CryoEM Structures of Native Quinol-Dependent Nitric Oxide Reductase in Resting and Quinol-Bound States

The membrane-bound quinol-dependent nitric oxide reductases (qNORs), which are members of the respiratory heme-copper oxidase superfamily, are of major importance to food production, environment, and human health. They are unique to bacteria and catalyze N-N bond formation, converting nitric oxide (NO) to generate the enzymatic product, nitrous oxide (N₂O), in agricultural and pathogenic conditions. High-resolution qNOR structures have been reported from two bacterial species, in which the molecular size of the protein was increased by the insertion of apocytochrome b₅₆₂ (BRIL) at the C-terminus to facilitate cryoEM structure determination. However, it remains uncertain how BRIL fusion alters the native structure of these metalloenzymes. Here, we present the first high-resolution structure of Achromobacter xylosoxidans qNOR (AxqNOR) determined without a fusion tag at two different pH values, revealing structural differences near the catalytic core as well as overall conformational changes between the native and fusion-tagged structures. The native enzyme shows a bell-shaped pH dependence of enzymatic activity, like nitrite reductase, the preceding enzyme in the denitrification pathway, which generates the substrate NO. In addition, we report structures of AxqNOR bound to quinol and hydroxyquinol that provide valuable insight into the potential electron transfer pathway originating from Trp718 to the redox centers.