Elucidating the biodegradation potential of Nudix hydrolase from Bacillus paranthracis via different approaches.

Abstract

The Nudix hydrolase from Bacillus paranthracis MBBL1 was investigated using in silico approaches. Polyfluoroalkyl substances (PFAS) are persistent environmental contaminants associated with serious health and ecological risks because of their stable chemical nature and strong resistance to breakdown. The enzyme sequence was retrieved from NCBI (Accession No. MFQ6175622.1), and its secondary structure revealed 33 alpha-helices, 50 beta-strands, and 66 coil regions, suggesting a balanced structural conformation. Tertiary structure prediction using AlphaFold3 achieved a high-confidence model with 94.5 % residues in the most favored regions of the Ramachandran plot and an ERRAT quality score of 96.99 %, validating its stereochemical reliability. Physicochemical profiling indicated a molecular weight of 17 kDa, a theoretical pI of 4.86, and a GRAVY index of -0.245, confirming its hydrophilic and slightly acidic nature. Two active-sites were predicted by PrankWeb, with Pocket 1 showing a high binding score of 6.46. Molecular docking against twelve PFAS derivatives showed favorable binding affinities ranging from -6.4 to -9.5 kcal/mol. Perfluorodecanoic acid demonstrated the strongest interaction (-9.5 kcal/mol), followed by H-PFOS (-9.0 kcal/mol) and perfluorooctanesulfonic acid (-8.8 kcal/mol). Interaction analysis identified key residues such as ALA22, THR40, ASP42, and ASN133 forming multiple hydrogen, halogen, and electrostatic bonds. These findings suggest that Nudix hydrolase may have structural and functional attributes relevant to PFAS biodegradation. Acknowledging the computational nature of this study, experimental validation will be required to confirm biodegradation activity.