2AB0

Crystal Structure of E. coli protein YajL (ThiJ)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2005.08.033

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YajL
A, B
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yajL (thiJ)
EC: 3.1.2.-, 3.5.1.-, 3.5.1.124
Find proteins for Q46948 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46948
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.722α = 90.00
b = 78.475β = 90.00
c = 99.946γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXL-97refinement
SHELXmodel building
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance