Nitronate monooxygenase (NMO) catalyzes the flavin-dependent oxidation of propionate 3-nitronate (P3N) via the formation of an anionic flavosemiquinone. The oxidation of substrate includes the formation of a peroxy-nitro acid intermediate. P3N is activated to its radical form via a single electron transfer onto the FMN cofactor forming the anionic flavosemiquinone. Reoxidation of FMN cofactor from the anionic semiquinone has been proposed to go through two routes dependent upon which radical species oxygen reacts with first, radical P3N or the semiquinone. The recent crystallographic determination of NMO from Cyberlindnera saturnus and steady-state kinetics revealed an allosteric activation effect on the enzyme by PEG 3350 with respect to P3N.

Choline oxidase (CHO) catalyzes the two-step oxidation of choline to glycine betaine via an enzyme-bound FAD cofactor. In the first redox reaction, choline is activated to it alkoxide form by means of an enzyme-derived catalytic base, H466. This histidine residue has been shown to not only act as a general base but an electrostatic catalyst stabilizing the negative charge accumulated on the reduced flavin species as shown by replacing the residue with alanine, aspartate, and glutamine using site-directed mutagenesis. CHO was also observed to catalyze excited state reactions as facilitated by H466. Evidence for the ESR comes from the observation of a pL-dependence on the fluorescence emission of CHO in H₂O and D₂O. Using fluorescence spectroscopy and pH effects, a hydroxy-C4a flavin intermediate was detected in the wild-type and S101A variant with and without oxygen indicating the adduct formation was with an active site hydroxide ion. The mechanism of formation has been elucidated.