Proteomics 2015, 15, 1693–1705 1693 DOI 10.1002/pmic.201400421 REVIEW Structural and functional evolution of chitinase-like proteins from plants Pooja Kesari, Dipak Narhari Patil, Pramod Kumar, Shailly Tomar, Ashwani Kumar Sharma and Pravindra Kumar Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India Received: August 31, 2014 Revised: January 16, 2015 Accepted: February 24, 2015 The plant genome contains a large number of sequences that encode catalytically inactive chitinases referred to as chitinase-like proteins (CLPs). Although CLPs share high sequence and structural homology with chitinases of glycosyl hydrolase 18 (TIM barrel domain) and 19 families, they may lack the binding/catalytic activity. Molecular genetic analysis revealed that gene duplication events followed by mutation in the existing chitinase gene have resulted in the loss of activity. The evidences show that adaptive functional diversification of the CLPs has been achieved through alterations in the flexible regions than in the rigid structural elements. The CLPs plays an important role in the defense response against pathogenic attack, biotic and abiotic stress. They are also involved in the growth and developmental processes of plants. Since the physiological roles of CLPs are similar to chitinase, such mutations have led to plu- rifunctional enzymes. The biochemical and structural characterization of the CLPs is essential for understanding their roles and to develop potential utility in biotechnological industries. This review sheds light on the structure–function evolution of CLPs from chitinases. Keywords: Chitinase-like proteins / Glycosyl hydrolase family / N-Acetylglucosamine / Plant proteomics / TIM barrel 1 Introduction Nature has equipped plants with chitinases to protect them from chitin-containing pathogens. Chitinases are also ex- pressed in response to abiotic stress and during developmen- tal processes of plants [1–3]. These proteins are primarily categorized into glycosyl hydrolase (GH) 18 and 19 families. The cDNA-deduced sequence of the proteins from both the families shows that the chitinases are composed of an N- terminal signal peptide of variable lengths [4–6]. As per the revised chitinase gene classification, they are mainly grouped Correspondence: Dr. Pravindra Kumar, Department of Biotechnol- ogy, Indian Institute of Technology Roorkee, Roorkee, UK 247667, India E-mail: pravindrak.iitr@gmail.com Fax: +91-1332-273560 Abbreviations: AFPs, antifreeze proteins; CBD, chitin-binding do- main; CHRK, chitinase-related receptor-like kinase; CLP, chitinase- like proteins; CTL, chitinase-like; GH, glycosyl hydrolase; Glc- NAc, N-acetylglucosamine; PPL2, Parkia platycephala lectin 2; PR, pathogenesis related; TCLL, tamarind CTL lectin; XAIP, xylanase and -amylase inhibitor protein; XIP-I, xylanase inhibitor protein I into six classes I to VI [7]. The classes III and V belong to the GH18, whereas classes I, II, IV, and VI belong to the GH19 family. The classes III and V show very less homol- ogy with each other and no sequence similarity to enzymes of GH19 family. The chitinases of GH18 family adopt / barrel fold, whereas the GH19 chitinases have a high helical content because of the presence of nonpolar residues in the core region [8]—and show structural similarity to chitosanase and lysozyme [9]. Both families exhibit diversity in their se- quences, domain orientation, and hydrolytic mechanisms. Along with active chitinases, the plant genome also consists of a large number of sequences that encode catalytically inac- tive chitinases also referred to as chitinase-like (CTL) proteins (CLPs). The CLPs share high sequence and structural similar- ity with chitinases of GH18 and 19 families; but they may lack the binding/catalytic activity due to the presence of substitu- tions in the chitin-binding domain (CBD) or CatD. Molecular genetic analysis reveals that gene duplication events followed by mutation in the existing chitinase gene have resulted in the loss of activity [10]. CLPs have evolved through two different evolutionary pathways. In the first category, a mutation has led to loss of catalytic potential “Glu” residue. These CLPs do not C  2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com