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Santhiagu, A.
- Phyre 2 and I-Tasser Web Portal for Protein Modeling, Prediction and Validation of Gel Q and Gel K Genes from Gellan Gum Producing Bacterial Strain Sphingomonas paucimobilis ATCC 31461
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Authors
Affiliations
1 School of Biotechnology, National Institute of Technology, Calicut-673601, Kerala, IN
2 Department of Pharmaceutical Biotechnology, MNR College of Pharmacy, Sangareddy-502294, IN
1 School of Biotechnology, National Institute of Technology, Calicut-673601, Kerala, IN
2 Department of Pharmaceutical Biotechnology, MNR College of Pharmacy, Sangareddy-502294, IN
Source
Research Journal of Pharmacy and Technology, Vol 12, No 1 (2019), Pagination: 27-36Abstract
Gellan gum, an anionic, high-molecular-weight, hetero exo-polysaccharide produced by Sphingomonas paucimobilis ATCC 31461 has potential applications in food and pharmaceutical industries, as a gelling agent, a highly-viscous biogum, a stabilizing agent etc. Three dimensional structure of a protein encoded by a gene could be useful to identify the function of the gene. This study investigates about the 3-D structure prediction of gel Q and gel K protein of Sphingomonas paucimobilis ATCC 31461 using two different protein modeling tools, Phyre2 and I-Tasser. Amplified gel Q and gel K genes were sequenced and the template protein structure identification was carried out using BLASTp with PDB. Superpositioning of the model with the template was analyzed with PyMol. Structure Validation servers of RAMPAGE, PROSA, Verify 3D, ERRAT and Qmean endorsed the 3D structure. The Phyre2 and I-Tasser model of gel Q protein showed best probability conformation with 94.3% and 80.7% residue respectively in the core region of Ramachandran plot showing greater accuracy of model prediction compared to gel K protein with 92.3% and 78.6% residue for Phyre2 and ITasser models respectively. Phyre2 server generated a finer prediction, analysis and validation for gel Q and gel K protein structure than the I-Tasser server. The results generated using Expasy tool also suggested that glycosyl transferase protein, encoded by the genes gel Q and gel K in the gel cluster may be directly involved in the fourth sugar addition of the repeating unit and in the incorporation of GlcA from UDP-glucuronic acid, into glucosyl-α-pyrophosphorylpolyprenol intermediate respectively. In order to develop a recombinant Sphingomonas paucimobilis ATCC 31461, gel Q and gel K gene might be a powerful successor for the overexpression of the gene to enhance gellan gum production.Keywords
Sphingomonas paucimobilis ATCC 31461, Gel Q, Gel K, Phyre2, I-Tasser, RAMPAGE.
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- Homology Modeling and Structural Validation of Gel C Gene Involved in the Biosynthesis of Gellan from Sphingomonas paucimobilis ATCC 31461
Abstract Views :153 |
PDF Views:0
Authors
Affiliations
1 School of Biotechnology, National Institute of Technology, Calicut-673601, Kerala, IN
2 Department of Pharmaceutical Biotechnology, MNR College of Pharmacy, Sangareddy- 502294, IN
1 School of Biotechnology, National Institute of Technology, Calicut-673601, Kerala, IN
2 Department of Pharmaceutical Biotechnology, MNR College of Pharmacy, Sangareddy- 502294, IN
Source
Research Journal of Pharmacy and Technology, Vol 12, No 3 (2019), Pagination: 1044-1050Abstract
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.Keywords
Homology Modelling, Phyre 2, I –TASSER, Blastp, RAMPAGE, QMEAN.References
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