As early as 1974, reports have confirmed the anticancer activity of pterin deaminase isolated from fungi. The enzyme has also been reported in bacteria, fungi and slime mold genera, but the enzyme characterization was effetely done. The present study attempted to purify and characterize pterin deaminase enzyme from Saccharomyces cerevisiae NCIM 3458. The protein was extracted from the extracellular extract by using the ethanol precipitation method. Partial purification of pterin deaminase enzyme was achieved by ion exchange chromatography (Hi-Trap QFF) by fast protein liquid chromatography (AKTA purifier). The molecular weight of the protein was apparently determined by SDS-PAGE, and the presence of pterin deaminase was confirmed by activity staining. The purified enzyme was further biochemically characterized. Molecular docking studies showed higher binding affinity towards folic acid interaction. The structural characterization of this protein may open the windows for new drug targets for cancer therapy.