Identification of Cucumis Sativus Urease as a Potential Urea Binding Enzyme by Computational Methods

Abstract

Urea is the most commonly used solid nitrogenous fertilizer owing to the fact that it contains high nitrogen content and also plays a significant role in the growth of plants. Many plant ureases catalyze the conversion of urea to ammonia and carbon dioxide. Identification of high-affinity plant ureases is considered to be one of the burning topics among several researchers for the development of Genetically Modified (GMO) crops. In the current study, the binding affinity of urea was compared with some of the plant ureases. In regard to this Pigeon pea Urease (PpU) was fixed as a reference to predict the binding pocket and thereby compare the binding affinity with urea. Cucumis sativus Urease (CsU) and Fragaria vesca Urease (FvU) were screened for comparison. Performing Molecular Dynamics (MD) simulation, molecular docking, and binding free energy calculation, it was observed that the structure of CsU was relatively stable and had a greater affinity of -3.37 kcal/mol with urea when compared with PpU and FvU. Predominantly, we report here that comparatively, CsU is a potential urea binding enzyme. Our findings in this study would be a useful tool in engineering novel high-affinity plant ureases drugs.