Feedback inhibition of DszC, a crucial enzyme for crude oil biodessulfurization

03 March 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


The Ideonella sakaiensis bacterium has a tremendous industrial interest as it can remove sulfur from crude oil through its four-enzyme (DszA-D) 4S metabolic pathway. DszC is one of the rate-limiting enzymes of the pathway and the one that most suffers from feedback inhibition. We have combined molecular docking and molecular dynamics simulations to identify binding sites through which two products of the 4S pathway, 2-hydroxybiphenyl, and 2'-hydroxybiphenyl-2-sulfinate, induce DszC feedback inhibition. We have identified four potential binding sites: two adjacent binding sites close to the 280-295 lid loop proposed to contribute to DszC oligomerization and proper binding of the flavin mononucleotide cofactor, and two other close to the active site of DszC and the substrate binding site. By considering i) the occupancy of the binding sites and ii) the similar inhibitor poses, we propose that the mechanism of feedback inhibition of DszC occurs through disturbance of the DszC oligomerization and consequent binding of the flavin mononucleotide due to the weakening of the interactions between the 280-295 lid loop and both the 131-142 loop and the C-terminal tail. Nevertheless, inhibitor binding close to the active site or the substrate binding sites also compromises critical interactions within the active site of DszC. The disclosed molecular details provide valuable insight for future rational enzyme engineering protocols to develop DszC mutants more resistant against the observed feedback inhibition mechanism.


4S pathway
noncompetitive inhibition
enzyme engineering
molecular docking
molecular dynamics simulations

Supplementary materials

Gromacs files
Starting coordinate files, system topologies, Gromacs input files.
Gromacs analysis
Raw output datafiles for contact, clustering and root-mean-square-fluctuation analsysis.


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