Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol

Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP-veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065 s(-1), followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (k(cat)) of 0.07 s(-1) and 0.07 s(-1), respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates.

Automated summary

This study delves into the oxidation reactions of veratryl alcohol (VA), 2,6-dimethoxyphenol (DMP), and guaiacol by Dye-decolorizing peroxidases (DyPs), revealing their comparable binding affinity and assisting in modulating BsDyP's structure engineering for enhanced activity towards a wide range of substrates.