The crystal structures of xenobiotic reductase A and B from pseudomonas putida II-B and pseudomonas fluorescens I-C: structural insight into regiospecific reactions with nitrocompounds
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Nitrochemicals are currently widely used as solvents, drugs, biocides, fuels and explosives and are consequently widely distributed in the environment. The reductive nitrite elimination from explosive compounds is catalyzed by two FMN-dependent, xenobiotic reductases (XenA or XenB). These genes for these regiospecific enzymes were cloned from Pseudomonas putida and P. fluorescens I-C respectively and isolated from the soil of a contaminated World War II munitions manufacturing plant. These enzymes enable the microbes to fulfill their nitrogen requirements from nitroglycerin by catalyzing the regiospecific, NADPH dependent, reductive denitration of nitroglycerin with differing selectivities. The two enzymes also transform a number of additional nitrocompounds in vitro, e.g. TNT and metronidazole, a leading drug in the treatment of Helicobacter pylori, a causative agent of human ulcers. Single crystals were obtained for XenA and XenB and complete X-ray diffraction datasets have been collected and analyzed to better understand these characteristics. The 1.6 Å resolution structure of XenA reveals a dimer of β/α)₈-TIM barrels, but the 2.3 Å resolution structure for XenB is a monomer. The (β/α)₈-TIM barrel protein fold is the most common fold in the PDB. However, the XenA structure exhibits a unique, C-terminal domain-swapped topology. Thus a portion of each active site is comprised of residues from the neighboring monomer. To probe the reaction cycle, crystal structures of ligand complexes and the reduced enzyme have been refined. For example, our structure of the XenA-metronidazole complex shows that ligands bind parallel to the FMN si-face. Our 1.5 Å resolution structure for reduced XenA reveals an FMN isoalloxazine ring with an angle of ~165° along the N5-N10 axis. We have also generated models of the reduced enzyme-nitroglycerin complexes by molecular dynamics. The results with both XenA and XenB reveal differences in enzyme-ligand hydrogen bonding. These differences correlate remarkably well with the regiospecific differences observed for nitrite elimination from nitroglycerin and reduction of TNT by the two enzymes.