Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Vol. 12 No. 2 (2022)

In Silico Molecular Characterization of a Putative Haloacid Dehalogenase Type II from Genomic of Mesorhizobium loti Strain TONO: In Silico Molecular Characterization of a Putative Haloacid Dehalogenase Type II

Sefatullah Zakary (Lecturer at Kabul University)
Hamida Mashal (Department of Botany, Faculty of Biology, Kabul University, 1006 Dehbori, Kabul, Afghanistan)
Abdul Rahman Osmani (Department of Zoology, Faculty of Biology, Kabul University, 1006 Dehbori, Kabul, Afghanistan)
Habeebat Adekilekun Oyewus (Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB 5351, Ekiti State, Nigeria)
Fahrul Huyop (Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM, Johor Bahru, Malaysia)
Muzhgan Mohammad Nasim (Department of Chemical and Environmental Engineering, Faculty of Malaysia Japan International Institute of Technology, University Technology Malaysia, 50100 UTM, Kuala Lumpur, Malaysia)



Article Info

Publish Date
17 Jun 2022

Abstract

Halogenated organic compounds are found as waste in the biosphere and can causenumerous dilemmas because of their toxicity and persistence in the environment. Theyplay a major role in the quality of life of both, human beings and other living organisms. Degradation of these compounds by microorganisms is significant to reduce recalcitrant and cost. Thus, in the current study, an in-silico approach was used for homology modelling and docking assessment of a newly identified DehLt4, type IIdehalogenase to predict its ability to degrade selected haloalkanoic acids and haloacetates. The study aimed to establish the catalytic tendencies of the enzyme to optimallydegrade the selected halogenated haloacids. The refined modelled structure of DehLt4using GROMACS 5.1.2 software revealed satisfactory scores of ERRAT (94.73%),Verify3D (90.83%) and PROCHECK (99.05 %) assessments. Active site predictionby blind docking and multiple sequence alignment indicated the catalytic triads forDehLt4 were Asp9-Lys149-Asn175. Both L-2-chloropropionic acid (L-2-CP) and trichloroacetate (TCA) docked with DehLt4 exhibited binding energy of -3.9 kcal/mol.However, the binding energy for D-2-chloropropionic acid (D-2-CP) and monochloroacetate (MCA) was -3.8 kcal/mol and -3.1 kcal/mol, respectively. Thus, the findingsof the study successfully identified the catalytic important residues of DehLt4 for possible pollutant degradation. The in-silico study as such has a good potential for characterization of newly identified dehalogenases based on basic molecular structure andfunctions analysis.Keywords: Dehalogenase, Haloacid dehalogenase, Mesorhizobium loti strain TONO,Protein structure

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Journal Info

Abbrev

jtrolis

Publisher

Subject

Agriculture, Biological Sciences & Forestry Environmental Science

Description

The Journal of Tropical Life Science (JTLS) provides publication of full-length papers, short communication and review articles describing of new finding or theory in living system, cells and molecular level in tropical life science and related areas. The journal publishes articles that report novel ...