Glutathione reductase (GR) is a flavoprotein that catalyses the reduction of oxidized glutathione (GSSG) to reduced glutathione (2GSH) in the presence of coenzyme NADPH. The importance of glutathione stems from the fact that it serves an important role in various metabolic processes. Plants growing in highly polluted areas are exposed to higher concentration of metal ions; thereby feeling abiotic stress and affecting various regulatory enzyme activities. In this study, effect of metal ions has been studied on GR. Phytocystatins show an increased expression in abiotic stress conditions. Here in, the effect of cystatin isolated from yellow mustard seeds (YMP) on heavy metals induced conformational changes in GR was investigated making use of GR activity assay, UV-absorption spectroscopy, fluorescence spectroscopy, FTIR, CD, ITC and SEM analysis. The results obtained clearly reveals that metal ions like Cu2+ and Zn+2 induces concentration dependent conformational changes in GR; YMP restores these alterations in way decreasing the effective concentration of metal ions.