ORIGINAL PAPER A comparative proteomic approach to analyse structure, function and evolution of rice chitinases: a step towards increasing plant fungal resistance Kishore Sarma & Budheswar Dehury & Jagajjit Sahu & Ranjan Sarmah & Smita Sahoo & Mousumi Sahu & Priyabrata Sen & Mahendra Kumar Modi & Madhumita Barooah Received: 9 February 2012 / Accepted: 14 May 2012 / Published online: 9 June 2012 # Springer-Verlag 2012 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 chi- tinases 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 pres- ent 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 dif- fered from each other forming two different clusters and may have evolved differentially. More structural study of this en- zyme from different plants is required to enhance the knowl- edge of catalytic mechanism and substrate binding. Keywords Chitinase . Comparative modeling . Phylogeny . Proteomic Introduction Plants represent the major component of earth’ s biota and are capable of producing their food through the process of photosynthesis. A multitude of pathogens cause loss in the crop yield every year which is often severe across the globe. Plants are equipped with a variety of defense mechanisms to protect themselves against the attack of pathogens. Some of these are constitutive while others are induced upon the attack by pathogens. The interaction of plant and pathogens induces a variety of defense mechanisms which include cell wall strengthening [1], de novo production of antimicrobial compounds (pathogenesis response proteins) and secondary metabolites [2, 3]. In the case of pathogenesis related pro- teins (PR), chitinase and glucanase play a crucial role since they attack directly on the fungal and insect structural com- ponent whereas enzymes of plant secondary metabolite pathway including Chalcone synthase [4] and Phenylalanine ammonia lyase [5] play significant roles due to antimicrobial nature of secondary metabolites. Chitinases (EC 3.2.1.14), which are found in a wide range of organisms catalyse the hydrolysis of chitin and play a major role in plant defense mechanism against fungal pathogens. Chitinase catalyses the hydrolysis of β-1-4-link- age of the N-acetylglucosamine polymer of chitins, a major component of fungal cell walls [6]. Plant chitinases usually have a wide range of optimum pH (pH 4–9) and are gener- ally stable at temperature up to 60 °C [7]. These enzymes K. Sarma : B. Dehury : J. Sahu : R. Sarmah : S. Sahoo : M. Sahu : P. Sen : M. K. Modi : M. Barooah (*) Agri-Bioinformatics Promotion Programme, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013 Assam, India e-mail: m17barooah@yahoo.co.in J Mol Model (2012) 18:4761–4780 DOI 10.1007/s00894-012-1470-8