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In silico characterization, homology modeling of Camellia sinensis chitinase and its evolutionary analyses with other plant chitinases

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Proceedings of the National Academy of Sciences, India Section B: Biological Sciences Aims and scope Submit manuscript

Abstract

Camellia sinensis (L.) Kuntze (commonly called tea plant) is an economically important cash crop in India. This plant is prone to infection by several fungal pathogens. Chitinases (EC 3.2.1.14) are enzymes that play a significant role in plants by hydrolyzing the N-acetylglucosamine polymer chitin. The present study entails different in silico characterization of chitinase enzyme using complete chitinase cDNA sequence from C. sinensis (CsChi). Template crystal structure of class I chitinase from Oryza sativa (PDB ID: 2DKV) was used for homology modeling of the CsChi enzyme. The model structure was refined and verified by using Structural Analysis and Verification Server (SAVES). The predicted model was submitted to the Protein Model Data Base (PMDB ID: PM0079561) and was docked with the chitin ligand, obtained from ChemSpider database. The results revealed that Serine in the predicted active site at position 199 of the enzyme is responsible for strong hydrogen bonding affinity with the ligand. Results of the evolutionary analysis showed that the obtained amino acid sequence of the CsChi enzyme belongs to class Ib chitinase.

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Authors and Affiliations

  1. Molecular and Applied Mycology and Plant Pathology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India

    Swarnendu Chandra, Arun Kumar Dutta & Krishnendu Acharya

  2. Division of Plant Physiology & Biotechnology, UPASI Tea Research Institute, Nirar Dam P.O., Coimbatore Dist., Valparai, Tamil Nadu, 642127, India

    Krishnappa Nagarathana Chandrashekara

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  1. Swarnendu Chandra
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  2. Arun Kumar Dutta
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Correspondence to Krishnendu Acharya.

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Chandra, S., Dutta, A.K., Chandrashekara, K.N. et al. In silico characterization, homology modeling of Camellia sinensis chitinase and its evolutionary analyses with other plant chitinases. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 87, 685–695 (2017). https://doi.org/10.1007/s40011-015-0634-6

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  • DOI: https://doi.org/10.1007/s40011-015-0634-6

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