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Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum

Abstract

A novel cytoplasmic dye-decolorizing peroxidase from Dictyostelium discoideum 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 Dictyostelium DyPA. In solution, Dictyostelium 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 Dictyostelium 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 Dictyostelium 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 H2O2 during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in Dictyostelium DyPA. Further, we identified two substrate-binding pockets per monomer in Dictyostelium 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.

Funding source: D.J.M. is a member of the Cluster of Excellence RESIST (EXC 2155) with support from the DFG—Project ID 39087428-B11 and the European Joint Project on Rare Diseases Consortium “PredACTINg” with support from the German Federal Ministry of Education and Research under Grant Agreement 01GM1922B.
Related subjects: Production & Supply Chain
Countries: Germany
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/content/journal2199
2021-06-10
2021-07-24
http://instance.metastore.ingenta.com/content/journal2199
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