Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from <i>Dictyostelium discoideum</i>
A novel cytoplasmic dye-decolorizing peroxidase from <i>Dictyostelium discoideum</i> 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 glyc...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-06-01
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| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/22/12/6265 |
| Summary: | A novel cytoplasmic dye-decolorizing peroxidase from <i>Dictyostelium discoideum</i> 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 <i>Dictyostelium</i> DyPA. In solution, <i>Dictyostelium</i> 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 <i>Dictyostelium</i> 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 <i>Dictyostelium</i> DyPA has a hexa-coordinated heme iron with a histidine residue at the proximal axial position and either an activated oxygen or CN<sup>−</sup> molecule at the distal axial position. Asp149 is in an optimal conformation to accept a proton from H<sub>2</sub>O<sub>2</sub> during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in <i>Dictyostelium</i> DyPA. Further, we identified two substrate-binding pockets per monomer in <i>Dictyostelium</i> 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. |
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| ISSN: | 1661-6596 1422-0067 |