Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)

Abstract

The development of biocatalytic desulfurization strategies of petroleum and its derivatives could result in more economic alternatives than the widely used chemical desulfurization. The organism Rhodococcus erythropolis IGTS8 has been shown to metabolize organic sulfur compounds through a mechanism known as 4S pathway, which involves four enzymes (DszA, DszB, DszC, and DszD) and has been explored in biodesulfurization. Here we have applied QM/MM methods to study the catalytic mechanism of the enzyme DszD, a NADH-FMN oxidoreductase that occupies a central place on the 4S pathway by catalyzing the formation of the FMNH2 that is used by the two monooxynases in the cycle: DszA and DszC. In addition, to clarify the catalytic mechanism of this enzyme, this study analyzed in detail the role played by the active site Thr residue and of Asn and Ala enzyme mutants. The results help to explain previous experimental evidence and suggest new strategies for improving biodesulfurization through an increase in the activity of DszD.

Transfer hydrogenation catalysis in cells

“…The electron acceptor is the isoalloxazine ring of FMN. 64,65 NADH is oxidized to NAD + by the enzymes NADH dehydrogenase and NADH:ubiquinone reductase, or during oxidative phosphorylation to generate ATP. 44,45 Phosphorylation of NAD + by NAD + kinases leads to the synthesis of NADP + , which in turn is reduced to NADPH by glucose-6-phosphate dehydrogenase (G6PDH) in the first step of the pentose phosphate pathway.…”

Whole Cell Actinobacteria as Biocatalysts

“…Among PAHs, sulfur (hetero-PAHs) in the form of thiophenic compounds such as benzothiophene (BT), dibenzothiophene (DBT), and their alkylated homologs (Khedkar and Shanker, 2015) have attracted increasingly stringent regulations due to their harmful effects on the environment and human health (Brinkmann et al, 2014; Sousa et al, 2016). The harmful effects of PAHs, particularly hetero-PAHs well documented (Brinkmann et al, 2014) and associated with mutagenic effects, chromosome aberrations, toxicity to daphnia and green algae, embryotoxicity of the zebrafish, and respiratory system irritations.…”

“…(Kirimura et al, 2001) have been studied for their ability to metabolize various polyaromatic sulfur heterocycles (PASHs) including BT and DBT (Aggarwal et al, 2013). The process adopted by this organism is known as the 4S pathway and involves four enzymes: DszA, DszB, DszC, and DszD (Wang et al, 2013; Sousa et al, 2016). DszA and DszC are monooxygenases that insert oxygen into the sulfur compounds, while DszB is a desulphinase that removes sulfur in the form of sulfite.…”

Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD)

“…An NADH dependent FMN oxidoreductase, DszD enzyme, encoded by the chromosomally-located dszD gene, provides FMNH 2 required for the activities of DszC and DszA enzymes. The DszD enzyme with 192 residues and a molecular weight of ∼22 kD is a key enzyme which is proposed to be responsible for the rate-limiting step of the 4S pathway (Sousa et al., 2016).…”