NAD(P)H͞quinone acceptor oxidoreductase (QR1, NQO1, formerly DT-diaphorase; EC 1.6.99.2) protects animal cells from the deleterious and carcinogenic effects of quinones and other electrophiles. In this paper we report the apoenzyme structures of human (at 1.7-Å resolution) and mouse (2.8 Å) QR1 and the complex of the human enzyme with the substrate duroquinone (2.5 Å) (2,3,5,6-tetramethyl-p-benzoquinone). In addition to providing a description and rationale of the structural and catalytic differences among several species, these structures reveal the changes that accompany substrate or cofactor (NAD) binding and release. Tyrosine-128 and the loop spanning residues 232-236 close the binding site, partially occupying the space left vacant by the departing molecule (substrate or cofactor). These changes highlight the exquisite control of access to the catalytic site that is required by the ping-pong mechanism in which, after reducing the flavin, NAD(P) ؉ leaves the catalytic site and allows substrate to bind at the vacated position. In the human QR1-duroquinone structure one ring carbon is significantly closer to the flavin N5, suggesting a direct hydride transfer to this atom.DT diaphorase ͉ cancer ͉ chemoprotection ͉ chemotherapy N AD(P)H:Quinone acceptor oxidoreductase type 1 (QR1, NQO1; EC 1.6.99.2) is a flavoenzyme (homodimer of 273 residues, one FAD per monomer) that catalyzes the obligatory two-electron reduction of quinones to hydroquinones (1-3). This reaction prevents the one-electron reduction of quinones by cytochrome P450 reductase and other flavoproteins, resulting in oxidative cycling of deleterious radical species. The enzyme is inducible by a wide variety of Michael reaction acceptors and other electrophiles (4, 5). In addition to its possible role in the detoxification of dietary quinones, the enzyme has been shown to catalyze the reductive activation of quinolic chemotherapeutic compounds such as mitomycins (6), anthracyclines, and aziridinyl-benzoquinones. Overexpression of QR1 in many tumors, including those of lung, colon, liver, and breast, makes this enzyme an ideal target for the development of additional activatable cytotoxic compounds.We previously reported the crystal structures of rat liver quinone reductase (rQR1) in complex with NADP ϩ and the ternary complex with the inhibitor Cibacron Blue (CB) and the substrate duroquinone (2,3,5,6-tetramethyl-1,2-benzoquinone; DQ) (7). These structures have revealed insight into many biochemical and physiological properties of QRs, as well as the mechanism of quinone reduction. These structures have provided a wealth of information, including the overall fold, the nature of the dimer, the interactions of the FAD cofactor, and the possibility of hydride transfer between the NADH and FAD cofactors and from FADH 2 to the quinone substrate. Nonetheless many important aspects of QR1 function remain elusive. This is caused in part by the lack of structural information about the apoenzyme (apo) containing only the FAD prosthetic group (apo QR1) or of QR1...