Cloning, sequence analysis, and molecular docking of nuclease B from Bacillus paralicheniformis str. PMp/10

Abstract

Bacterial biofilms cause serious problems in the industrial sector and human healthcare. Nucleases are characterized as biofilm-degrading enzymes. In this work, the extracellular nuclease nucB gene from a new isolate Bacillus paralicheniformis str. PMp/10 was isolated and cloned successfully into the cloning vector pET 29a+, then transformed into E. coli DH5α. The nucB gene has a molecular weight of 429 bp, its sequence was uploaded to the NCBI GenBank database under the accession number OP712506 which is the first report for B. paralicheniformis. The gene encoded a nuclease B enzyme consisting of 142 amino acids with an estimated molecular weight of 13 kDa. The 3D and 2D structure of nuclease B was predicted and the NucB enzyme's secondary structure prediction showed that it has five β-strands and three α-helices. Finally, the Molecular docking interaction between NucB and deoxyribonucleic acid was performed successfully with a high binding affinity (−7.1 kcal/mol).