Implication of Molecular Conservation on Computational Designing of Haloarchaean Urease with Novel Functional Diversity

Objective: The objective was to design an enzyme construct with diverse function from urease sequences of haloarchaean, Haloarcula marismortui ATCC 43049 based on its conserved domain consisting metal-binding region and active sites. Methods: Complete urease sequences of haloarchaea were retrieved from National Center for Biotechnology Information and then homology models generated, and validated. The best protein models were selected for docking with respective substrates using Ligand Fit program. The lowest energetic conformers were generated from these protein models by molecular dynamics methods. Urease construct-substrate complex was chosen based on the mode of catalysis, types of molecular interactions, and binding energy. Results: The resulted construct has a monomeric structure consisting of 3 helixes and 6 turns with 97 amino acids in length. The side chains of Asp49, Gly50 and Gln51 were predicted as functional residues in this construct. Urease construct was predicted to show catalytic function as similar to aliphatic nitrile hydradase and acrylamide hydro-lyase. Binding affinity of construct was more significant, which was better than to native urease. Urease construct was showed high binding affinity with semicarbazide and acrylamide wherein it has formed favorable hydrogen bonds. Conclusion: Substrate-binding region and active sites in the conserved domain of haloarchaean ureases are evolutionarily conserved at sequence as well as structural level. Substrate docking study supports the strong molecular interactions between construct and relative substrates. Thus, the present approach provides an insight to design urease construct with diverged catalytic function.