Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey

Abstract

This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of −2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of −4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (−21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.

Communicated by Ramaswamy H. Sarma

Keywords:

• DehLBHS1
• dehalogenase
• alkalotolerant
• dichloropropionate
• haloalkanoic acid
• homology modelling

Disclosure statement

No potential conflict of interest was reported by the authors.

Acknowledgments

The authors would like to express their gratitude to the Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, and the Department of Biotechnology, Faculty of Science, International Islamic University Malaysia, for providing the necessary facilities for this work.

Additional information

Funding

The project was funded by the Scientific Technological Research Council of Turkey (TÜBİTAK) Program 2221-Fellowship for visiting Scientists and Scientists on Sabbatical Leave [grant no. 1059B11800242], and was jointly supported by Ondokuz Mayis University through BAP No. PYO.ZRT.1904.17.059. Additionally, Habeebat Adekilekun Oyewusi was a researcher at Universiti Teknologi Malaysia, working under the Post-Doctoral Fellowship Scheme for the project titled "Catalytic-Enzyme degradation of toxic environmental pollutants by Bacillus megaterium H2: An in-silico approach."