In silico structural and functional analysis of copalyl diphosphate synthase enzyme in Andrographis paniculata (Burm. f.) Wall. ex Nees: A plant of immense pharmaceutical value

Abstract

Andrographis paniculata (Burm. f.) Wa ll. ex Nees (Acanthaceae) with immense medicinal importance lacks information on its biosynthetic pathway genes and their regulatory role in the production of pharmaceutically important andrographolide. Copalyl diphosphate synthase (CPS) is involved in the production of copalyl diphosphate, a precursor for many bioactive compounds with particular reference to diterpene lactone. In this study, we elucidated the structural and functional aspects of A. paniculata CPS (ApCPS). Composition of amino acids and hydrophobic nature of ApCPS were analysed and identified as non trans-membrane protein. A chloroplast transit peptide and mitochondrial targeting peptide in ApCPS were identified. Protein secondary structure prediction has given insight on the distribution of helix (52.52%), loop (45.91%) and strands (1.56%) in ApCPS. The homology modelling of ApCPS was carried out with SWISS MODEL. The validation of 3D model using PROCHECK revealed that 91.74% of the residues have averaged 3D-1D score >= 0.2 which is structurally reliable. In Ramachandran plot, 90.9% amino acid residues were found in most favoured region. Phylogenetic tree was constructed using MEGA 7.0 by taking eudicots, monocots, gymnosperms and fungal species. Among them, ApCPS was clustered within eudicots and closely related to Sesumum indicum in Laminales. Protein-protein interaction study using STRING10 revealed that CPS interacts with gibberilic acid and terpene synthase related proteins. In Arabidopsis thaliana, CPS coexpression was seen with gibberelic acid related proteins. The present in silico analysis will be useful in understanding the structural, functional and evolutionary diversification of ApCPS.