Identification and Characterization of a Multifunctional Dye Peroxidase from a Lignin-Reactive Bacterium

Plant biomass represents a renewable feedstock that has not yet been fully tapped because of the difficulty in accessing the carbon in its structural biopolymers. Lignin is an especially challenging substrate, but select microbes have evolved complex systems of enzymes for its breakdown through a radical-mediated oxidation process. Fungal systems are well-characterized for their ability to depolymerize lignin, but the ability of bacteria to react with this substrate remains elusive. We have therefore focused on elucidating strategies used by lignin-reactive soil bacteria and describing their oxidative enzyme systems. We now report the identification and characterization of an unusual C-type dye-decolorizing peroxidase from Amycolatopsis sp. 75iv2 (DyP2), which belongs to a family of heme peroxidases reported to be involved in bacterial lignin degradation. Biochemical studies indicate that DyP2 has novel function for this family, with versatile and high activity both as a peroxidase and Mn peroxidase (k_cat/K_M ≈ 10⁵-10 ⁶ M^-1 s^-1). It also has a Mn-dependent oxidase mode of action that expands its substrate scope. Crystallographic studies of DyP2 at 2.25 Å resolution show the existence of a Mn binding pocket and support its key role in catalysis.