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A comparative proteomic approach to analyse structure, function and evolution of rice chitinases: a step towards increasing plant fungal resistance

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Abstract

Glycoside hydrolase family 19 chitinases (EC 3.2.1.14) widely distributed in plants, bacteria and viruses catalyse the hydrolysis of chitin and play a major role in plant defense mechanisms and development. Rice possesses several classes of chitinase, out of which a single structure of class I has been reported in PDB to date. In the present study an attempt was made to gain more insight into the structure, function and evolution of class I, II and IV chitinases of GH family 19 from rice. The three-dimensional structures of chitinases were modelled and validated based on available X-ray crystal structures. The structural study revealed that they are highly α-helical and bilobed in nature. These enzymes are single or multi domain and multi-functional in which chitin-binding domain (CBD) and catalytic domain (CatD) are present in class I and IV whereas class II lacks CBD. The CatD possesses a catalytic triad which is thought to be involved in catalytic process. Loop III, which is common in all three classes of chitinases, reflects that it may play a significant role in their function. Our study also confirms that the absence and presence of different loops in GH family 19 of rice may be responsible for various sized products. Molecular phylogeny revealed chitinases in monocotyledons and dicotyledons differed from each other forming two different clusters and may have evolved differentially. More structural study of this enzyme from different plants is required to enhance the knowledge of catalytic mechanism and substrate binding.

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Acknowledgments

The authors thankfully acknowledge the financial support for Agri-Bioinformatics Promotion Program by Bioinformatics Initiative Division, Department of Information Technology, Ministry of Communications & Information Technology, Government of India, New Delhi as well as Biotechnology Information System Network, Department of Biotechnology, Government of India. Also the authors are grateful to Assam Agricultural University, Jorhat, Assam for providing the necessary facilities, constant support to carryout our research endeavour.

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  1. Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India

    Kishore Sarma, Budheswar Dehury, Jagajjit Sahu, Ranjan Sarmah, Smita Sahoo, Mousumi Sahu, Priyabrata Sen, Mahendra Kumar Modi & Madhumita Barooah

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  1. Kishore Sarma
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  2. Budheswar Dehury
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Correspondence to Madhumita Barooah.

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Sarma, K., Dehury, B., Sahu, J. et al. A comparative proteomic approach to analyse structure, function and evolution of rice chitinases: a step towards increasing plant fungal resistance. J Mol Model 18, 4761–4780 (2012). https://doi.org/10.1007/s00894-012-1470-8

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