4OGG

Crystal Structure of Arabidopsis thaliana DJ-1d with glyoxylate as substrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1111/febs.13085
  • Primary Citation of Related Structures:  

  • 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) c ...

    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.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein DJ-1 homolog D
A, B, C
388Arabidopsis thalianaMutation(s): 0 
Gene Names: DJ1D
Find proteins for Q9M8R4 (Arabidopsis thaliana)
Go to UniProtKB:  Q9M8R4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGV
Query on CGV
A, B, C
L-PEPTIDE LINKINGC5 H9 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.685α = 90.00
b = 92.922β = 90.00
c = 138.242γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
Cootmodel building
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2014-12-24
    Type: Database references