Structural study of the X-ray-induced enzymatic reduction of molecular oxygen to water bySteccherinum murashkinskyilaccase: insights into the reaction mechanism

Harnessing the power of bacterial laccases for xenobiotic degradation in water: A 10-year overview

Industrialization and population growth are leading to the production of significant amounts of sewage containing hazardous xenobiotic compounds. These compounds pose a threat to human and animal health, as well as the overall ecosystem. To combat this issue, chemical, physical, and biological techniques have been used to remove these contaminants from water bodies affected by human activity. Biotechnological methods have proven effective in utilizing microorganisms and enzymes, particularly laccases, to address this problem. Laccases possess versatile enzymatic characteristics and have shown promise in degrading different xenobiotic compounds found in municipal, industrial, and medical wastewater. Both free enzymes and crude enzyme extracts have demonstrated success in the biotransformation of these compounds. Despite these advancements, the widespread use of laccases for bioremediation and wastewater treatment faces challenges due to the complex composition, high salt concentration, and extreme pH often present in contaminated media. These factors negatively impact protein stability, recovery, and recycling processes, hindering their large-scale application. These issues can be addressed by focusing on large-scale production, resolving operation problems, and utilizing cutting-edge genetic and protein engineering techniques. Additionally, finding novel sources of laccases, understanding their biochemical properties, enhancing their catalytic activity and thermostability, and improving their production processes are crucial steps towards overcoming these limitations. By doing so, enzyme-based biological degradation processes can be improved, resulting in more efficient removal of xenobiotics from water systems. This review summarizes the latest research on bacterial laccases over the past decade. It covers the advancements in identifying their structures, characterizing their biochemical properties, exploring their modes of action, and discovering their potential applications in the biotransformation and bioremediation of xenobiotic pollutants commonly present in water sources.

Fungal Laccases: Fundamentals, Engineering and Classification Update

Multicopper oxidases (MCOs) share a common catalytic mechanism of activation by oxygen and cupredoxin-like folding, along with some common structural determinants. Laccases constitute the largest group of MCOs, with fungal laccases having the greatest biotechnological applicability due to their superior ability to oxidize a wide range of aromatic compounds and lignin, which is enhanced in the presence of redox mediators. The adaptation of these versatile enzymes to specific application processes can be achieved through the directed evolution of the recombinant enzymes. On the other hand, their substrate versatility and the low sequence homology among laccases make their exact classification difficult. Many of the ever-increasing amounts of MCO entries from fungal genomes are automatically (and often wrongly) annotated as laccases. In a recent comparative genomic study of 52 basidiomycete fungi, MCO classification was revised based on their phylogeny. The enzymes clustered according to common structural motifs and theoretical activities, revealing three novel groups of laccase-like enzymes. This review provides an overview of the structure, catalytic activity, and oxidative mechanism of fungal laccases and how their biotechnological potential as biocatalysts in industry can be greatly enhanced by protein engineering. Finally, recent information on newly identified MCOs with laccase-like activity is included.

Radiation damage to biological macromolecules∗

In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.

Exoproteomic Study and Transcriptional Responses of Laccase and Ligninolytic Peroxidase Genes of White-Rot Fungus Trametes hirsuta LE-BIN 072 Grown in the Presence of Monolignol-Related Phenolic Compounds

Being an abundant renewable source of aromatic compounds, lignin is an important component of future bio-based economy. Currently, biotechnological processing of lignin through low molecular weight compounds is one of the conceptually promising ways for its valorization. To obtain lignin fragments suitable for further inclusion into microbial metabolism, it is proposed to use a ligninolytic system of white-rot fungi, which mainly comprises laccases and peroxidases. However, laccase and peroxidase genes are almost always represented by many non-allelic copies that form multigene families within the genome of white-rot fungi, and the contributions of exact family members to the overall process of lignin degradation has not yet been determined. In this article, the response of the Trametes hirsuta LE-BIN 072 ligninolytic system to the presence of various monolignol-related phenolic compounds (veratryl alcohol, p-coumaric acid, vanillic acid, and syringic acid) in culture media was monitored at the level of gene transcription and protein secretion. By showing which isozymes contribute to the overall functioning of the ligninolytic system of the T. hirsuta LE-BIN 072, the data obtained in this study will greatly contribute to the possible application of this fungus and its ligninolytic enzymes in lignin depolymerization processes.

Structural Insight into the Amino Acid Environment of the Two-Domain Laccase's Trinuclear Copper Cluster

Laccases are industrially relevant enzymes. However, their range of applications is limited by their functioning and stability. Most of the currently known laccases function in acidic conditions at temperatures below 60 °C, but two-domain laccases (2D) oxidize some substrates in alkaline conditions and above 70 °C. In this study, we aim to establish the structural factors affecting the alkaline activity of the 2D laccase from Streptomyces griseoflavus (SgfSL). The range of methods used allowed us to show that the alkaline activity of SgfSL is influenced by the polar residues located close to the trinuclear center (TNC). Structural and functional studies of the SgfSL mutants Met199Ala/Asp268Asn and Met199Gly/Asp268Asn revealed that the substitution Asp268Asn (11 Å from the TNC) affects the orientation of the Asn261 (the second coordination sphere of the TNC), resulting in hydrogen-bond-network reorganization, which leads to a change in the SgfSL-activity pH profile. The combination of the Met199Gly/Arg240His and Asp268Asn substitutions increased the efficiency (kcat/KM) of the 2,6-DMP oxidation by 34-fold compared with the SgfSL. Our results extend the knowledge about the structure and functioning of 2D laccases' TNC active sites and open up new possibilities for the directed engineering of laccases.

Laccase: A potential biocatalyst for pollutant degradation

In the continual march to a predominantly urbanized civilization, anthropogenic activities have increased scrupulously, industrialization have occurred, economic growth has increased, and natural resources are being exploited, causing huge waste management problems, disposal issues, and the evolution of several pollutants. In order to have a sustainable environment, these pollutants need to be removed and degraded. Bioremediation employing microorganisms or enzymes can be used to treat the pollutants by degrading and/or transforming the pollutants into different form which is less or non-toxic to the environment. Laccase is a diverse enzyme/biocatalyst belonging to the oxidoreductase group of enzymes produced by microorganisms. Due to its low substrate specificity and monoelectronic oxidation of substrates in a wide range of complexes, it is most commonly used to degrade chemical pollutants. For degradation of emerging pollutants, laccase can be efficiently employed; however, large-scale application needs reusability, thermostability, and operational stability which necessitated strategies like immobilization and engineering of robust laccase possessing desirable properties. Immobilization of laccase for bioremediation, and treatment of wastewater for degrading emerging pollutants have been focussed for sustainable development. Challenges of employing biocatalysts for these applications as well as engineering robust laccase have been highlighted in this study.

Nanozyme-based pollutant sensing and environmental treatment: Trends, challenges, and perspectives

Nanozymes are defined as nanomaterials exhibiting enzyme-like properties, and they possess both catalytic functions and nanomaterial's unique physicochemical characteristics. Due to the excellent stability and improved catalytic activity in comparison to natural enzymes, nanozymes have established a wide base for applications in environmental pollutants monitoring and remediation. Nanozymes have been applied in the detection of heavy metal ions, molecules, and organic compounds, both quantitatively and qualitatively. Additionally, within the natural environment, nanozymes can be employed for the degradation of organic and persistent pollutants such as antibiotics, phenols, and textile dyes. Further, the potential sphere of applications for nanozymes traverses from indoor air purification to anti-biofouling agents, and even they show promise in combatting pathogenic bacteria. However, nanozymes may have inherent toxicity, which can restrict their widespread utility. Thus, it is important to evaluate and monitor the interaction and transformation of nanozymes towards biosphere damage when employed within the natural environment in a cradle-to-grave manner, to assure their utmost safety. In this context, various studies have concluded that the green synthesis of nanozymes can efficiently overcome the toxicity limitations in real life applications, and nanozymes can be well utilized in the sensing and degradation of several toxic pollutants including metal ions, pesticides, and chemical warfare agents. In this seminal review, we have explored the great potential of nanozymes, whilst addressing a range of concerns, which have often been overlooked and currently restrict widespread applications and commercialization of nanozymes.

Fungal Laccases: The Forefront of Enzymes for Sustainability

Enzymatic catalysis is one of the main pillars of sustainability for industrial production. Enzyme application allows minimization of the use of toxic solvents and to valorize the agro-industrial residues through reuse. In addition, they are safe and energy efficient. Nonetheless, their use in biotechnological processes is still hindered by the cost, stability, and low rate of recycling and reuse. Among the many industrial enzymes, fungal laccases (LCs) are perfect candidates to serve as a biotechnological tool as they are outstanding, versatile catalytic oxidants, only requiring molecular oxygen to function. LCs are able to degrade phenolic components of lignin, allowing them to efficiently reuse the lignocellulosic biomass for the production of enzymes, bioactive compounds, or clean energy, while minimizing the use of chemicals. Therefore, this review aims to give an overview of fungal LC, a promising green and sustainable enzyme, its mechanism of action, advantages, disadvantages, and solutions for its use as a tool to reduce the environmental and economic impact of industrial processes with a particular insight on the reuse of agro-wastes.

The β-hairpin from the Thermus thermophilus HB27 laccase works as a pH-dependent switch to regulate laccase activity

The multi-copper oxidase from the hyper-thermophilic bacteria Thermus thermophilus (Tth-MCO), has been previously characterized and described as an example of a laccase with low catalytic properties, especially when it is compared with the activity of fungal laccases, but it is active at high temperatures. Structurally, Tth-MCO has a unique feature: a β-hairpin near the T1Cu site, which is not present in any other laccases deposited at the PDB. This β-hairpin has an expected crystallographic behavior in solvent-exposed areas of a crystallized protein: lack of electron density, high B-values and several crystalline contacts with neighboring crystallographic copies; however, its dynamical behavior in solution and its biological implications have not been described. Here, we describe four new Tth-MCO crystallographic structures, and the β-hairpin behavior has been analyzed by molecular dynamics simulations, considering the effect of pH and temperature. The β-hairpin new crystallographic conformations described here, together with their dynamics, were used to understand the pH-restrained laccase activity of Tth-MCO against substrates as syringaldazine. Remarkably, there are insertions in laccases from Thermus and Meiothermus genus, sharing the same position and a methionine-rich composition of the Tth-MCO β-hairpin. This unique high methionine content of the Tth-MCO β-hairpin is responsible to coordinate, Ag⁺¹ and Hg⁺¹ in oxidative conditions, but Cu⁺¹ and Cu⁺² are not coordinated in crystallographic experiments, regardless of the redox conditions; however, Ag⁺¹ addition does not affect Tth-MCO laccase activity against syringaldazine. Here, we propose that the pH-dependent β-hairpin dynamical behavior could explain, at least in part, the inefficient laccase activity displayed by Tth-MCO in acidic pH values.

The role of positive charged residue in the proton-transfer mechanism of two-domain laccase from Streptomyces griseoflavus Ac-993

Multi-copper oxidases are capable of coupling the one-electron oxidation of four substrate equivalents to the four-electron reduction of dioxygen to two molecules of water. This process takes place at the trinuclear copper center of the enzymes. Previously, the main catalytic stages for three-domain (3D) laccases have been identified. However, for bacterial small two-domain (2D) laccases several questions remain to be answered. One of them is the nature of the protonation events upon the reductive cleavage of dioxygen to water. In 3D laccases, acidic residues play a key role in the protonation mechanisms. In this study, the role of the Arg240 residue, located within the T2 tunnel of 2D laccase from Streptomyces griseoflavus Ac-993, was investigated. X-ray structural analysis and kinetic characterization of two mutants, R240A and R240H, have provided support for a role of this residue in the protonation events. Communicated by Ramaswamy H. Sarma.

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

An obligate mutualistic relationship exists between the fungus Amylostereum areolatum and woodwasp Sirex noctilio. The fungus digests lignin in the host pine, providing essential nutrients for the growing woodwasp larvae. However, the functional properties of this symbiosis are poorly described. In this study, we identified, cloned, and characterized 14 laccase genes from A. areolatum. These genes encoded proteins of 508 to 529 amino acids and contained three typical copper-oxidase domains, necessary to confer laccase activity. Besides, we performed molecular docking and dynamics simulation of the laccase proteins in complex with lignin compounds (monomers, dimers, trimers, and tetramers). AaLac2, AaLac3, AaLac6, AaLac8, and AaLac10 were found that had low binding energies with all lignin model compounds tested and three of them could maintain stability when binding to these compounds. Among these complexes, amino acid residues ALA, GLN, LEU, PHE, PRO, and SER were commonly present. Our study reveals the molecular basis of A. areolatum laccases interacting with lignin, which is essential for understanding how the fungus provides nutrients to S. noctilio. These findings might also provide guidance for the control of S. noctilio by informing the design of enzyme mutants that could reduce the efficiency of lignin degradation.

A Fungal Ascorbate Oxidase with Unexpected Laccase Activity

Ascorbate oxidases are an enzyme group that has not been explored to a large extent. So far, mainly ascorbate oxidases from plants and only a few from fungi have been described. Although ascorbate oxidases belong to the well-studied enzyme family of multi-copper oxidases, their function is still unclear. In this study, Af_AO1, an enzyme from the fungus Aspergillus flavus, was characterized. Sequence analyses and copper content determination demonstrated Af_AO1 to belong to the multi-copper oxidase family. Biochemical characterization and 3D-modeling revealed a similarity to ascorbate oxidases, but also to laccases. Af_AO1 had a 10-fold higher affinity to ascorbic acid (K_M = 0.16 ± 0.03 mM) than to ABTS (K_M = 1.89 ± 0.12 mM). Furthermore, the best fitting 3D-model was based on the ascorbate oxidase from Cucurbita pepo var. melopepo. The laccase-like activity of Af_AO1 on ABTS (V_max = 11.56 ± 0.15 µM/min/mg) was, however, not negligible. On the other hand, other typical laccase substrates, such as syringaldezine and guaiacol, were not oxidized by Af_AO1. According to the biochemical and structural characterization, Af_AO1 was classified as ascorbate oxidase with unusual, laccase-like activity.

Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase

Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.

Inhibition in multicopper oxidases: a critical review

This review critiques the literature on inhibition of O₂-reduction catalysis in multicopper oxidases like laccase and bilirubin oxidase and provide recommendations for best practice when carrying out experiments and interpreting published data.

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

There is a high number of well characterized, commercially available laccases with different redox potentials and low substrate specificity, which in turn makes them attractive for a vast array of biotechnological applications. Laccases operate as batteries, storing electrons from individual substrate oxidation reactions to reduce molecular oxygen, releasing water as the only by-product. Due to society’s increasing environmental awareness and the global intensification of bio-based economies, the biotechnological industry is also expanding. Enzymes such as laccases are seen as a better alternative for use in the wood, paper, textile, and food industries, and they are being applied as biocatalysts, biosensors, and biofuel cells. Almost 140 years from the first description of laccase, industrial implementations of these enzymes still remain scarce in comparison to their potential, which is mostly due to high production costs and the limited control of the enzymatic reaction side product(s). This review summarizes the laccase applications in the last decade, focusing on the published patents during this period.

Laccases: structure, function, and potential application in water bioremediation

The global rise in urbanization and industrial activity has led to the production and incorporation of foreign contaminant molecules into ecosystems, distorting them and impacting human and animal health. Physical, chemical, and biological strategies have been adopted to eliminate these contaminants from water bodies under anthropogenic stress. Biotechnological processes involving microorganisms and enzymes have been used for this purpose; specifically, laccases, which are broad spectrum biocatalysts, have been used to degrade several compounds, such as those that can be found in the effluents from industries and hospitals. Laccases have shown high potential in the biotransformation of diverse pollutants using crude enzyme extracts or free enzymes. However, their application in bioremediation and water treatment at a large scale is limited by the complex composition and high salt concentration and pH values of contaminated media that affect protein stability, recovery and recycling. These issues are also associated with operational problems and the necessity of large-scale production of laccase. Hence, more knowledge on the molecular characteristics of water bodies is required to identify and develop new laccases that can be used under complex conditions and to develop novel strategies and processes to achieve their efficient application in treating contaminated water. Recently, stability, efficiency, separation and reuse issues have been overcome by the immobilization of enzymes and development of novel biocatalytic materials. This review provides recent information on laccases from different sources, their structures and biochemical properties, mechanisms of action, and application in the bioremediation and biotransformation of contaminant molecules in water. Moreover, we discuss a series of improvements that have been attempted for better organic solvent tolerance, thermo-tolerance, and operational stability of laccases, as per process requirements.

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

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.

Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase from Streptomyces griseoflavus Ac-993

Laccases (EC 1.10.3.2) are multicopper oxidoreductases acting on diphenols and related substances. Laccases are highly important for biotechnology and environmental remediation. These enzymes contain mononuclear one T2 copper ion and two T3 copper ions (Cu3_α and Cu3_β), which form the so-called trinuclear center (TNC). Along with the typical three-domain laccases Bacteria produce two-domain (2D) enzymes, which are active at neutral and basic pH, thermostable, and resistant to inhibitors. In this work we present the comparative analysis of crystal structures and catalytic properties of recombinant 2D laccase from Streptomyces griseoflavus Ac-993 (SgfSL) and its four mutant forms with replacements of two amino acid residues, located at the narrowing of the presumable T3-solvent tunnels. We obtained inactive enzymes with substitutions of His165, with Phe, and Ile170 with Ala or Phe. His165Ala variant was more active than the wild type. We suggest that His165 is a “gateway” at the O₂-tunnel leading from solvent to the Cu3_β of the enzyme. The side chain of Ile170 could be indirectly involved in the coordination of copper ions at the T3 center by maintaining the position of the imidazole ring of His157 that belongs to the first coordination sphere of Cu3_α.

A comparative structural analysis of the surface properties of asco-laccases

Laccases of different biological origins have been widely investigated and these studies have elucidated fundamentals of the generic catalytic mechanism. However, other features such as surface properties and residues located away from the catalytic centres may also have impact on enzyme function. Here we present the crystal structure of laccase from Myceliophthora thermophila (MtL) to a resolution of 1.62 Å together with a thorough structural comparison with other members of the CAZy family AA1_3 that comprises fungal laccases from ascomycetes. The recombinant protein produced in A. oryzae has a molecular mass of 75 kDa, a pI of 4.2 and carries 13.5 kDa N-linked glycans. In the crystal, MtL forms a dimer with the phenolic substrate binding pocket blocked, suggesting that the active form of the enzyme is monomeric. Overall, the MtL structure conforms with the canonical fold of fungal laccases as well as the features specific for the asco-laccases. However, the structural comparisons also reveal significant variations within this taxonomic subgroup. Notable differences in the T1-Cu active site topology and polar motifs imply molecular evolution to serve different functional roles. Very few surface residues are conserved and it is noticeable that they encompass residues that interact with the N-glycans and/or are located at domain interfaces. The N-glycosylation sites are surprisingly conserved among asco-laccases and in most cases the glycan displays extensive interactions with the protein. In particular, the glycans at Asn88 and Asn210 appear to have evolved as an integral part of the asco-laccase structure. An uneven distribution of the carbohydrates around the enzyme give unique properties to a distinct part of the surface of the asco-laccases which may have implication for laccase function–in particular towards large substrates.