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Structural and biochemical characterization of a dye-decolorizing peroxidase from Dictyostelium discoideum.
Int. J. Mol. Sci. 22:6265 (2021)
A novel cytoplasmic dye-decolorizing peroxidase from Dictyostelium discoideum was investi-gated 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 Dicty-ostelium 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 acti-vated 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.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
B-type Dyp ; Compound I ; Crystal Structure ; Dictyostelium Discoideum ; Dye-decolorizing-type Peroxidase ; Electron Paramagnetic Resonance (epr) Spectroscopy ; Enzyme Kinetics ; Heme Peroxidases ; Lignin Degradation ; Long-range Electron Transfer; Electron-paramagnetic-resonance; Cytochrome-c Peroxidase; Substrate-interaction-sites; Crystal-structure; Lignin Peroxidase; Horseradish-peroxidase; Catalase-peroxidase; Thermobifida Fusca; Heme-binding; Oxidation
ISSN (print) / ISBN
1422-0067
e-ISSN
1661-6596
Quellenangaben
Volume: 22,
Issue: 12,
Article Number: 6265
Publisher
MDPI
Publishing Place
Basel
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Medicinal Chemistry (IMC)
Grants
German Federal Ministry of Education and Research
DFG
DFG