Engineering substrate promiscuity in 2,4-dichlorophenol hydroxylase by in silico design

2,4-Dichlorophenol hydroxylase (2,4-DCP hydroxylase) is a key enzyme in the degradation of 2,4-dichlorophenoxyacetic acid in the hydroxylation step in many bacteria. Our previous study demonstrated that a 2,4-DCP hydroxylase (TfdB-JLU) exhibits broad substrate specificity for chlorophenols (CPs) and their homologues. In this study, TfdB-JLU has been engineered by rational design to further broaden its substrate scope towards CPs. We dissect the architectures of enzymes from oxidoreductase families to discover their underlying structural sources of substrate promiscuity. A homology model of TfdB-JLU has been built and docking experiments of this homology model with its natural substrate 2,4-DCP reveal that the phenyl rings of 2,4-DCP form strong interactions with residues His47, Ile48, Trp222, Pro316, and Phe424. These residues are found to be important for substrate binding in the active site. Then, the site-directed mutagenesis strategy has been applied for redesigning substrate promiscuity in TfdB-JLU. The TfdB-JLU-P316Q variant obtained shows a significant enhancement of activity (up to 3.4-fold) toward 10 CP congeners compared to wild-type TfdB-JLU. Interestingly, the active improvements of TfdB-JLU-P316Q toward CP congeners show significant difference, especially for active improvements of positional congeners such as 3-CP (1.1-fold) compared to 4-CP (3.0-fold), as well as 2,3-DCP (1.2-fold) compared to 2,5-DCP (3.4-fold). Structural analysis results indicate that the improvement in substrate promiscuity of the variant enzyme compared to the wild-type enzyme is possibly due to the increase of non-bonding interaction. The results suggest that exploiting enzyme-substrate promiscuity is promising, which would provide a starting point for designing and engineering novel biological catalysts for pollution removal.

Self-assembled 2,4-dichlorophenol hydroxylase-inorganic hybrid nanoflowers with enhanced activity and stability

2,4-Dichlorophenol hydroxylase (2,4-DCP hydroxylase) is a key enzyme in the degradation of 2,4-dichlorophenoxyacetic acid in the hydroxylation step in many bacteria. Our previous study demonstrated that a cold-adapted 2,4-DCP hydroxylase (tfdB-JLU) exhibits broad substrate specificity for chlorophenols, biphenyl derivatives and their homologues. However, the stability of this enzyme is not satisfactory in practical use. There have been no reports of immobilizing a cold-adapted enzyme to improve its activity and stability so far. This study for the first time reports a facile approach for the synthesis of hybrid nanoflowers (hNFs) formed from cold-adapted 2,4-dichlorophenol hydroxylase (tfdB-JLU) and Cu₃(PO₄)₂·3H₂O. The influence of experimental factors, such as the pH of the solution mixture and the enzyme and Cu²⁺ concentrations, on the activity of the prepared tfdB-JLU-hNFs is investigated. The morphologies of the tfdB-JLU-hNFs are further analyzed by SEM and TEM. Compared to the free enzyme, the tfdB-JLU-hNFs exhibit up to 162.46 ± 1.53% enhanced 2,4-dichlorophenol degradation activity when encapsulated at different enzyme concentrations. The tfdB-JLU-hNFs exhibit excellent durability with 58.34% residual activity after six successive cycles, and up to 90.58% residual activity after 20 days of storage. These results demonstrate that this multistage and hierarchical flower-like structure can effectively increase enzyme activity and stability with respect to those of the free enzyme. The satisfactory removal rate of 2,4-dichlorophenol catalyzed by tfdB-JLU-hNFs suggests that this immobilized enzyme exhibits great potential for application in bioremediation.

Highly stable and active hydroxylase-inorganic hybrid nanoflowers with great potential for application in bioremediation were obtained.