Homology Modelling and Docking Studies of Arsenate Reductase of Bacillus megaterium

Arbi, Mst. Nusrat Jahan; Thahsin, Naima; Nurjahan, Azmery; Sharmin, Sabrina; Islam, Md. Zahidul; Zohora, Umme Salma; Ruma, Mastura Khatun; Moni, Ripa; Rahman, Mohammad Shahedur

doi:10.30491/jabr.2021.302174.1437

Homology Modelling and Docking Studies of Arsenate Reductase of Bacillus megaterium

Document Type : Original Article

Authors

Mst. Nusrat Jahan Arbi ¹

Naima Thahsin ¹

Azmery Nurjahan ¹

Sabrina Sharmin ²

Md. Zahidul Islam ¹

Umme Salma Zohora ¹

Mastura Khatun Ruma ¹

Ripa Moni ¹

Mohammad Shahedur Rahman ¹

¹ Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh

² Department of Pharmacy, Brac University, 66 Mohakhali, Dhaka 1212, Bangladesh

10.30491/jabr.2021.302174.1437

Abstract

Introduction: Bacillus megaterium is a ubiquitous bacterial strain that produces the enzyme arsenate reductase that catalyzes the reduction of less toxic arsenate (V) to more toxic arsenite (III). Due to the functional significance of this enzyme, the present study was carried out to construct and validate the Three Dimensional (3D) structure of arsenate reductase of B. megaterium and study its interaction with arsenate.
Materials and Methods: The 3D model was generated by MODELLER using the known crystal structure of the enzyme. The superimposition of the model with the template structures was done by PyMOL. PATCHDOCK was used to perform molecular docking of the enzyme with arsenate ion and Fire Dock was used to refining the docked complexes. The highest geometric score containing docked complex was visualized and the intra-molecular interaction within it was evaluated.
Results: The evaluation of the 3D computed model showed good qualities including fine stereochemical properties, satisfactory compatibility between the structure and its amino acid sequence, acceptable residues error value, etc. The model as well as its phylogenetic relatives (Bacillus and Staphylococcus) showed the same active site motif which is CTGNSCRS. The crucial amino acids involved in binding with the arsenate ion (AsO4^3-) were Cys10, Thr11, Gly12, Asn13, Ser14, Cys15, His43, and Asp106. Among these, the first six amino acids fell in the conservative motif (CTGNSCRS).
Conclusions: Studying this interaction can be helpful for more research to inhibit the binding or any other approach that will stop the inimical conversion of less toxic arsenate to more toxic arsenite.

Keywords

Bacillus megaterium

Arsenate Reductase

Arsenate

Homology Modeling

Molecular Docking