Rai, Amrita ; Klare, Johann P. ; Reinke, Patrick Y. A. ; Englmaier, Felix ; Fohrer, Jörg ; Fedorov, Roman ; Taft, Manuel H. ; Chizhov, Igor ; Curth, Ute ; Plettenburg, Oliver ; Manstein, Dietmar J. (2024)
Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum.
In: International Journal of Molecular Sciences, 2021, 22 (12)
doi: 10.26083/tuprints-00022211
Artikel, Zweitveröffentlichung, Verlagsversion
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Kurzbeschreibung (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.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2024 |
| Autor(en): | Rai, Amrita ; Klare, Johann P. ; Reinke, Patrick Y. A. ; Englmaier, Felix ; Fohrer, Jörg ; Fedorov, Roman ; Taft, Manuel H. ; Chizhov, Igor ; Curth, Ute ; Plettenburg, Oliver ; Manstein, Dietmar J. |
| Art des Eintrags: | Zweitveröffentlichung |
| Titel: | Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum |
| Sprache: | Englisch |
| Publikationsjahr: | 12 Januar 2024 |
| Ort: | Darmstadt |
| Publikationsdatum der Erstveröffentlichung: | 2021 |
| Ort der Erstveröffentlichung: | Basel |
| Verlag: | MDPI |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | International Journal of Molecular Sciences |
| Jahrgang/Volume einer Zeitschrift: | 22 |
| (Heft-)Nummer: | 12 |
| Kollation: | 25 Seiten |
| DOI: | 10.26083/tuprints-00022211 |
| URL / URN: | https://tuprints.ulb.tu-darmstadt.de/22211 |
| Zugehörige Links: | |
| Herkunft: | Zweitveröffentlichung DeepGreen |
| Kurzbeschreibung (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. |
| Freie Schlagworte: | dye-decolorizing-type peroxidase, heme peroxidases, lignin degradation, Dictyostelium discoideum, B-type DyP, electron paramagnetic resonance (EPR) spectroscopy, compound I, enzyme kinetics, crystal structure, long-range electron transfer |
| Status: | Verlagsversion |
| URN: | urn:nbn:de:tuda-tuprints-222117 |
| Zusätzliche Informationen: | This article belongs to the Special Issue Universe of DyP-type Peroxidase |
| Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 500 Naturwissenschaften und Mathematik > 540 Chemie 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie |
| Fachbereich(e)/-gebiet(e): | 07 Fachbereich Chemie 07 Fachbereich Chemie > Clemens-Schöpf-Institut > Fachgebiet Organische Chemie |
| Hinterlegungsdatum: | 12 Jan 2024 13:57 |
| Letzte Änderung: | 15 Jan 2024 08:54 |
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- Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum. (deposited 12 Jan 2024 13:57) [Gegenwärtig angezeigt]
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