Modeling Based Structural Insights into Biodegradation of the Herbicide Diuron by Laccase-1 from Ceriporiopsis subvermispora

Abstract

The herbicide diuron (3-(3,4-dichlorophenyl)-1,1-dimethylurea) is used in many agricultural crops and non-crop areas worldwide, leading to the pollution of the aquatic environment by soil leaching. White rot fungi and its lignin modifying enzymes, peroxidases and laccases, are responsible for its degradation. Therefore, it is of interest to explore the potential use of Ceriporiopsis subvermispora laccase (CersuLac1) in the biotransformation of this herbicide by using its enzyme laccase. However, the structure of laccase from Ceriporiopsis subvermispora is still unknown. Hence, a model of laccase was constructed using homology modeling. The model was further used to dock p-methylbenzoate in the presence of four copper ions to analyze molecular basis of its binding and interaction. The ligand-protein interaction is stereo-chemically favorable in nature. The presence of the single protonated Lys457 was necessary for catalysis, being coordinated by a cupper ion. The best pose of diuron on CersuLac1 has a theoretical Ki of 2.91 mM. This is comparable to the KM values for laccases from other organisms with similar compounds. Thus, we document the insights for the potential use of laccase from Ceriporiopsis subvermispora in the biotransfrormation of diuron.

Predicting the Biodegradability Nature of Imidazole and Its Derivatives by Modulating Two Histidine Degradation Enzymes (Urocanase and Formiminoglutamase) Activities

“…Thus, to overcome problem, molecular docking approaches has been explored in recent years. For instance, molecular modeling of laccase was carried out to study the biodegradation nature of herbicide diuron [13].…”

Rice (Oryza sativa) Laccases Involved in Modification and Detoxification of Herbicides Atrazine and Isoproturon Residues in Plants

“…Laccases (EC 1.10.3.2) constitute a family of copper-containing oxidase enzymes that use molecular oxygen to catalyze the monoelectronic oxidation of natural metabolites or artificial substrates (e.g., phenolic and aromatic substrates) via a mechanism involving redicals. , Laccases exist in many fungi and plants, and more than a hundred compounds have been identified as substrates for fungal laccases. − Typical substrates of laccases include monophenols, polyamines, aminophenol, aryl diamine, and some inorganic ions (e.g., Cu). The major biological functions of laccase are involved in lignin biodegradation, , cell wall lignification, and detoxification of some toxic compounds such as polyaromatic hydrocarbons (PAHs), , organophosphorus pesticides, or azodyes. , It is apparent that molecular modification and detoxification could be one of the major functions for laccases in organisms. To date, most studies have concerned functional laccases on xenobiotics (e.g., pesticides or herbicides) in fungi and bacteria, but very few have described laccase working against toxic compounds in higher plants. , …”

“…The major biological functions of laccase are involved in lignin biodegradation, , cell wall lignification, and detoxification of some toxic compounds such as polyaromatic hydrocarbons (PAHs), , organophosphorus pesticides, or azodyes. , It is apparent that molecular modification and detoxification could be one of the major functions for laccases in organisms. To date, most studies have concerned functional laccases on xenobiotics (e.g., pesticides or herbicides) in fungi and bacteria, but very few have described laccase working against toxic compounds in higher plants. , …”

“…To date, most studies have concerned functional laccases on xenobiotics (e.g., pesticides or herbicides) in fungi and bacteria, but very few have described laccase working against toxic compounds in higher plants. 9,12 The presence of pesticides in the environment is a matter of particular concern for the conservation of ecosystems. It is also the major problem for crop production because soil contamination with such compounds risks food safety and human health.…”