA substrate specificity.


    Organizational Affiliation

    MPI für Biochemie, Abteilung Membranbiochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany. zeth@biochem.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protein yljA
A
106Escherichia coli (strain K12)Gene Names: clpS (yljA)
Find proteins for P0A8Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8Q6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP dependent clp protease ATP-binding subunit clpA
B
146Escherichia coli (strain K12)Gene Names: clpA (lopD)
Find proteins for P0ABH9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABH9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPK
Query on SPK

Download SDF File 
Download CCD File 
B
SPERMINE (FULLY PROTONATED FORM)
C10 H30 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-R
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.252 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.654α = 90.00
b = 93.654β = 90.00
c = 78.889γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
CNSphasing
XDSdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation