In silico model of DSF synthase RpfF protein from Xanthomonas oryzae pv. Oryzae: A novel target for bacterial blight of rice disease



Vidavaluru Sravani Reddy1, Yellapu Nanda Kumar1, Aminedi Raghavendra2, Gopal Sowjenya3, Suman Kumar4, Guggulla Ramyasree1 & Gottiprolu Rajarami Reddy1*



1Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India-517502; 2Department of Biotechnology and Environmental Sciences, Thapar University, Patiala, Punjab, India -147004; 3Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tiruapati, AP, India-517507; 4Noni Biotech Pvt ltd. Rajiv Gandhi road, OMR, Perungudi, Chennai, 600096


Email; *Corresponding author


Article Type




Received May 19, 2012; Accepted May 27, 2012; Published June 16, 2012


Background: Rice plant diseases play a major role as biological constraints on production. One of such rice disease is bacterial leaf blight, caused by Xanthomonas oryzae pv. Oryzae (Xoo). The diffusible signal factor (DSF) synthesized by Xoo has a major role in virulence to rice plant. The DSF synthase RpfF protein, which is related to crotonase superfamily is responsible for the maintaining concentration of DSF. DSF-dependent quorum sensing (QS) system adopts protein- protein interaction mechanism to auto regulates the production of DSF. The antibacterial activity of pesticides against Xoo has not yet been completely understood. Three dimensional structure of RpfF protein was predicted using homology modeling method by MODELLER 9V9 software, SWISS MODEL and GENO3D online tools and structures were validated by Ramachandran plot, TM-Score and RMSD. 3D structure of RpfF (accession number AAL06345) was predicted using DSF synthase of Xanthomonas campestris pv. campestris (Xcc) (PDB ID: 3M6M ) as a template. The stereo chemical check reveals the structure developed from the modeller was the best one and the potential ligand binding sites were identified by CASTp Server. The predicted RpfF model provides insight into its structure, active sites and aid in the development of novel inhibitors to control bacterial leaf blight in rice plant. DSF synthase RpfF protein could be used as a novel target to control infection



Xanthomonas oryzae, RpfF, DSF, Homology modeling



Reddy et al. Bioinformation 8(11): 504-507 (2012)

Edited by

P Kangueane






Biomedical Informatics



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