Biomimetic mineralization of enzymes for enhanced stability and activity is an important area of research due to its potential applications. Inorganic materials with enzymes coated and or embedded in them, viz., protein-inorganic hybrid nanomaterials with distinctive morphology and surface characteristics are promising candidates for exploring their elevated enzymatic activity. In this work, we have developed two different types of protein inorganic nanohybrid materials using a 120 kDa lectin purified from bitter gourd seeds (Momordica charantia lectin, MCL), and copper phosphate nanoflowers to result in a protein – inorganic nano hybrid material CuPNF_MCL and encapsulating this in zeolitic imidazole framework, ZIF8_MCL. While CuPNF_MCL showed floral morphology, the ZIF8_MCL mostly showed hexapod morphology as noticed from the microscopy data. Both the nanomaterials showed a distinctive trend of decrease in size with increase in the protein concentration used during the preparation. The nanoflowers also showed an increase in the tightness of the packing of the petals with increase in the protein concentration. Powder X-Ray diffraction studies confirmed the crystallinity of the inorganic frameworks. The Fourier Transform infrared spectroscopy studies coupled with confocal imaging of the fluorophore tagged MCL embedded hybrids confirmed the presence of the protein. The MCL protein was examined for its ability to cleave DNA, i.e., nuclease activity using pBR322, wherein the form I plasmid is completely transformed into the form II / III at 2 mg/mL concentration of the protein. However, both the hybrids showed a superior nuclease activity as compared to the protein, wherein the CuPNF_MCL showed a threefold greater nuclease activity as compared to the ZIF8_MCL. The greater nuclease activity of CuPNF_MCL is attributable to its mesoporous nature with higher pore size and pore volume as compared to that in case of ZIF8_MCL, which is microporous in nature. Thus, in this paper, we have purified a nuclease like lectin from bitter gourd seeds and improved its nuclease property by converting it into inorganic hybrid nanomaterial of two types wherein higher activity was observed in the material having better porosity and surface area characteristics.