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Article

Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I

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Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico
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Department of Biocatalysis, Institute of Catalysis and Petrochemistry, CSIC, 28049 Madrid, Spain
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Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
*
Authors to whom correspondence should be addressed.
On sabbatical leave at Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico.
Int. J. Mol. Sci. 2020, 21(16), 5734; https://doi.org/10.3390/ijms21165734
Received: 26 July 2020 / Revised: 7 August 2020 / Accepted: 7 August 2020 / Published: 10 August 2020
(This article belongs to the Special Issue OxiZymes)
Unspecific peroxygenases (UPOs) are fungal heme-thiolate enzymes able to catalyze a wide range of oxidation reactions, such as peroxidase-like, catalase-like, haloperoxidase-like, and, most interestingly, cytochrome P450-like. One of the most outstanding properties of these enzymes is the ability to catalyze the oxidation a wide range of organic substrates (both aromatic and aliphatic) through cytochrome P450-like reactions (the so-called peroxygenase activity), which involves the insertion of an oxygen atom from hydrogen peroxide. To catalyze this reaction, the substrate must access a channel connecting the bulk solution to the heme group. The composition, shape, and flexibility of this channel surely modulate the catalytic ability of the enzymes in this family. In order to gain an understanding of the role of the residues comprising the channel, mutants derived from PaDa-I, a laboratory-evolved UPO variant from Agrocybe aegerita, were obtained. The two phenylalanine residues at the surface of the channel, which regulate the traffic towards the heme active site, were mutated by less bulky residues (alanine and leucine). The mutants were experimentally characterized, and computational studies (i.e., molecular dynamics (MD)) were performed. The results suggest that these residues are necessary to reduce the flexibility of the region and maintain the topography of the channel. View Full-Text
Keywords: biocatalysis; molecular dynamics; oxizyme engineering; peroxygenases; structure–function relationship biocatalysis; molecular dynamics; oxizyme engineering; peroxygenases; structure–function relationship
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MDPI and ACS Style

Ramirez-Ramirez, J.; Martin-Diaz, J.; Pastor, N.; Alcalde, M.; Ayala, M. Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I. Int. J. Mol. Sci. 2020, 21, 5734. https://doi.org/10.3390/ijms21165734

AMA Style

Ramirez-Ramirez J, Martin-Diaz J, Pastor N, Alcalde M, Ayala M. Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I. International Journal of Molecular Sciences. 2020; 21(16):5734. https://doi.org/10.3390/ijms21165734

Chicago/Turabian Style

Ramirez-Ramirez, Joaquin, Javier Martin-Diaz, Nina Pastor, Miguel Alcalde, and Marcela Ayala. 2020. "Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I" International Journal of Molecular Sciences 21, no. 16: 5734. https://doi.org/10.3390/ijms21165734

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