A novel cytoplasmic dye-decolorizing peroxidase from was investigated that oxidizes anthraquinone dyes, lignin model compounds, and general peroxidase substrates such as ABTS efficiently. Unlike related enzymes, an aspartate residue replaces the first glycine of the conserved GXXDG motif in DyPA. In solution, DyPA exists as a stable dimer with the side chain of Asp146 contributing to the stabilization of the dimer interface by extending the hydrogen bond network connecting two monomers. To gain mechanistic insights, we solved the DyPA structures in the absence of substrate as well as in the presence of potassium cyanide and veratryl alcohol to 1.7, 1.85, and 1.6 Å resolution, respectively. The active site of DyPA has a hexa-coordinated heme iron with a histidine residue at the proximal axial position and either an activated oxygen or CN molecule at the distal axial position. Asp149 is in an optimal conformation to accept a proton from HO during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in DyPA. Further, we identified two substrate-binding pockets per monomer in DyPA at the dimer interface. Long-range electron transfer pathways associated with a hydrogen-bonding network that connects the substrate-binding sites with the heme moiety are described.
Pseudomonas sp. AU10 is an Antarctic psychrotolerant bacterium that produces a dye-decolorizing peroxidase (DyP-AU10). The recombinant enzyme (rDyP-AU10) is a heme-peroxidase that decolors dyes and modifies kraft lignin.
Encapsulins are self-assembling protein compartments found in prokaryotes and specifically encapsulate dedicated cargo enzymes. The most abundant encapsulin cargo class are Dye-decolorizing Peroxidases (DyPs). It has been previously suggested that DyP encapsulins are involved in oxidative stress resistance and bacterial pathogenicity due to DyPs' inherent ability to reduce and detoxify hydrogen peroxide while oxidizing a broad range of organic co-substrates.
Fungal enzyme systems for the degradation of plant cell wall lignin, consisting of, among others, laccases and lignin-active peroxidases, are well characterized. Additionally, fungi and bacteria contain dye-decolorizing peroxidases (DyP), which are also capable of oxidizing and modifying lignin constituents. Studying DyP activity on lignocellulose poses challenges due to the heterogeneity of the substrate and the lack of continuous kinetic methods.
A study investigated a white-rot fungus known for its ligninolytic enzymes, focusing on a dye-decolorizing peroxidase (DyP) and its potential to biotransform antibiotics.
The enzyme was cloned, expressed, and characterized, revealing optimal activity at pH 3 and stability between 30 °C and 50 °C, with the ability to decolorize various industrial dyes.
Results showed that DyP1 effectively biotransformed several fluoroquinolone antibiotics, highlighting its potential for biotechnological use in environmental applications.
Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan.
Iron is an essential element for bacterial survival. Bacterial pathogens have therefore developed methods to obtain iron. Vibrio cholerae, the intestinal pathogen that causes cholera, utilizes heme as an iron source.
