Homology Modeling and Structural Validation of Gel C gene involved in the biosynthesis of Gellan from Sphingomonas paucimobilis ATCC 31461

Abstract

Gellan gum is an anionic exopolysaccharide produced by S. Paucimobilis ATCC 31461. Gellan have wide applications in food industry, pharmaceutical and cosmetic industries. Gel cluster involved in the biosynthesis of dTDP-L-Rha, glycosyltransferases and proteins requisite for gellan polymerization and export comprises of 18 genes. This study focuses on homology modelling of gel C, a component of gellan gum gene cluster using known protein structure of PDB server by Swiss, Phyre 2 and I-TASSER. Secondary structure prediction was analyzed using I-TASSER. Appropriate template for the modeling was determined using Protein BLAST. Visualization of the protein models was done using online software tool PyMOL. Structure validation was performed using various programs such as RAMPAGE, PROSA, VERIFY3D, ERRAT and QMEAN. RAMPAGE revealed that the predicted model has 94% amino acids in the core region of Ramachandran plot. Quality of the generated 3D models was validated using ProSA which display two characteristics of the input structure: Z-score and energy plots. Protein models with 3-D sequence profiles were retreived using VERIFY3D. Amino acid environment was evaluated by ERRAT and unreliable regions were identified using QMEAN. In our study, the protein modelling using Phyre 2 was found to be the most adequate when compared to modeling by Swiss model and I-TASSER model. Structural validation confirmed the reliability of model. The results indicated that gel C plays a crucial role in the polysaccharide chain length determination and so it can be a potential candidate for multiple expressions in Sphingomonas paucimobilis ATCC 31461.