Dehydrogenase versus oxidase function: the interplay between substrate binding and flavin microenvironment

Redox enzymes, mostly equipped with metal or organic cofactors, can vary their reactivity with oxygen by orders of magnitudes. Understanding how oxygen reactivity is controlled by the protein milieu remains an open issue with broad implications for mechanistic enzymology and enzyme design. Here, we address this problem by focusing on a widespread group of flavoenzymes that oxidize phenolic compounds derived from microbial lignin degradation, using either oxygen or a cytochrome c as electron acceptors. A comprehensive phylogenetic analysis revealed conserved amino acid motifs in their flavin-binding site. Using a combination of kinetics, mutagenesis, structural, and computational methods, we examined the role of these residues. Our results demonstrate that subtle and localized changes in the flavin environment can drastically impact on oxygen reactivity. These effects are afforded through the creation or blockade of pathways for oxygen diffusion. Substrate binding plays a crucial role by potentially obstructing oxygen access to the flavin, thus influencing the enzyme's reactivity. The switch between oxidase and dehydrogenase functionalities is thereby achieved through targeted, site-specific amino acid replacements that finely tune the microenvironment around the flavin. Our findings explain how very similar enzymes can exhibit distinct functional properties, operating as oxidases or dehydrogenases. They further provide valuable insights for the rational design and engineering of enzymes with tailored functions.