Shorter Alkanesulfonate Carbon Chains Destabilize the Active Site Architecture of SsuD for Desulfonation

Abstract

Bacteria have evolved to utilize alternative organosulfur sources when sulfur is limiting. The SsuE/SsuD and MsuE/MsuD enzymes expressed when sulfur sources are restricted, are responsible for providing specific bacteria with sulfur in the form of alkanesulfonates. In this study, we evaluated why two structurally and functionally similar FMNH2-dependent monooxygenase enzymes (MsuD and SsuD) are needed for the acquisition of alkanesulfonates in some bacteria. In desulfonation assays, MsuD was able to utilize the entire range of alkanesulfonates (C1–C10). However, SsuD was not able to utilize smaller alkanesulfonate substrates. Interestingly, SsuD had a similar binding affinity for methanesulfonate (MES) (15 ± 1 μM) as MsuD (12 ± 1 μM) even though SsuD was not able to catalyze the desulfonation of the MES substrate. SsuD and MsuD showed decreased proteolytic susceptibility in the presence of FMNH2 with MES and octanesulfonate (OCS). Tighter loop closure was observed for the MsuD/FMNH2 complex with MES and OCS compared to SsuD under comparable conditions. Analysis of the SsuD/FMNH2/MES structure using accelerated molecular dynamics simulations found three different conformations for MES, demonstrating the instability of the bound structure. Even when MES was bound in a similar fashion to OCS within the active site, the smaller alkane chain resulted in a shift of FMNH2 so that it was no longer in a position to catalyze the desulfonation of MES. The active site of SsuD requires a longer alkane chain to maintain the appropriate architecture for desulfonation.

Mycobactin analogue interacting with siderophore efflux-pump protein: insights from molecular dynamics simulations and whole-cell assays

“…Within proteins, p-p interactions generally have intermolecular distances ranging from ≤ 5.6 Å and dihedral angles, g, ranging from 50°to 90°for non-substituted aromatic rings such as phenyls while substituted aromatic rings, like hydroxyphenyls slightly shift these ranges (Zhao et al, 2015). To account for p-p stacking interactions, normalized vectors centered on the mass of the hydroxyphenyl rings of the ligand and Y273 were used to compute the angle between them while centers of mass were leveraged to compute intermolecular distances (Figure 7) (Zhao et al, 2015;Hayatshahi et al, 2018;Somai et al, 2023). To estimate for p-p stacking interactions, a distance cutoff of ≤ 5.0 Å denoted by R cen and an angle cut-off of 0°to 180°was utilized, resulting in compound Il when in orientation-3 exhibiting stacking behavior for 81.8% of the trajectory while orientations 1 and 2 yielded dismal results of 9.5% and 0.0%, respectively.…”