Crystal Structure of E. coli protein YajL (ThiJ)

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

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This is version 1.3 of the entry. See complete history


The Atomic Resolution Crystal Structure of the YajL (ThiJ) Protein from Escherichia coli: A Close Prokaryotic Homologue of the Parkinsonism-associated Protein DJ-1.

Wilson, M.A.Ringe, D.Petsko, G.A.

(2005) J Mol Biol 353: 678-691

  • DOI: https://doi.org/10.1016/j.jmb.2005.08.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Escherichia coli protein YajL (ThiJ) is a member of the DJ-1 superfamily with close homologues in many prokaryotes. YajL also shares 40% sequence identity with human DJ-1, an oncogene and neuroprotective protein whose loss-of-function mutants are associated with certain types of familial, autosomal recessive Parkinsonism. We report the 1.1 angstroms resolution crystal structure of YajL in a crystal form with two molecules in the asymmetric unit. The structure of YajL is remarkably similar to that of human DJ-1 (0.9 angstroms C(alpha) RMSD) and both proteins adopt the same dimeric structure. The conserved cysteine residue located in the "nucleophile elbow" is oxidized to either cysteine sulfenic or sulfinic acid in the two molecules in the asymmetric unit, and a mechanism for this oxidation is proposed that may be valid for other proteins in the DJ-1 superfamily as well. Rosenfield difference matrix analysis of the refined anisotropic displacement parameters in the YajL structure reveals significant differences in the intramolecular flexibility of the two non-crystallographic symmetry-related molecules in the asymmetric unit. Lastly, a comparison of the crystal structures of the four different E.coli members of the DJ-1 superfamily indicates that the variable oligomerization in this superfamily is due to a combination of protein-specific insertions into the core fold that form specific interfaces while occluding others plus optimization of residues in the structurally invariant regions of the core fold that facilitate protein-protein interactions.

  • Organizational Affiliation

    Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, MS 029, Waltham, MA 02454, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
205Escherichia coliMutation(s): 0 
Gene Names: thiJ
Find proteins for Q46948 (Escherichia coli (strain K12))
Explore Q46948 
Go to UniProtKB:  Q46948
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46948
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.722α = 90
b = 78.475β = 90
c = 99.946γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Refinement description