Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the “4S” Desulfurization Pathway

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.

Structures of the alkanesulfonate monooxygenase MsuD provide insight into C–S bond cleavage, substrate scope, and an unexpected role for the tetramer

“…Interestingly, S265, E266, and G267 are located within the active site lid, and D264 of the same region is observed to interact with a conserved arginine (R126) from near the phosphoryl binding site. The observed binding mode of FMN is expected to be similar for FMNHand is consistent with mutagenesis studies in the homolog BdsA, where mutations to residues corresponding to H123, R126, Y127 and S177 reduced the turnover rate by 45 -95% (45).…”

“…Available structures of group C FMN-dependent monooxygenases all contain a relatively open active site, despite positioning of the lid region when flavin binds.These proteins contain a long, disordered protein C terminus of unidentified function ( 30 , 33 , 37 , 45 , 48 ). To our surprise, the dataset of ternary-MsuD contained contiguous electron density for residues A355-A377 of the C terminus.…”

“…This article contains supporting information ( 17 , 26 , 30 , 31 , 35 , 37 , 42 , 43 , 45 , 46 , 48 , 81 , 82 , 83 , 84 , 85 , 86 , 87 ).…”

Bacterial Desulfurization of Dibenzothiophene by Pseudomonas Sp. Strain Kwn5 Immobilized in Alginate Beads

“…Crude oil has a high aromatic sulfur content, consist of benzothiophene (BT), dibenzothiophene (DBT), and its derivatives [10]. It is difficult to remove aromatic sulfur in crude oil through the process of hydrodesulfurization (HDS) because it was harder to desulfurize heterocyclic aromatic sulfur compounds (Polyaromatic Sulfur Heterocycles; PASHs) found in larger fractions [11,12].…”

Devulcanization of natural rubber vulcanizates by Bacillus cereus TISTR 2651

“…Recycling of the vulcanized rubber is an alternative method that converts the rubber waste into value added products [5][6][7]. Devulcanization is one form of recycling, where the crosslinked bonds in the rubber chains are cleaved, and can be classified into the three broad processes of physical [8][9][10][11][12][13][14], chemical [12,13,[15][16][17][18][19][20] and biological [12,[21][22][23][24][25][26][27][28][29] devulcanization processes. Physical devulcanization generally requires a high temperature or external energy for cleavage of the crosslinked bonds and so this process has a high cost and high energy consumption, challenging its economic and environmental viability.…”