The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism

Abstract

Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X‐ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented. Three series of X‐ray diffraction data sets were collected with increasing doses of absorbed X‐ray radiation from a native S. murashkinskyi laccase crystal and from crystals of complexes of the laccase with chloride and fluoride ions. The data for the native laccase crystal confirmed the previously deduced enzymatic mechanism of molecular oxygen reduction. The structures of the complexes allowed the localization of chloride and fluoride ions in the channel near the T2 copper ion. These ions replace the oxygen ligand of the T2 copper ion in this channel and can play the role of this ligand in the enzymatic reaction. As follows from analysis of the structures from the increasing dose series, the inhibition of laccases by chloride and fluoride anions can be explained by the fact that the binding of these negatively charged ions at the position of the oxygen ligand of the T2 copper ion impedes the reduction of the T2 copper ion.

Genes Identification, Molecular Docking and Dynamics Simulation Analysis of Laccases from Amylostereum areolatum Provides Molecular Basis of Laccase Bound to Lignin

“…We searched potential templates for different laccase proteins in the Protein Data Bank database and the SWISS-MODEL template library. Based on high similarity scores, the optimal crystal structures (Protein Data Bank codes shown in Table 2 ) were selected as templates [ 78 , 79 , 80 , 81 , 82 ], and homology modelings of AaLac proteins were carried out using the SWISS-MODEL web server ( ) [ 83 ]. The GalaxyRene server ( ) [ 84 ] was used to optimize the side chain conformation of the modeled AaLac proteins and minimize the energy of each conformation.…”

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

“…For example, the influenza virus uses the haemagglutinin glycoprotein to recognise and bind sialic acid decorations of human cells in the respiratory tract [7]. Glycosylation is also used by pathogens to evade the host's immune system via glycan shields [8][9][10], and thereby to delay Figure 1: Comparison of the glycan features in electron density maps over a range of resolutions from selected glycoprotein structures (PDB entries: 6RI6 [19]; 6MZK [20]; 4O5I [21]). The electron density maps were obtained with X-ray crystallography.…”

“… Comparison of the glycan features in electron density maps over a range of resolutions from selected glycoprotein structures (PDB entries: 6RI6 [ 19 ]; 6MZK [ 20 ]; 4O5I [ 21 ]). The electron density maps were obtained with X-ray crystallography.…”

Applications of Microbial Laccases: Patent Review of the Past Decade (2009–2019)

“…Inhibitors of laccase activity include several metals, EDTA, L-cysteine, azide, cyanide, glutathione, dithiothreitol, and thiourea, among others [18]. Recent data regarding the structural basis of laccase inhibition by metals revealed the binding of chloride and fluoride anions to the T2 copper center, and thus the inhibition of oxygen reduction [19].…”