Nitin Kumar Verma1*, Atal Bihari Bajpai2, Vibha3 and Saurab Kumar Yadav4
1. Department of Biotechnology and Bioinformatics, Uttaranchal College of Science
and Technology, Dehradun
2. Department of Botany, D.B.S. (P.G.) College, Dehradun
3. Genetics and Tree Propagation Division, Forest Research Institute, Dehradun
4. Department of Biotechnology, OPJS University, Rajasthan
Received-01.12.2016, Revised-10.03.2017
Abstract: Phosphoenolpyruvate carboxykinase (PEPCK) is an enzyme in the lyase family. PEPCK is an ATP-dependent that is involved in the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide. In this study, the results of structural and physiochemical study of Medicago truncatula PEPCK has explored. The conceptual three-dimensional structure investigated while there was no structural information available in any other database. Computational analysis performed on Medicago truncatula PEPCK and developed a three-dimensional structure of PEPCK enzyme using comparative modeling approach. The modeled enzyme includes N-terminal and C-Terminal domains with a mixed α/β topology. The energy of constructing models was minimized and the quality of the models was evaluated by VERRIFY_3D and PROCHECK. Ramachandran plot analysis showed the confirmation of 100 % amino acid residues was within the most favored regions. Multiple sequence alignment of the PEPCK protein sequence of different plant sources revealed the conserved region and constructed a phylogenetic tree. The stability of model checked through Gromacs 4.5. The final three-dimensional structure submitted in the protein model database (PMDB). This study may play keystone role in in-vivo and in-vitro studies.
Keyword Phosphoenolpyruvate carboxykinase, phylogenetic tree, Gromacs, MD simulation, Homology Modeling
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