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In silico analysis of peroxidase from Luffa acutangula

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Abstract

Peroxidases are oxidoreductase enzymes that widely gained attention as biocatalysts for their robust catalytic activity, specificity, and regioselective functionality for phenolic compounds. The study of molecular aspects of peroxidases is as crucial as that of the physicochemical aspects. A bioinformatics approach is utilized in this study to investigate the structural aspects and functions of luffa peroxidase (LPrx) from Luffa acutangula. The evolutionary relationship of LPrx with other class III peroxidases was studied by constructing a neighbour-joining phylogenetic tree. An analysis of the phylogenetic tree revealed that plant peroxidases share a common ancestor. The gene ontology term showed that LPrx had a molecular functionality of the oxidation–reduction process, heme binding and peroxidase-like activity, and the biological function of hydrogen peroxide scavenging activity. The enzyme-ligand interactions were studied from a catalytic point of view using the molecular docking technique. The molecular docking was carried out with LPrx as a receptor and guaiacol, m-cresol, p-cresol, catechol, quinol, pyrogallol, 2,4-dimethoxyphenol, gallic acid, aniline, and o-phenylenediamine as ligands. The results presented in the current communication will have a significant implication in proteomics, biochemistry, biotechnology, and the potential applications of peroxidases in the biotransformations of organic compounds.

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Acknowledgements

The authors thank the Department of Chemistry, North Eastern Regional Institute of Science and Technology, Nirjuli, Arunachal Pradesh, India, for providing adequate lab facilities and the Sandor Speciality Diagnostics Pvt. Ltd. for the MALDI-TOF MS data. The authors also thank the Ministry of Tribal Affairs, New Delhi, India, for providing fellowship to Dencil Basumatary under the “National Fellowship and Scholarship for Higher Education for ST Students” scheme.

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Authors and Affiliations

  1. Department of Chemistry, North Eastern Regional Institute of Science and Technology, Nirjuli, Arunachal Pradesh, 791109, India

    Dencil Basumatary, Shilpa Saikia, Hardeo Singh Yadav & Meera Yadav

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  1. Dencil Basumatary
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  2. Shilpa Saikia
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  3. Hardeo Singh Yadav
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  4. Meera Yadav
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Contributions

DB has performed all experimental and software analyses and written the manuscript. SS has investigated and edited the manuscript. HSY and MY supervised and reviewed the manuscript. All authors reviewed and approved the final manuscript.

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Correspondence to Dencil Basumatary.

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Basumatary, D., Saikia, S., Yadav, H.S. et al. In silico analysis of peroxidase from Luffa acutangula. 3 Biotech 13, 25 (2023). https://doi.org/10.1007/s13205-022-03432-8

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