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Title

Molecular modeling and docking characterization of CzR1, a CC-NBS-LRR R-gene from Curcuma zedoaria Loeb. that confers resistance to Pythium aphanidermatum

 

Authors

Raj Kumar Joshi1*, Satyabrata Nanda1, Ellojita Rout1, Basudeba Kar1, Pradeep Kumar Naik2 & Sanghamitra Nayak1

 

Affiliation

1Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India; 2Dept. of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India.

 

Email

rajkumar.joshi@yahoo.co.in; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received May 25, 2013; Accepted May 27, 2013; Published June 29, 2013

 

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 Glu187ľAsp355 pair is well within the distance of 5┼ 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.

 

Keywords

Curcuma zedoaria, Pythium aphanidermatum, CC-NBS-LRR, molecular docking, β-(1, 3)-D-Glucan.

 

Citation

Joshi et al.  Bioinformation 9(11): 560-564 (2013)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.