Comparative Molecular Docking Analysis in Two Legume Species: Glycine max and Medicago truncatula

Urease (EC 3.5.1.5) is an enzyme responsible for the hydrolysis of urea into ammonia and carbon dioxide which results in the release of two molecules of ammonia and one molecule of carbon dioxide as follows: (NH₂)2CO + H₂O → CO₂ + 2NH_3. Ureases are known to be present in several bacteria, fungi, algae, plants and invertebrates. They are nickel-containing metalloenzymes of high molecular weight. This study investigates primary, secondary and tertiary structures of G. max and M. truncatula ureases. 3D models are generated and docking analyses with urea were performed. In addition to mutation analysis, a structure-based phylogenetic tree was constructed. According to our findings, ureases belong to two species show similarity in terms of primary, secondary and tertiary structures.

In phylogenetic tree, plant and bacterial ureases were distinct, and plant ureases exhibited more conserved 3D structures. A common interacting residue in both Glycine (2.2 Å) and Medicago (2.8 Å) was found as Glutamic acid (Glu). Besides highly mutable amino acids were demonstrated; Arg435 in Medicago and Arg437 in Glycine. Urea-urease complexes in both plants and bacteria were measured for their free binding energies (ΔG) which ranged from -3.8 to -4.2 kcal/mol. This study provides insight for future studies of urea-urease binding interactions in plants, especially in legumes.