In the absence of oxygen and in the presence of nitrate, Escherichia coli induces the production of two energy-converting enzymes: formate dehydrogenase-N (FdnGHI) and dissimilatory nitrate reductase A (NarGHI).3 These two complexes cooperate in generating a proton motive force through the redox loop mechanism as originally envisaged by Peter Mitchell in his chemiosmotic hypothesis (1). The separation of positive and negative charges across the cytoplasmic membrane is achieved through electron transfer from the formate oxidation site in the periplasm to the nitrate reduction site located on the cytoplasmic space with mena-or ubiquinone/quinol cycling between them (2, 3). The heterotrimeric NarGHI complex is composed of (i) a nitrate-reducing subunit NarG containing a Mo-bis-MGD cofactor (Moco) and a [4Fe-4S] cluster FeS0 with unusual His coordination (4, 5), (ii) an electron transfer subunit NarH carrying four FeS clusters (6), and (iii) a membrane anchor subunit NarI containing two b-type hemes termed b D and b P to indicate their distal and proximal positions with respect to the nitratereducing site (7-9). These prosthetic groups define an electron transfer pathway from a periplasmically oriented quinol oxidation site (Q D ) to a cytoplasmically oriented nitrate reduction site.Although considerable research has been devoted to nitrate reductase functioning, only partial information has been gained about the number, the structure, and the specificity of quinol binding sites within NarGHI. For instance, some studies have reported on mena-and ubiquinol analogue binding (10 -20), whereas the molecular details of the interaction between natural quinols and NarGHI remain to be established.Despite the absence of bound quinones in the available high resolution structures of NarGHI (7,20), the crystal structure of the enzyme in complex with pentachlorophenol (PCP), an inhibitor of the quinol oxidase activity, has been determined (20). Based on mutagenesis data, biochemical analyses, and molecular modeling, a model of the Q D quinol binding site has been proposed (20). In this working model, a quinone carbonyl group interacts with the protein via a hydrogen bond to a histidine residue (His-66), which is one of the axial ligands of heme b D . Molecular modeling of a menaquinone in the PCP binding site suggested that the opposite carbonyl group could form a hydrogen bond to . Additionally, an elongated