1R6Q

ClpNS with fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic investigation of peptide binding sites in the N-domain of the ClpA chaperone.

Xia, D.Esser, L.Singh, S.K.Guo, F.Maurizi, M.R.

(2004) J.Struct.Biol. 146: 166-179

  • DOI: 10.1016/j.jsb.2003.11.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Escherichia coli ClpA, an Hsp100/Clp chaperone and an integral component of the ATP-dependent ClpAP protease, participates in the dissolution and degradation of regulatory proteins and protein aggregates. ClpA consists of three functional domains: an ...

    Escherichia coli ClpA, an Hsp100/Clp chaperone and an integral component of the ATP-dependent ClpAP protease, participates in the dissolution and degradation of regulatory proteins and protein aggregates. ClpA consists of three functional domains: an N-terminal domain and two ATPase domains, D1 and D2. The N-domain is attached to D1 by a mobile linker and is made up of two tightly bound, identically folded alpha-helical bundles related by a pseudo 2-fold symmetry. Between the halves of the pseudo-dimer is a large flexible acidic loop that becomes better ordered upon binding of the small adaptor protein, ClpS. We have identified a number of structural features in the N-domain, including a Zn(++) binding motif, several interfaces for binding to ClpS, and a prominent hydrophobic surface area that binds peptides in different configurations. These structural motifs may contribute to binding of protein or peptide substrates with weak affinity and broad specificity. Kinetic studies comparing wild-type ClpA to a mutant ClpA with its N-domain deleted show that the N-domains contribute to the binding of a non-specific protein substrate but not of a folded substrate with the specific SsrA recognition tag. A functional model is proposed in which the N-domains in ClpA function as tentacles to weakly hold on to proteins thereby enhancing local substrate concentration.


    Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. dixia@helix.nih.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease ATP-binding subunit clpA
A, B
143Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: clpA (lopD)
Find proteins for P0ABH9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABH9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease adaptor protein clpS
C, D
106Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: clpS (yljA)
Find proteins for P0A8Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8Q6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YBT
Query on YBT

Download SDF File 
Download CCD File 
A, B
BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANE YTTRIUM
C8 H19 N O5 Y
KSJVCBJVYSTBHB-UXIAQZODAR
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Y1
Query on Y1

Download SDF File 
Download CCD File 
C, D
YTTRIUM ION
Y
KAJPZYFHSCFBCI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.913α = 90.00
b = 87.913β = 90.00
c = 209.420γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance