Prenyl transferase enzyme is widely distributed among plants. This enzyme catalyses prenylation reaction, that leads to increased flavonoid's activity. In this research, highly conserved polyprenyl patterns have been analysed in plants. Prenyl transferase in Triticum urartu, Oryza sativa japonica and Zea mays share presence of conserved motif LIhDDviDdsgmRRG. This protein share the presence of motif LVlDDimDnsqtRRG in Lupinus albus and Phaseolus vulgaris, both motifs belong to polyprenyl signature 1. Prenyl transferase of Triticum urartu do not contain polyprenyl signature 2. Here, polyprenyl signature 2 motif has been inserted into the protein of Triticum urartu at 273 position, which was extracted from above plants. Structural variations have been analysed using homology modelling after insertion of LGlsFQVvDDIlD and MGtyFQVqDDYlD motifs into protein of Triticum urartu. Modifications in protein do not show any unfavourable changes or disruption in structure. Analysis of Conserved domain Trans-Isoprenyl Diphosphate Synthases shows presence of enhanced substrate binding pocket, catalytic residues in modified Prenyl Transferase.