Crystallization and preliminary X-ray diffraction analysis of ydjA, a minimal nitroreductase from Escherichia coli K12

Nitroreductases that reduce hazardous nitroaromatic compounds are of interest because of their central role in nitroaromatic toxicity, their potential use in bioremediation and their utility in activating prodrugs in directed anticancer therapies. To provide the molecular background to the enzymatic mechanism of the ydjA nitroreductase, which is one of the smallest nitroreductases, the ydjA gene from Escherichia coli K12 was cloned and expressed and the expressed protein Ec_ydjA was purified. Ec_ydjA was crystallized from 20%(w/v) polyethylene glycol 1000, 0.2 M lithium sulfate and 0.1 M phosphate–citrate pH 4.2. Diffraction data were collected to 2.00 Å resolution using synchrotron radiation. The crystal belongs to the monoclinic space group C2, with unit-cell parameters a = 87.55, b = 129.28, c = 36.88 Å, α = 90, β = 103.8, γ = 90°. With two Ec_ydjA molecules in the asymmetric unit, the Matthews coefficient was 2.43 ų Da⁻¹ and the solvent content was 48.33%.