› 4ogg

X-ray diffraction
1.6Å resolution

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

Released:
DOI: 10.2210/pdb4ogg/pdb
PDB entry 4ogg coloured by chain, front view.
PDB entry 4ogg coloured by chain, side view.
PDB entry 4ogg coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Stereospecific mechanism of DJ-1 glyoxalases inferred from their hemithioacetal-containing crystal structures.
Choi D, Kim J, Ha S, Kwon K, Kim EH, Lee HY, Ryu KS, Park C
FEBS J 281 5447-62 (2014)
PMID: 25283443

Function and Biology Details

Reaction catalysed: 
(R)-S-lactoylglutathione = glutathione + methylglyoxal
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192381 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protein DJ-1 homolog D Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 388 amino acids
Theoretical weight: 41.91 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9M8R4 (Residues: 3-388; Coverage: 100%)
Gene names: At3g02720, DJ1D, F13E7.34
Sequence domains: DJ-1/PfpI family
Structure domains: Rossmann fold

Ligands and Environments

No bound ligands
1 modified residue:
Ligand CGV 6 x CGV

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P212121
Unit cell:
a: 83.685Å b: 92.922Å c: 138.242Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.185 0.212
Expression system: Escherichia coli

Quick links

Citations

4 review citations

D-Lactic Acid as a Metabolite: Toxicology, Diagnosis, and Detection.
Pohanka M. (2020)
3 more

2 mentions without citation

Stereospecific mechanism of DJ-1 glyoxalases inferred from their hemithioacetal-containing crystal structures.
Choi et al. (2014)
1 more