Andrographis paniculata (Burm.f.) Wall. ex Nees is as an important medicinal plant from centuries for treating infectious diseases in India and other countries. Active principles of this plant are diterpene lactones, specifically andrographolides and are synthesised via two independent biosynthetic pathways, i.e., mevalonic acid (MVA) and methyl-erythritol phosphate (MEP) pathway. Very meagre genomic and proteomic information is available about the genes and enzymes involved in these biosynthetic pathways. In this study, we have performed in silico characterization of a vital rate limiting enzyme 1-deoxy-D-xylulose 5phospahte synthase (DXS) of MEP pathway in A. paniculata. Structural and functional characterization of A. paniculata DXS (ApDXS) revealed its hydrophobic nature and a non trans-membrane protein was found to be present in chloroplast stroma. Predicted 3D structure with phyre2 tool had shown 85% of amino acids in the most favoured region as revealed by Ramachandran plot and was 96.32% structurally reliable. The phylogenetic analysis of ApDXS by MEGA7 revealed evolutionarily close relationship with Lamiaceae (Phlomis umbrosa/ Phlomoides umbrosa, Plectranthus barbatus, Lavandula angustifolia and Salvia miltiorrhiza) and Pedaliaceae (Sesamum indicum) families. Protein-protein interaction study revealed the interface of ApDXS with other MEP pathway proteins such as HDS, HDR, DXR and CDPMEK. Further, interaction was also evident with MVA pathway protein HMGS and downstream proteins, viz., GPS1, IPPI1 of diterpenoid pathway. The findings on the interactions of ApDXS with HMGS has given insight to the cross talk between MEP and MVA pathways. Prediction of bio-physico-chemical properties, secondary and tertiary structures will be of significance in protein purification processes. In addition, it will also be advantageous for drug designing applications with particular reference to manipulation of biosynthetic pathway, involving diterpene lactones in A. paniculata.