In-silico Characterization, Structural Modelling, Docking Studies and Phylogenetic Analysis of 5-Enolpyruvylshikimate-3-Phosphate Synthase Gene of Oryza sativa L.

Abstract

The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is one of the vital enzymes of the shikimate pathway which is involved in the biosynthesis of secondary metabolites and several amino acids. The multiple sequence alignment of these EPSPS protein sequences from different plants showed conserved regions at different stretches with maximum homology in amino acid residues. We revealed the homology model of Oryza sativa EPSPS (OsEPSPS) protein using the structure of E. coli EPSPS as template. The resulting model structure was refined by PROCHECK, RAMPAGE server, ProSA, Verify3D etc. that indicated the model structure is reliable. Ramachandran plot analysis showed that conformations for 94.3% of amino acid residues are within the most favoured regions. Through motif analysis, it was revealed that a conserved EPSPS domain is uniformly found in all EPSPS proteins irrespective of variable plant species suggesting its possible role in cellular and metabolic functions. The phylogenetic tree constructed revealed different clusters based on EPSPS in respect of bacteria, monocot and dicot plants. The interacting partners of the gene shows the importance of this gene family in regulating developmental and metabolic functions. The two conserved motifs LP(G/S)KSLSNRILLLAAL and LFLGNAGTAMRPL present in almost all EPSPS plant species may function as the catalytic domains of EPSPS enzymes and are supposed to contribute in the glyphosate binding site.