On the basis of the observation that nitrate reductase from Escherichia coli is sensitive to UV irradiation with an action spectrum indicative of a naphthoquinone (F. Brito and M. Dubourdieu, Biochem. Int. 15:1079-1088, 1987), we extracted and characterized quinone components from two different preparations of purified nitrate reductase. A soluble form of nitrate reductase, composed of ␣ and  subunits, was purified after release from the membrane fraction by heat treatment, and a detergent-solubilized form, containing ␣, , and ␥ (cytochrome b NR ) subunits, was purified in the presence of Triton X-100. Extraction of soluble ␣ form with chloroform-methanol yielded several UV-absorbing components, which were characterized as menaquinone-9 with an oxidized side chain and further photodestruction products of the menaquinone. The total amount of menaquinone extracted into the organic phase was estimated to be 0.97 mol/mol of ␣ dimer. Extraction of the detergent-solubilized ␣␥ form by a similar procedure yielded two naphthoquinone-like components which were characterized by mass spectrometry as the oxidized forms of menaquinone-9 and demethylmenaquinone-9. In this case, the molar ratio of total naphthoquinone to the ␣ dimer was estimated to be greater than 6:1. When cytochrome b NR and detergent were eliminated from the detergent-solubilized enzyme by heat treatment and ion-exchange chromatography, only menaquinone-9 could be identified in the organic extract of the active ␣ product. These results suggest that menaquinone-9 is specifically bound to the ␣ dimer and may be the UV-sensitive component in the pathway of electron transfer catalyzed by nitrate reductase.Nitrate reductase in Escherichia coli is the terminal component of a membrane-bound electron transfer system which catalyzes the reduction of nitrate to nitrite in order to generate energy under anaerobic growth conditions (16). Nitrate reductase, assayed with reduced methyl viologen (MVH) as an artificial electron donor, has been purified by several different procedures, and its chemical and physical properties have been studied in some detail (6,13,23). When purified after solubilization from membranes with detergents, nitrate reductase is composed of three subunits, ␣, , and ␥ (cytochrome b NR ), with approximate molecular masses of 145, 60, and 25 kDa, respectively (5), and contains molybdopterin cofactor (18), several iron-sulfur centers (19), and heme groups (12). An active, soluble form of the enzyme can be released from the membranes in the absence of detergents by heat treatment which, when purified, is composed of only the ␣ and  subunits and contains the molybdopterin cofactor and iron-sulfur centers (19,23,24). Quinols, the presumed physiological electron donors for nitrate reductase, serve as electron donors for nitrate reduction with the detergent-extracted preparation but not with the heat-released enzyme which lacks the cytochrome b NR subunit (28). MVH, which is an effective electron donor for either preparation, apparently donates ...