Details
| Original language | English |
|---|---|
| Article number | 6265 |
| Journal | International Journal of Molecular Sciences |
| Volume | 22 |
| Issue number | 12 |
| Publication status | Published - 10 Jun 2021 |
Abstract
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.
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
ASJC Scopus subject areas
- Chemical Engineering(all)
- Catalysis
- Biochemistry, Genetics and Molecular Biology(all)
- Molecular Biology
- Chemistry(all)
- Spectroscopy
- Computer Science(all)
- Computer Science Applications
- Chemistry(all)
- Physical and Theoretical Chemistry
- Chemistry(all)
- Organic Chemistry
- Chemistry(all)
- Inorganic Chemistry
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In: International Journal of Molecular Sciences, Vol. 22, No. 12, 6265, 10.06.2021.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Structural and biochemical characterization of a dye-decolorizing peroxidase from dictyostelium discoideum
AU - Rai, Amrita
AU - Klare, Johann P.
AU - Reinke, Patrick Y.A.
AU - Englmaier, Felix
AU - Fohrer, Jörg
AU - Fedorov, Roman
AU - Taft, Manuel H.
AU - Chizhov, Igor
AU - Curth, Ute
AU - Plettenburg, Oliver
AU - Manstein, Dietmar J.
N1 - Funding Information: 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.
PY - 2021/6/10
Y1 - 2021/6/10
N2 - 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.
AB - 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.
KW - B-type DyP
KW - Compound I
KW - Crystal structure
KW - Dictyostelium discoideum
KW - Dye-decolorizing-type peroxidase
KW - Electron paramagnetic resonance (EPR) spectroscopy
KW - Enzyme kinetics
KW - Heme peroxidases
KW - Lignin degradation
KW - Long-range electron transfer
UR - http://www.scopus.com/inward/record.url?scp=85107497894&partnerID=8YFLogxK
U2 - 10.3390/ijms22126265
DO - 10.3390/ijms22126265
M3 - Article
C2 - 34200865
AN - SCOPUS:85107497894
VL - 22
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
SN - 1661-6596
IS - 12
M1 - 6265
ER -