Molecular modeling and docking characterization of CzR1, a CC-NBS-LRR R-gene from Curcuma zedoaria Loeb. that confers resistance to Pythium aphanidermatum |
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Authors: | Raj Kumar Joshi Satyabrata Nanda Ellojita Rout Basudeba Kar Pradeep Kumar Naik Sanghamitra Nayak |
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Institution: | 1.Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India;2.Dept. of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India |
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Abstract: | Plant NBS-LRR R-genes recognizes several pathogen associated molecular patterns (PAMPs) and limit pathogen infection through
a multifaceted defense response. CzR1, a coiled-coil-nucleotide-binding-site-leucine-rich repeat R-gene isolated from Curcuma
zedoaria L exhibit constitutive resistance to different strains of P. aphanidermatum. Majority of the necrotrophic oomycetes are
characterized by the presence of carbohydrate PAMPs β-glucans in their cell walls which intercat with R-genes. In the present
study, we predicted the 3D (three dimensional) structure of CzR1 based on homology modeling using the homology module of
Prime through the Maestro interface of Schrodinger package ver 2.5. The docking investigation of CzR1 with β-glucan using the
Glide software suggests that six amino acid residues, Ser186, Glu187, Ser263, Asp264, Asp355 and Tyr425 act as catalytic residues
and are involved in hydrogen bonding with ligand β-(1,3)-D-Glucan. The calculated distance between the carboxylic oxygen atoms
of Glu187–Asp355 pair is well within the distance of 5Å suggesting a positive glucanase activity of CzR1. Elucidation of these
molecular characteristics will help in in silico screening and understanding the structural basis of ligand binding to CzR1 protein
and pave new ways towards a broad spectrum rhizome rot resistance development in the cultivated turmeric. |
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Keywords: | Curcuma zedoaria Pythium aphanidermatum CC-NBS-LRR molecular docking β -(1 3)-D-Glucan |
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