› 5bk9

X-ray diffraction
1.51Å resolution

AAD-1 Bound to the Vanadyl Ion and Succinate

Released:
DOI: 10.2210/pdb5bk9/pdb
PDB entry 5bk9 coloured by chain, front view.
PDB entry 5bk9 coloured by chain, side view.
PDB entry 5bk9 coloured by chain, top view.
Source organism: Delftia acidovorans
Primary publication:
Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants.
Chekan JR, Ongpipattanakul C, Wright TR, Zhang B, Bollinger JM, Rajakovich LJ, Krebs C, Cicchillo RM, Nair SK
Proc Natl Acad Sci U S A 116 13299-13304 (2019)
PMID: 31209034

Function and Biology Details

Reaction catalysed: 
(R)-(2,4-dichlorophenoxy)propanoate + 2-oxoglutarate + O(2) = 2,4-dichlorophenol + pyruvate + succinate + CO(2)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160686 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 295 amino acids
Theoretical weight: 33.25 KDa
Source organism: Delftia acidovorans
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P83310 (Residues: 1-295; Coverage: 100%)
Gene name: rdpA
Sequence domains: Taurine catabolism dioxygenase TauD, TfdA family

Ligands and Environments

3 bound ligands:
Ligand SIN 1 x SIN
Ligand VVO 2 x VVO
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21212
Unit cell:
a: 85.915Å b: 97.868Å c: 69.855Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.196 0.217
Expression system: Escherichia coli K-12

Quick links

Citations

1 review citation

Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools.
Zallot et al. (2021)
4 other articles

2 mentions without citation

Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015.
Santos et al. (2023)
1 more