The crystal structure of a major oxygen-insensitive nitroreductase (NfsA) from Escherichia coli has been solved by the molecular replacement method at 1.7-Å resolution. This enzyme is a homodimeric flavoprotein with one FMN cofactor per monomer and catalyzes reduction of nitrocompounds using NADPH. The structure exhibits an ␣ ؉ -fold, and is comprised of a central domain and an excursion domain. The overall structure of NfsA is similar to the NADPH-dependent flavin reductase of Vibrio harveyi, despite definite difference in the spatial arrangement of residues around the putative substrate-binding site. Nitroaromatic compounds including nitrofurans, nitropyrenes, and nitrobenzenes have been used as antimicrobial agents, food additives and raw materials in several industrial processes (1-5), and as a result are distributed widely around the environment. Many of these compounds are toxic, mutagenic, or carcinogenic (6 -8). It is believed that enzymatic transformation is needed for nitroaromatic compounds to show these serious effects (9, 10). The reduction of a nitro group of a parent nitrocompound is a key step of this process (11,12). Enzymes, which catalyze the reduction of nitrocompounds using a reduced pyridine nucleotide, are termed nitroreductases and are distinguished by their sensitivity of activity to oxygen (9, 10).The oxygen-sensitive enzymes can catalyze nitroreduction only under anaerobic conditions. A nitro-anion radical formed by a one-electron transfer is immediately reoxidized in the presence of oxygen to a parent nitrocompound and superoxide (13,14). In this futile cycle, reducing equivalents are consumed without the progress of nitroreduction and nitrocompounds perform as a catalyst to reduce oxygen. On the other hand, the oxygen-insensitive enzymes catalyze an obligatory two-electron reduction. A nitro group of a parent nitrocompound is reduced by a series of two-electron transfers, through nitroso and hydroxylamine intermediates, and finally to an amino group (13). The hydroxylamine intermediate arising from the four-electron transfer in total is found to be toxic, carcinogenic, or mutagenic.Three proteins with oxygen-insensitive nitroreductase activity in Escherichia coli have been identified (15). NfsA 1 is the major component, while NfsB and NfsC are minor components. NfsA and NfsB have been well studied relative to NfsC. NfsA and NfsB have similar enzymatic property, although NfsA has only 7% identity with NfsB on the amino acid sequence alignment. Both NfsA and NfsB are flavoenzymes with FMN as the prosthetic group and catalyze the reduction of nitrocompounds by Ping Pong Bi Bi kinetics (16,17). Counterparts of NfsA and NfsB, found in luminescent bacteria (16,17), are flavin reductase (FRP) of Vibrio harveyi (18) and flavin reductase (FRase I) of Vibrio fischeri (19), respectively. Enzyme that resembles FRP in the amino acid sequence alignment is also found in Bacillus subtilus and is called NfrA1 (20). A comparison of * This work was supported in part by grants-in-aid for Scientific Res...