Abstract
Dibenzothiophene (DBT) and their derivatives, accounting for the major part of the sulfur components in crude oil, make one of the most significant pollution sources. The DBT sulfone monooxygenase BdsA, one of the key enzymes in the “4S” desulfurization pathway, catalyzes the oxidation of DBT sulfone to 2′-hydroxybiphenyl 2-sulfonic acid (HBPSi). Here, we determined the crystal structure of BdsA from Bacillus subtilis WU-S2B, at the resolution of 2.2 Å, and the structure of the BdsA-FMN complex at 2.4 Å. BdsA and the BdsA-FMN complex exist as tetramers. DBT sulfone was placed into the active site by molecular docking. Seven residues (Phe12, His20, Phe56, Phe246, Val248, His316, and Val372) are found to be involved in the binding of DBT sulfone. The importance of these residues is supported by the study of the catalytic activity of the active site variants. Structural analysis and enzyme activity assay confirmed the importance of the right position and orientation of FMN and DBT sulfone, as well as the involvement of Ser139 as a nucleophile in catalysis. This work combined with our previous structure of DszC provides a systematic structural basis for the development of engineered desulfurization enzymes with higher efficiency and stability.
Highlights
The burning of fossil fuels causes worldwide environmental pollution because of the sulfur compounds present in fossil fuels
The crystal structure of apo-BdsA from Bacillus subtilis belongs to the P21212 space group with the cell dimension a = 132.494 Å, b = 174.574 Å, and c = 85.345 Å
The BdsA monomer contains nine β-strands (β1–β9) and 13 α-helices (α1–α13), which fold into a triosephosphate isomerase (TIM)-barrel with five extended insertion regions (Figure 2B)
Summary
The burning of fossil fuels causes worldwide environmental pollution because of the sulfur compounds present in fossil fuels. Hydrodesulfurization (HDS) can remove sulfur from petroleum, but heterocyclic sulfur compounds are difficult to remove completely. Reducing the presence of heterocyclic sulfur compounds, such as dibenzothiophene (DBT) and alkylated DBTs, has become increasingly important. Physical and chemical methods of desulfurization are not economically viable and may cause additional environmental pollution. Biological desulfurization (BDS) for the treatment of recalcitrant organic sulfur compounds has gained attention (Monticello et al, 1985; Gray et al, 2003). Numerous efforts have been focused on investigating biodesulfurization systems, using DBT or its alkylated derivatives as model compounds. The pathway cleaving the C-S bond during metabolic desulfurization has been termed the “4S” pathway (Figure 1)
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