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Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17

BACKGROUND: Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H(2)O(2) as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (Il-DyP4, corresponding to GenBank MG209114), obtained by heterologous ex...

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Autores principales: Li, Liuqing, Wang, Tao, Chen, Taohua, Huang, Wenhan, Zhang, Yinliang, Jia, Rong, He, Chao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8165797/
https://www.ncbi.nlm.nih.gov/pubmed/34059116
http://dx.doi.org/10.1186/s13068-021-01978-y
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author Li, Liuqing
Wang, Tao
Chen, Taohua
Huang, Wenhan
Zhang, Yinliang
Jia, Rong
He, Chao
author_facet Li, Liuqing
Wang, Tao
Chen, Taohua
Huang, Wenhan
Zhang, Yinliang
Jia, Rong
He, Chao
author_sort Li, Liuqing
collection PubMed
description BACKGROUND: Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H(2)O(2) as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (Il-DyP4, corresponding to GenBank MG209114), obtained by heterologous expression, exhibits a high catalytic efficiency for phenolic compounds and a strong decolorizing ability toward various synthetic dyes. However, the enzyme structure and the catalytic residues involved in substrate oxidation remain poorly understood. RESULTS: Here, we obtained a high-resolution structure (2.0 Å, PDB: 7D8M) of Il‑DyP4 with α-helices, anti-parallel β-sheets and one ferric heme cofactor sandwiched between two domains. The crystal structure of Il‑DyP4 revealed two heme access channels leading from the enzyme molecular surface to its heme region, and also showed four conserved amino acid residues forming the pocket for the conversion of hydrogen peroxide into the water molecule. In addition, we found that Trp264 and Trp380, were two important residues with different roles in Il‑DyP4, by using site-directed mutagenesis and an electron paramagnetic resonance (EPR) study. Trp264 is a noncatalytic residue that mainly is used for maintaining the normal spatial conformation of the heme region and the high-spin state of heme Fe(3+) of Il‑DyP4, while Trp380 serves as the surface-exposed radical-forming residue that is closely related to the oxidation of substrates including not only bulky dyes, but also simple phenols. CONCLUSIONS: This study is important for better understanding the catalytic properties of fungal DyPs and their structure–function relationships. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-021-01978-y.
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spelling pubmed-81657972021-06-01 Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17 Li, Liuqing Wang, Tao Chen, Taohua Huang, Wenhan Zhang, Yinliang Jia, Rong He, Chao Biotechnol Biofuels Research BACKGROUND: Dye-decolorizing peroxidases (DyPs) represent a novel family of heme peroxidases that use H(2)O(2) as the final electron acceptor to catalyze the oxidation of various organic compounds. A DyP from Irpex lacteus F17 (Il-DyP4, corresponding to GenBank MG209114), obtained by heterologous expression, exhibits a high catalytic efficiency for phenolic compounds and a strong decolorizing ability toward various synthetic dyes. However, the enzyme structure and the catalytic residues involved in substrate oxidation remain poorly understood. RESULTS: Here, we obtained a high-resolution structure (2.0 Å, PDB: 7D8M) of Il‑DyP4 with α-helices, anti-parallel β-sheets and one ferric heme cofactor sandwiched between two domains. The crystal structure of Il‑DyP4 revealed two heme access channels leading from the enzyme molecular surface to its heme region, and also showed four conserved amino acid residues forming the pocket for the conversion of hydrogen peroxide into the water molecule. In addition, we found that Trp264 and Trp380, were two important residues with different roles in Il‑DyP4, by using site-directed mutagenesis and an electron paramagnetic resonance (EPR) study. Trp264 is a noncatalytic residue that mainly is used for maintaining the normal spatial conformation of the heme region and the high-spin state of heme Fe(3+) of Il‑DyP4, while Trp380 serves as the surface-exposed radical-forming residue that is closely related to the oxidation of substrates including not only bulky dyes, but also simple phenols. CONCLUSIONS: This study is important for better understanding the catalytic properties of fungal DyPs and their structure–function relationships. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-021-01978-y. BioMed Central 2021-05-31 /pmc/articles/PMC8165797/ /pubmed/34059116 http://dx.doi.org/10.1186/s13068-021-01978-y Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Li, Liuqing
Wang, Tao
Chen, Taohua
Huang, Wenhan
Zhang, Yinliang
Jia, Rong
He, Chao
Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17
title Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17
title_full Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17
title_fullStr Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17
title_full_unstemmed Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17
title_short Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17
title_sort revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from irpex lacteus f17
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8165797/
https://www.ncbi.nlm.nih.gov/pubmed/34059116
http://dx.doi.org/10.1186/s13068-021-01978-y
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