1LZW

Structural basis of ClpS-mediated switch in ClpA substrate recognition

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 Biol 9: 906-911

  • DOI: 10.1038/nsb869
  • Primary Citation of Related Structures:  
    1LZW, 1MG9

  • 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 specificity is modified by adaptor proteins, such as ClpS ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein yljAA106Escherichia coliMutation(s): 1 
UniProt
Find proteins for P0A8Q6 (Escherichia coli (strain K12))
Explore P0A8Q6 
Go to UniProtKB:  P0A8Q6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8Q6
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent clp protease ATP-binding subunit ClpAB146Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ABH9 (Escherichia coli (strain K12))
Explore P0ABH9 
Go to UniProtKB:  P0ABH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABH9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT
Download Ideal Coordinates CCD File 
C [auth B]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.88α = 90
b = 114.59β = 90
c = 38.49γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations