Crystal Structure of Arabidopsis thaliana DJ-1d

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.243 

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Stereospecific mechanism of DJ-1 glyoxalases inferred from their hemithioacetal-containing crystal structures.

Choi, D.Kim, J.Ha, S.Kwon, K.Kim, E.H.Lee, H.Y.Ryu, K.S.Park, C.

(2014) FEBS J 281: 5447-5462

  • DOI: https://doi.org/10.1111/febs.13085
  • Primary Citation of Related Structures:  
    4OFW, 4OGF, 4OGG

  • PubMed Abstract: 

    DJ-1 family proteins have recently been characterized as novel glyoxalases, although their cofactor-free catalytic mechanisms are not fully understood. Here, we obtained crystals of Arabidopsis thaliana DJ-1d (atDJ-1d) and Homo sapiens DJ-1 (hDJ-1) covalently bound to glyoxylate, an analog of methylglyoxal, forming a hemithioacetal that presumably mimics an intermediate structure in catalysis of methylglyoxal to lactate. The deuteration level of lactate supported the proton transfer mechanism in the enzyme reaction. Differences in the enantiomeric specificity of d/l-lactacte formation observed for the DJ-1 superfamily proteins are explained by the presence of a His residue in the active site with essential Cys and Glu residues. The model for the stereospecificity was further evaluated by a molecular modeling simulation with methylglyoxal hemithioacetal superimposed on the glyoxylate hemithioacetal. The mechanism of DJ-1 glyoxalase provides a basis for understanding the His residue-based stereospecificity. Structural data have been submitted to the Protein Data Bank under accession numbers 4OFW (structure of atDJ-1d), 4OGF (structure of hDJ-1 with glyoxylate) and 4OGG (structure of atDJ-1d with glyoxylate).

  • Organizational Affiliation

    Division of Magnetic Resonance Research, Korea Basic Science Institute, Chungcheongbuk-Do, South Korea; Department of Biological Science, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein DJ-1 homolog D
A, B, C, D, E
A, B, C, D, E, F
387Arabidopsis thalianaMutation(s): 0 
Gene Names: DJ1DAt3g02720F13E7.34
Find proteins for Q9M8R4 (Arabidopsis thaliana)
Explore Q9M8R4 
Go to UniProtKB:  Q9M8R4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M8R4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.556α = 90
b = 115.047β = 91.51
c = 115.531γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
Cootmodel building
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description