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Abstract (in English)
Halogenated organic compounds exist in great quantity in the biosphere and can cause extensive problems due to their toxic properties and persistence in nature. They can affect the quality of life of human beings and other living organisms. The degradation of these compounds by microorganisms is salient in reducing pollutants. Bradyrhizobium elkanii is a nitrogen-fixing bacteria that lives in symbiosis with plant roots, particularly legumes. To the best of our knowledge, up to now, there is no evidence to indicate that Bradyrhizobium elkanii can produce haloacid dehalogenase type II enzymes. Thus, the current study used proteogenomics techniques for homology modeling and docking assessment of a newly identified dehalogenase type II (namely, DehlB4) to predict its ability to degrade selected halogenated compounds. A total of sixty-seven genomes of Bradyrhizobium elkanii strains from the National Center for Biotechnology Information (NCBI) were searched for dehalogenase genes. These strains notably carry dehalogenase genes. Surprisingly, Bradyrhizobium elkanii strain BR29 contains five dehalogenases, and therefore strain BR29 was further characterized. The study aimed to probe the enzyme's catalytic tendencies to optimally breakdown the selected haloacids. The modeled structure of DehlB4 was composed of a core and a cap domain. The modeled structure of DehlB4 revealed satisfactory scores on the ERRAT (90.65%), Verify3D (88.54%), and PROCHECK (100%) assessments. The active site was anticipated by docking and multiple sequence alignment assessments for possible pollutant degradation. The amino acids R40 and N174 were predicted to be catalytically important. The indispensable residue D9 which acts as a nucleophile was conserved with the crystalized structure of DehIVa and L-DEX consequently indicating a robust result of the current research. The proteogenomics study as such has a good potential for screening new types of dehalogenases and characterization of newly identified dehalogenases based on basic molecular structure and function analysis.