ArticleThe Biochemical journal2015
Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.
Article in The Biochemical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 98 citations in OpenAlex.
- Review
- Unveiling the mechanism of dye-decolorizing peroxidase (DyP): unique anthraquinone-directed catalysis exposes a dual-function peroxidase.Applied and environmental microbiology · 2026Article
- The oligomeric states of dye-decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation.Protein science : a publication of the Protein Society · 2024Article
- The chemical logic of enzymatic lignin degradation.Chemical communications (Cambridge, England) · 2024Review
- New insights into controlling radical migration pathways in heme enzymes gained from the study of a dye-decolorising peroxidase.Chemical science · 2023Article
- Lignin-degrading enzymes from a pathogenic canker-rot fungus Inonotus obliquus strain IO-B2.AMB Express · 2023Article
- Unexpected diversity of dye-decolorizing peroxidases.Biochemistry and biophysics reports · 2023Article
- Efficient Degradation of Tetracycline Antibiotics by Engineered Myoglobin with High Peroxidase Activity.Molecules (Basel, Switzerland) · 2022Article
- Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes.Applied microbiology and biotechnology · 2022Article
- Design and Engineering of an Efficient Peroxidase Using Myoglobin for Dye Decolorization and Lignin Bioconversion.International journal of molecular sciences · 2021Article
- Loops around the Heme Pocket Have a Critical Role in the Function and Stability ofInternational journal of molecular sciences · 2021Article
- Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of FeJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2021Review
- First Dye-Decolorizing Peroxidase from an Ascomycetous Fungus Secreted byBiomolecules · 2021Article
- Rigidifying aACS catalysis · 2021Article
- In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase-The Interplay of Key Amino Acids, pH, Buffer and Glycerol.International journal of molecular sciences · 2021Article
- Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase.The FEBS journal · 2021Article
- Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17.Biotechnology for biofuels · 2021Article
- DyP-Type Peroxidases: Recent Advances and Perspectives.International journal of molecular sciences · 2021Review
- Characterization of a Dye-Decolorizing Peroxidase fromJournal of fungi (Basel, Switzerland) · 2021Article
- Exploring the Diversity of Fungal DyPs in Mangrove Soils to Produce and Characterize Novel Biocatalysts.Journal of fungi (Basel, Switzerland) · 2021Article
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Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H₂O₂-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (k(cat) > 200 s⁻¹) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 k(cat) ~20 s⁻¹) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.
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