Crystal structures of chloroperoxidase with its bound substrates and complexed with formate, acetate, and nitrate

Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst

Oxidoreductases are enzymes with distinctive characteristics that favor their use in different areas, such as agriculture, environmental management, medicine, and analytical chemistry. Among these enzymes, oxidases, dehydrogenases, peroxidases, and oxygenases are very interesting. Because their substrate diversity, they can be used in different biocatalytic processes by homogeneous and heterogeneous catalysis. Immobilization of these enzymes has favored their use in the solution of different biotechnological problems, with a notable increase in the study and optimization of this technology in the last years. In this review, the main structural and catalytical features of oxidoreductases, their substrate specificity, immobilization, and usage in biocatalytic processes, such as bioconversion, bioremediation, and biosensors obtainment, are presented.

Enabling Peroxygenase Activity in Cytochrome P450 Monooxygenases by Engineering Hydrogen Peroxide Tunnels

Given prominent physicochemical similarities between H₂O₂ and water, we report a new strategy for promoting the peroxygenase activity of P450 enzymes by engineering their water tunnels to facilitate H₂O₂ access to the heme center buried therein. Specifically, the H₂O₂-driven activities of two native NADH-dependent P450 enzymes (CYP199A4 and CYP153A_M.aq) increase significantly (by >183-fold and >15-fold, respectively). Additionally, the amount of H₂O₂ required for an artificial P450 peroxygenase facilitated by a dual-functional small molecule to obtain the desired product is reduced by 95%-97.5% (with ∼95% coupling efficiency). Structural analysis suggests that mutating the residue at the bottleneck of the water tunnel may open a second pathway for H₂O₂ to flow to the heme center (in addition to the natural substrate tunnel). This study highlights a promising, generalizable strategy whereby P450 monooxygenases can be modified to adopt peroxygenase activity through H₂O₂ tunnel engineering, thus broadening the application scope of P450s in synthetic chemistry and synthetic biology.

Structure of the Green Heme Isolated from Allylbenzene-Modified Chloroperoxidase: A Novel Heme Architecture Implicating the Mechanisms of CPO Inactivation and Epoxidation

The chemical identification of the modified heme (the green heme) during chloroperoxidase catalyzed epoxidation of allylbenzene remains unestablished due to its high instability within the protein matrix, the absence of paramagnetically shifted signals, and the difficulty in obtaining crystals of the modified enzyme. We have established the unambiguous structure of the modified prosthetic heme group, which was extracted from the protein matrix using ²D NMR spectroscopy and LC-MS spectrometry. The modified heme was isolated as a µ-oxo dimer that can be quantitatively converted to the corresponding monomer. The depolymerized green heme displayed characteristic NMR signatures of iron porphyrin complexes, but no Nuclear Overhauser Effect was observable to assist in signal assignment. An alternative strategy was applied by removing the iron center of the green heme, resulting in a stable demetallated green porphyrin species. Complete assignment of all the NMR resonances in the demetallated green heme allowed us to establish the molecular architecture of the modified species as a novel N-alkylated heme. Decisive space correlations between the propyl protons of allylbenzene and the γ meso proton coupled with clear dipolar connectivities between the propyl-2H of the substrate and the β proton in the side chain of the propionic acid at carbon-6 of the porphyrin ring, clearly indicate that allylbenzene was covalently attached to the nitrogen atom of the pyrrole ring III of the prosthetic heme. In this study, the mechanism of green CPO formation and its relation to CPO catalyzed chiral transformations are also discussed. It is concluded that the double-phenyl clamp formed by two phenylalanine residues at the distal heme pocket plays a critical role in fine-tuning substrate orientation that determines the outcome of CPO catalyzed epoxidation of substituted styrenes.

Chemoenzymatic Synthesis of Sterically Hindered Biaryls by Suzuki Coupling and Vanadium Chloroperoxidase Catalyzed Halogenations

Halogenated biaryls are vital structural skeletons in bioactive products. In this study, an effective chemoenzymatic halogenation by vanadium-dependent chloroperoxidase from Camponotus inaequalis (CiVCPO) enabled the transformation of freely rotating biaryl bonds to sterically hindered axis. The yields were up to 84 % for the tribrominated biaryl products and up to 65 % when isolated. Furthermore, a one-pot, two-step chemoenzymatic strategy by incorporating transition metal catalyzed Suzuki coupling and the chemoenzymatic halogenation in aqueous phase were described. This strategy demonstrates a simplified one-pot reaction sequence with organometallic and biocatalytic procedures under economical and environmentally beneficial conditions that may inspire further research on synthesis of sterically hindered biaryls.

Comparing the Catalytic and Structural Characteristics of a 'Short' Unspecific Peroxygenase (UPO) Expressed in Pichia pastoris and Escherichia coli

Unspecific peroxygenases (UPOs) have emerged as valuable tools for the oxygenation of non-activated carbon atoms, as they exhibit high turnovers, good stability and depend only on hydrogen peroxide as the external oxidant for activity. However, the isolation of UPOs from their natural fungal sources remains a barrier to wider application. We have cloned the gene encoding an 'artificial' peroxygenase (artUPO), close in sequence to the 'short' UPO from Marasmius rotula (MroUPO), and expressed it in both the yeast Pichia pastoris and E. coli to compare the catalytic and structural characteristics of the enzymes produced in each system. Catalytic efficiency for the UPO substrate 5-nitro-1,3-benzodioxole (NBD) was largely the same for both enzymes, and the structures also revealed few differences apart from the expected glycosylation of the yeast enzyme. However, the glycosylated enzyme displayed greater stability, as determined by nano differential scanning fluorimetry (nano-DSF) measurements. Interestingly, while artUPO hydroxylated ethylbenzene derivatives to give the (R)-alcohols, also given by a variant of the 'long' UPO from Agrocybe aegerita (AaeUPO), it gave the opposite (S)-series of sulfoxide products from a range of sulfide substrates, broadening the scope for application of the enzymes. The structures of artUPO reveal substantial differences to that of AaeUPO, and provide a platform for investigating the distinctive activity of this and related'short' UPOs.

Enhancing thermal stability and lytic activity of phage lysin PlyAB1 from Acinetobacter baumannii

With the increasingly serious drug resistance of Acinetobacter baumannii, it is urgent to find new antibacterial drugs. Phage lysin PlyAB1 has a bactericidal effect on drug-resistant Acinetobacter baumannii, which has the potential to replace antibiotics to fight infection caused by Acinetobacter baumannii. However, its application is limited by its thermal stability and lytic activity. To solve these problems, molecular dynamics (MD) simulations combined with Hotspot wizard 3.0 were used to identify key residue sites affecting thermal stability, and evolutionary analysis combined with multiple sequence alignment was used to identify key residue sites affecting lytic activity. Four single-point variants with significantly increased thermal stability and four single-point variants with significantly lytic activity were obtained, respectively. Furthermore, by superimposing mutations, we obtained three double-point variants G100Q/K69R, G100R/K69R, and G100K/K69R with significantly improved thermal stability and improved lytic activity. At 45℃, the lytic activity and half-life of the optimal variant G100Q/K69R were 1.51 folds and 24 folds higher than those of the wild PlyAB1, respectively. These results deepen our understanding of the structure and function of phage lysin and contribute to the application of phage lysin in antibiotic substitution. This article is protected by copyright. All rights reserved.

Halogenation in Fungi: What Do We Know and What Remains to Be Discovered?

In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.

Green remediation potential of immobilized oxidoreductases to treat halo-organic pollutants persist in wastewater and soil matrices - A way forward

The alarming presence of hazardous halo-organic pollutants in wastewater and soils generated by industrial growth, pharmaceutical and agricultural activities is a major environmental concern that has drawn the attention of scientists. Unfortunately, the application of conventional technologies within hazardous materials remediation processes has radically failed due to their high cost and ineffectiveness. Consequently, the design of innovative and sustainable techniques to remove halo-organic contaminants from wastewater and soils is crucial. Altogether, these aspects have led to the search for safe and efficient alternatives for the treatment of contaminated matrices. In fact, over the last decades, the efficacy of immobilized oxidoreductases has been explored to achieve the removal of halo-organic pollutants from diverse tainted media. Several reports have indicated that these enzymatic constructs possess unique properties, such as high removal rates, improved stability, and excellent reusability, making them promising candidates for green remediation processes. Hence, in this current review, we present an insight of green remediation approaches based on the use of immobilized constructs of phenoloxidases (e.g., laccase and tyrosinase) and peroxidases (e.g., horseradish peroxidase, chloroperoxidase, and manganese peroxidase) for sustainable decontamination of wastewater and soil matrices from halo-organic pollutants, including 2,4-dichlorophenol, 4-chlorophenol, diclofenac, 2-chlorophenol, 2,4,6-trichlorophenol, among others.

Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation

The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.

Histidine versus Cysteine-Bearing Heme-Dependent Halogen Peroxidases: Parallels and Differences for Cl- Oxidation

The homodimeric myeloperoxidase (MPO) features a histidine as a proximal ligand and a sulfonium linkage covalently attaching the heme porphyrin ring to the protein. MPO is able to catalyze Cl^- oxidation with about the same efficiency as chloroperoxidase at pH 7.0. In this study, we seek to explore the parallels and differences between the histidine and cysteine heme-dependent halogen peroxidases. Transition states, reaction barriers, and relevant thermodynamic properties are calculated on protein models. Together with electronic structure calculations, it gives an overview of the reaction mechanisms and of the factors that determine the selectivity between one- and two-electron paths. Conclusions point to the innate oxidizing nature of MPO with the ester and sulfonium linkages hiking up the reactivity to enable chloride oxidation. The installation of a deprotonated imidazolate as a proximal ligand does not shift the equilibrium from one- to two-electron events without influencing the chemistry of the oxidation reaction.

Riboflavin Is Directly Involved in N-Dealkylation Catalyzed by Bacterial Cytochrome P450 Monooxygenases

Like a vast number of enzymes in nature, bacterial cytochrome P450 monooxygenases require an activated form of flavin as a cofactor for catalytic activity. Riboflavin is the precursor of FAD and FMN that serves as indispensable cofactor for flavoenzymes. In contrast to previous notions, herein we describe the identification of an electron-transfer process that is directly mediated by riboflavin for N-dealkylation by bacterial P450 monooxygenases. The electron relay from NADPH to riboflavin and then via activated oxygen to heme was proposed based on a combination of X-ray crystallography, molecular modeling and molecular dynamics simulation, site-directed mutagenesis and biochemical analysis of representative bacterial P450 monooxygenases. This study provides new insights into the electron transfer mechanism in bacterial P450 enzyme catalysis and likely in yeasts, fungi, plants and mammals.

Effects of the deglycosylation on the structure and activity of chloroperoxidase: Molecular dynamics simulation approach

Chloroperoxidase (CPO) is a versatile fungal heme-thiolate protein that catalyzes a variety of one electron and two-electron oxidations. Chloroperoxidase is a versatile fungal heme-thiolate protein that catalyzes a variety of oxidations. CPO enzyme contains thirteen sugars, including five N-acetyl D-glucosamines (NAG) and eight mannoses (MAN), which are attached to the protein via the glycosidic bonds. Removal of the sugars from CPO leads to increase the hydrophobicity of the enzyme, as well as the reduction of the alkylation reactions. However, due to the lack of the proper force field for the sugars, they are ignored in the theoretical studies. The present study aims to assess the effects of the sugar segments on the structure and activity of CPO through the simulation of the halo structure and the structures without the sugar segment. Despite the difficulty of the process and being time-consuming, the suitable force field is introduced successfully for the sugars. According to molecular dynamics simulation (MD), seven channels and fifteen cavities are identified in the CPO structure. Two of the channels provide the substrate access to the active site. The MD simulation results reveal that the removal of NAG decreases the number of the cavities from fifteen to eleven. Besides, the removal of NAG is associated with removing the channel providing the substrate access. The number of the cavities decreases from fifteen to fourteen through the removal of MAN; however, channel providing the substrate access to the active site is partly preserved. The MD simulation results indicate that the structures without the sugar units are more compact in comparison with the halo structures. The removal of the sugar segments induces the significant changes in the flexibility of the residues that affect the catalytic activity of the enzyme. As a result, the enzyme activities, such as the oxidation, alkylation, halogenation, and epoxidation cannot occur when the sugar segments of the enzyme are removed.

Halogenating Enzymes for Active Agent Synthesis: First Steps Are Done and Many Have to Follow

Halogens can be very important for active agents as vital parts of their binding mode, on the one hand, but are on the other hand instrumental in the synthesis of most active agents. However, the primary halogenating compound is molecular chlorine which has two major drawbacks, high energy consumption and hazardous handling. Nature bypassed molecular halogens and evolved at least six halogenating enzymes: Three kind of haloperoxidases, flavin-dependent halogenases as well as α-ketoglutarate and S-adenosylmethionine (SAM)-dependent halogenases. This review shows what is known today on these enzymes in terms of biocatalytic usage. The reader may understand this review as a plea for the usage of halogenating enzymes for fine chemical syntheses, but there are many steps to take until halogenating enzymes are reliable, flexible, and sustainable catalysts for halogenation.

Biocatalysis Fueled by Light: On the Versatile Combination of Photocatalysis and Enzymes

Enzymes catalyze a plethora of highly specific transformations under mild and environmentally benign reaction conditions. Their fascinating performances attest to high synthetic potential that is often hampered by operational obstacles such as in vitro cofactor supply and regeneration. Exploiting light and combining it with biocatalysis not only helps in overcoming these drawbacks, but the fruitful liaison of these two fields of "green chemistry" also offers opportunities to unlock new synthetic reactivities. In this review we provide an overview of the wide variety of photo-biocatalysis, ranging from the photochemical delivery of electrons required in redox biocatalysis and photochemical cofactor and reagent (re)generation to direct photoactivation of enzymes enabling reactions unknown in nature. We highlight synthetically relevant transformations such as asymmetric reactions facilitated by the combination of light as energy source and enzymes' catalytic power.

Ligand and Redox Partner Binding Generates a New Conformational State in Cytochrome P450cam (CYP101A1)

It has become increasingly clear that cytochromes P450 can cycle back and forth between two extreme conformational states termed the closed and open states. In the well-studied cytochrome P450cam, the binding of its redox partner, putidaredoxin (Pdx), shifts P450cam toward the open state. Shifting to the open state is thought to be important in the formation of a proton relay network essential for O-O bond cleavage and formation of the active Fe(IV)═O intermediate. Another important intermediate is the oxy-P450cam complex when bound to Pdx. Trapping this intermediate in crystallo is challenging owing to its instability, but the CN^- complex is both stable and an excellent mimic of the O₂ complex. Here we present the P450cam-Pdx structure complexed with CN^-. CN^- results in large conformational changes including cis/trans isomerization of proline residues. Changes include large rearrangements of active-site residues and the formation of new active-site access channel that we have termed channel 2. The formation of channel 2 has also been observed in our previous molecular dynamics simulations wherein substrate binding to an allosteric site remote from the active site opens up channel 2. This new structure supports an extensive amount of previous work showing that distant regions of the structure are dynamically coupled and underscores the potentially important role that large conformational changes and dynamics play in P450 catalysis.

Structural Insights into the Substrate Promiscuity of a Laboratory-Evolved Peroxygenase

Because of their minimal requirements, substrate promiscuity and product selectivity, fungal peroxygenases are now considered to be the jewel in the crown of C-H oxyfunctionalization biocatalysts. In this work, the crystal structure of the first laboratory-evolved peroxygenase expressed by yeast was determined at a resolution of 1.5 Å. Notable differences were detected between the evolved and native peroxygenase from Agrocybe aegerita, including the presence of a full N-terminus and a broader heme access channel due to the mutations that accumulated through directed evolution. Further mutagenesis and soaking experiments with a palette of peroxygenative and peroxidative substrates suggested dynamic trafficking through the heme channel as the main driving force for the exceptional substrate promiscuity of peroxygenase. Accordingly, this study provides the first structural evidence at an atomic level regarding the mode of substrate binding for this versatile biocatalyst, which is discussed within a biological and chemical context.

Functional Enzyme Mimics for Oxidative Halogenation Reactions that Combat Biofilm Formation

Transition-metal oxide nanoparticles and molecular coordination compounds are highlighted as functional mimics of halogenating enzymes. These enzymes are involved in halometabolite biosynthesis. Their activity is based upon the formation of hypohalous acids from halides and hydrogen peroxide or oxygen, which form bioactive secondary metabolites of microbial origin with strong antibacterial and antifungal activities in follow-up reactions. Therefore, enzyme mimics and halogenating enzymes may be valuable tools to combat biofilm formation. Here, halogenating enzyme models are briefly described, enzyme mimics are classified according to their catalytic functions, and current knowledge about the settlement chemistry and adhesion of fouling organisms is summarized. Enzyme mimics with the highest potential are showcased. They may find application in antifouling coatings, indoor and outdoor paints, polymer membranes for water desalination, or in aquacultures, but also on surfaces for food packaging, door handles, hand rails, push buttons, keyboards, and other elements made of plastic where biofilms are present. The use of natural compounds, formed in situ with nontoxic and abundant metal oxide enzyme mimics, represents a novel and efficient "green" strategy to emulate and utilize a natural defense system for preventing bacterial colonization and biofilm growth.

Six-Coordinate Nitrato Complexes of Iron Porphyrins with Trans S-Donor Ligands

The reaction of dimethyl sulfide (DMS) and tetrahydrothiophene (THT) with thin, amorphous layers of the nitrato complexes Fe(Por)(η²-O₂NO) (Por = meso-tetraphenylporphyrinato dianion or meso-tetra- p-tolylporphyrinato dianion) at low temperature leads to formation of the corresponding six-coordinate complexes Fe(Por)(L)(η¹-ONO₂) (L = DMS, THT) as characterized by Fourier transform infrared and optical spectroscopy measurements. Adduct formation was accompanied by bidentate-to-monodentate linkage isomerization of the nitrato ligand, with the Fe^III center remaining in a high-spin electronic state. These adducts are thermally unstable; warming to room temperature restores the initial Fe(Por)(η²-O₂NO) species.

Dual-Functional Small Molecules for Generating an Efficient Cytochrome P450BM3 Peroxygenase

We report a unique strategy for the development of a H₂ O₂ -dependent cytochrome P450BM3 system, which catalyzes the monooxygenation of non-native substrates with the assistance of dual-functional small molecules (DFSMs), such as N-(ω-imidazolyl fatty acyl)-l-amino acids. The acyl amino acid group of DFSM is responsible for bounding to enzyme as an anchoring group, while the imidazolyl group plays the role of general acid-base catalyst in the activation of H₂ O₂ . This system affords the best peroxygenase activity for the epoxidation of styrene, sulfoxidation of thioanisole, and hydroxylation of ethylbenzene among those P450-H₂ O₂ system previously reported. This work provides the first example of the activation of the normally H₂ O₂ -inert P450s through the introduction of an exogenous small molecule. This approach improves the potential use of P450s in organic synthesis as it avoids the expensive consumption of the reduced nicotinamide cofactor NAD(P)H and its dependent electron transport system. This introduces a promising approach for exploiting enzyme activity and function based on direct chemical intervention in the catalytic process.

Development of Halogenase Enzymes for Use in Synthesis

Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.

Independent Evolution of Six Families of Halogenating Enzymes

Halogenated natural products are widespread in the environment, and the halogen atoms are typically vital to their bioactivities. Thus far, six families of halogenating enzymes have been identified: cofactor-free haloperoxidases (HPO), vanadium-dependent haloperoxidases (V-HPO), heme iron-dependent haloperoxidases (HI-HPO), non-heme iron-dependent halogenases (NI-HG), flavin-dependent halogenases (F-HG), and S-adenosyl-L-methionine (SAM)-dependent halogenases (S-HG). However, these halogenating enzymes with similar biological functions but distinct structures might have evolved independently. Phylogenetic and structural analyses suggest that the HPO, V-HPO, HI-HPO, NI-HG, F-HG, and S-HG enzyme families may have evolutionary relationships to the α/β hydrolases, acid phosphatases, peroxidases, chemotaxis phosphatases, oxidoreductases, and SAM hydroxide adenosyltransferases, respectively. These halogenating enzymes have established sequence homology, structural conservation, and mechanistic features within each family. Understanding the distinct evolutionary history of these halogenating enzymes will provide further insights into the study of their catalytic mechanisms and halogenation specificity.

Specific oxyfunctionalisations catalysed by peroxygenases: opportunities, challenges and solutions

Peroxygenases are promising oxyfunctionalisation catalysts for organic synthesis.

Formation mechanisms of trichloromethyl-containing compounds in the terrestrial environment: a critical review

Natural trichloromethyl compounds present in the terrestrial environment are important contributors to chlorine in the lower atmosphere and may be also a cause for concern when high concentrations are detected in soils and groundwater. During the last decade our knowledge of the mechanisms involved in the formation of these compounds has grown. This critical review summarizes our current understanding and uncertainties on the mechanisms leading to the formation of natural trichloromethyl compounds. The objective of the review is to gather information regarding the natural processes that lead to the formation of trichloromethyl compounds and then to compare these mechanisms with the much more comprehensive literature on the reactions occurring during chemical chlorination of organic material. It turns out that the reaction mechanisms during chemical chlorination are likely to be similar to those occurring naturally and that significant knowledge may therefore be transferred between the scientific disciplines of chemical chlorination and natural organohalogens. There is however still a need for additional research before we understand fully the mechanisms occurring during the formation of natural trichloromethyl compounds and open questions and future research needs are identified in the last part of the review.

Investigating chloroperoxidase-catalyzed formation of chloroform from humic substances using stable chlorine isotope analysis

Chloroperoxidase (CPO) is suspected to play an important role in the biosynthesis of natural chloroform. The aims of the present study are to evaluate the variability of the δ(37)Cl value of naturally produced chloroform and to better understand the reaction steps that control the chlorine isotope signature of chloroform. The isotope analyses have shown that the chlorination of the humic substances (HS) in the presence of high H3O(+) and Cl(-) concentrations induces a large apparent kinetic isotope effect (AKIE = 1.010-1.018) likely associated with the transfer of chlorine between two heavy atoms, whereas in the presence of low H3O(+) and Cl(-) concentrations, the formation of chloroform induces a smaller AKIE (1.005-1.006) likely associated with the formation of an HOCl-ferriprotoporphyrin IX intermediate. As the concentration of H3O(+) and Cl(-) in soils are generally at submillimolar levels, the formation of the HOCl-ferriprotoporphyrin IX intermediate is likely rate-limiting in a terrestrial environment. Given that the δ(37)Cl values of naturally occurring chloride tend to range between -1 and +1‰, the δ(37)Cl value of natural chloroform should vary between -5‰ and -8‰. As the median δ(37)Cl value of industrial chloroform is -3.0‰, the present study suggests that chlorine isotopic composition of chloroform might be used to discriminate industrial and natural sources in the environment.

Structural basis of substrate conversion in a new aromatic peroxygenase: cytochrome P450 functionality with benefits

Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.1). They catalyze, inter alia, oxyfunctionalization reactions of aromatic and aliphatic hydrocarbons with remarkable regio- and stereoselectivities. When compared with cytochrome P450, APOs appear to be the choice enzymes for oxyfunctionalizations in organic synthesis due to their independence from a cellular environment and their greater chemical versatility. Here, the first two crystal structures of a heavily glycosylated fungal aromatic peroxygenase (AaeAPO) are described. They reveal different pH-dependent ligand binding modes. We model the fitting of various substrates in AaeAPO, illustrating the way the enzyme oxygenates polycyclic aromatic hydrocarbons. Spatial restrictions by a phenylalanine pentad in the active-site environment govern substrate specificity in AaeAPO.

Differences in chemical properties and reactivity patterns of mono- and dioxomanganese(V) porphyrins as revealed by density functional theory

Recent experimental studies of Liu and Groves (J. Am. Chem. Soc. 2010; 132: 12847) on dioxomanganese(V) porphyrin complexes implicated substrate halogenation in good yield. Currently, little is known of this unique mechanism, therefore to gain understanding on the halogenation mechanism and the chemical features of this oxidant we decided to do a computational (density functional theory) study. We show that the dioxomanganese(V) complex has considerably different molecular (valence) orbitals as compared to monooxomanganese(V) porphyrin due to mixing of the metal 3d orbitals with 2p orbitals on both oxygen atoms. This results in a set of three pairs of orbitals of which the bonding and nonbonding pairs are doubly occupied and the antibonding orbitals are vacant. As a consequence, the bonding character along the Mn–O bond is less in dioxomanganese(V) as compared to monooxomanganese(V) complexes and therefore this bond can formally be described as a double bond rather than a triple bond. The differences in orbital interactions and orbital energies also affect the intrinsic chemical properties of the oxidants, such as the electron affinity and pKa values, which result in enhanced catalytic potential for dioxomanganese(V) porphyrin. Our calculations predict a halogenation mechanism in line with that proposed by experiment with an initial hydrogen atom abstraction followed by ligand exchange and halogen transfer.

Paramagnetic nuclear magnetic resonance relaxation and molecular mechanics studies of the chloroperoxidase-indole complex: insights into the mechanism of chloroperoxidase-catalyzed regioselective oxidation of indole

To unravel the mechanism of chloroperoxidase (CPO)-catalyzed regioselective oxidation of indole, we studied the structure of the CPO-indole complex using nuclear magnetic resonance (NMR) relaxation measurements and computational techniques. The dissociation constant (KD) of the CPO-indole complex was calculated to be approximately 21 mM. The distances (r) between protons of indole and the heme iron calculated via NMR relaxation measurements and molecular docking revealed that the pyrrole ring of indole is oriented toward the heme with its 2-H pointing directly at the heme iron. Both KD and r values are independent of pH in the range of 3.0-6.5. The stability and structure of the CPO-indole complex are also independent of the concentration of chloride or iodide ion. Molecular docking suggests the formation of a hydrogen bond between the NH group of indole and the carboxyl O of Glu 183 in the binding of indole to CPO. Simulated annealing of the CPO-indole complex using r values from NMR experiments as distance restraints reveals that the van der Waals interactions were much stronger than the Coulomb interactions in the binding of indole to CPO, indicating that the association of indole with CPO is primarily governed by hydrophobic rather than electrostatic interactions. This work provides the first experimental and theoretical evidence of the long-sought mechanism that leads to the "unexpected" regioselectivity of the CPO-catalyzed oxidation of indole. The structure of the CPO-indole complex will serve as a lighthouse in guiding the design of CPO mutants with tailor-made activities for biotechnological applications.

Assessing the role of trichloroacetyl-containing compounds in the natural formation of chloroform using stable carbon isotopes analysis

Chloroform (CHCl(3)) is an environmental contaminant widely distributed around world, as well as a natural compound formed in various aquatic and terrestrial environments. However, the chemical mechanisms leading to the natural formation of chloroform in soils are not completely understood. To assess the role of trichloroacetyl-containing compound (TCAc) in the natural formation of chloroform in forest soils, carbon stable isotope analyses of chloroform and TCAc in field samples and chlorination experiments were carried out. The isotope analysis of field samples have revealed that the δ(13)C value of natural chloroform (δ(13)C(mean)=-25.8‰) is in the same range as the natural organic matter (δ(13)C(mean)=-27.7‰), whereas trichloromethyl groups of TCAc are much more enriched in (13)C (δ(13)C(mean)=-9.8‰). A similar relationship was also observed for TCAc and chloroform produced by chlorination of natural organic matter with NaOCl. The strong depletion of (13)C in chloroform relative to TCAc can be explained by carbon isotope fractionation during TCAc hydrolysis. As shown using a mathematical model, when steady state between formation of TCAc and hydrolysis is reached, the isotope ratio of chloroform is expected to correspond to isotope composition of NOM while TCAc should be enriched in (13)C by about 18.3‰, which is in good agreement with field observations. Hence this study suggests that TCAc are likely precursors of chloroform and at the same time explains why natural chloroform has a similar isotope composition as NOM despite large carbon isotope fractionation during its release.

Chloroperoxidase-catalyzed epoxidation of cis-β-methylstyrene: distal pocket flexibility tunes catalytic reactivity

Chloroperoxidase, the most versatile heme protein, has a hybrid active site pocket that shares structural features with peroxidases and cytochrome P450s. The simulation studies presented here show that the enzyme possesses a remarkable ability to efficiently utilize its hybrid structure, assuming structurally different peroxidase-like and P450-like distal pocket faces and thereby enhancing the inherent catalytic capability of the active center. We find that, during epoxidation of cis-β-methylstyrene (CBMS), the native peroxidase-like aspect of the distal pocket is diminished as the polar Glu183 side chain is displaced away from the active center and the distal pocket takes on a more hydrophobic, P450-like, aspect. The P450-like distal pocket provides a significant enthalpic stabilization of ∼4 kcal/mol of the 14 kcal/mol reaction barrier for gas-phase epoxidation of CMBS by an oxyferryl heme-thiolate species. This stabilization comes from breathing of the distal pocket. As until recently the active site of chloroperoxidase was postulated to be inflexible, these results suggest a new conceptual understanding of the enzyme's versatility: catalytic reactivity is tuned by flexibility of the distal pocket.

Thirty years of heme catalases structural biology

About thirty years ago the crystal structures of the heme catalases from Penicillium vitale (PVC) and, a few months later, from bovine liver (BLC) were published. Both enzymes were compact tetrameric molecules with subunits that, despite their size differences and the large phylogenetic separation between the two organisms, presented a striking structural similarity for about 460 residues. The high conservation, confirmed in all the subsequent structures determined, suggested a strong pressure to preserve a functional catalase fold, which is almost exclusively found in these mono-functional heme catalases. However, even in the absence of the catalase fold an efficient catalase activity is also found in the heme containing catalase-peroxidase proteins. The structure of these broad substrate range enzymes, reported for the first time less than ten years ago from the halophilic archaebacterium Haloarcula marismortui (HmCPx) and from the bacterium Burkholderia pseudomallei (BpKatG), showed a heme pocket closely related to that of plant peroxidases, though with a number of unique modifications that enable the catalase reaction. Despite the wealth of structural information already available, for both monofunctional catalases and catalase-peroxidases, a number of unanswered major questions require continuing structural research with truly innovative approaches.

Enantiospecificity of chloroperoxidase-catalyzed epoxidation: biased molecular dynamics study of a cis-β-methylstyrene/chloroperoxidase-compound I complex

Molecular dynamics simulations of an explicitly solvated cis-β-methylstyrene/chloroperoxidase-Compound I complex are performed to determine the cause of the high enantiospecificity of epoxidation. From the simulations, a two-dimensional free energy potential is calculated to distinguish binding potential wells from which reaction to 1S2R and 1R2S epoxide products may occur. Convergence of the free energy potential is accelerated with an adaptive biasing potential. Analysis of binding is followed by analysis of 1S2R and 1R2S reaction precursor structures in which the substrate, having left the binding wells, places its reactive double bond in steric proximity to the oxyferryl heme center. Structural analysis of binding and reaction precursor conformations is presented. We find that 1), a distortion of Glu(183) is important for CPO-catalyzed epoxidation as was postulated previously based on experimental results; 2), the free energy of binding does not provide significant differentiation between structures leading to the respective epoxide enantiomers; and 3), CPO's enantiospecificity toward cis-β-methylstyrene is likely to be caused by a specific group of residues which form a hydrophobic core surrounding the oxyferryl heme center.

Crystallization of a 45 kDa peroxygenase/peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron

Some litter-decaying fungi secrete haem-thiolate peroxygenases that oxidize numerous organic compounds and therefore have a high potential for applications such as the detoxification of recalcitrant organic waste and chemical synthesis. Like P450 enzymes, they transfer oxygen functionalities to aromatic and aliphatic substrates. However, in contrast to this class of enzymes, they only require H(2)O(2) for activity. Furthermore, they exhibit halogenation activity, as in the well characterized fungal chloroperoxidase, and display ether-cleavage activity. The major form of a highly glycosylated peroxygenase was produced from Agrocybe aegerita culture media, purified to apparent SDS homogeneity and crystallized under three different pH conditions. One crystal form containing two molecules per asymmetric unit was solved at 2.2 A resolution by SAD using the anomalous signal of the haem iron. Subsequently, two other crystal forms with four molecules per asymmetric unit were determined at 2.3 and 2.6 A resolution by molecular replacement.

New and classic families of secreted fungal heme peroxidases

Heme-containing peroxidases secreted by fungi are a fascinating group of biocatalysts with various ecological and biotechnological implications. For example, they are involved in the biodegradation of lignocelluloses and lignins and participate in the bioconversion of other diverse recalcitrant compounds as well as in the natural turnover of humic substances and organohalogens. The current review focuses on the most recently discovered and novel types of heme-dependent peroxidases, aromatic peroxygenases (APOs), and dye-decolorizing peroxidases (DyPs), which catalyze remarkable reactions such as peroxide-driven oxygen transfer and cleavage of anthraquinone derivatives, respectively, and represent own separate peroxidase superfamilies. Furthermore, several aspects of the "classic" fungal heme-containing peroxidases, i.e., lignin, manganese, and versatile peroxidases (LiP, MnP, and VP), phenol-oxidizing peroxidases as well as chloroperoxidase (CPO), are discussed against the background of recent scientific developments.

Effects of substrate, protein environment, and proximal ligand mutation on compound I and compound 0 of chloroperoxidase

This paper investigates the enzyme chloroperoxidase (CPO) by means of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. The effects of anionic substrate, protein environment, and proximal ligand mutation on the high-valent iron-oxo species, compound I (Cpd I), and the ferric hydroperoxide complex, compound 0 (Cpd 0), are studied. The results indicate that the presence of an anionic substrate (acetate) and the protonation state of one critical residue (Glu104) have a considerable impact on the relative stabilities of Cpd I and Cpd 0. In the absence of the substrate or when the substrate is protonated, Cpd I is considerably more stable, and its formation barrier is smaller than in the case where the substrate is in its anionic state and when Glu104 is deprotonated. This trend, which is shown to be a simple manifestation of the Hammond principle, reproduces the experimental observation that the working pH of the enzyme is acidic. Furthermore, in the absence of substrate (or when it is protonated), the relative Cpd 0/Cpd I energies are found to be a good index of Cpd I stability in heme enzymes and to follow the experimental order: horseradish peroxidase (HRP) > CPO > P450. In silico mutation of the proximal ligand from cysteine to selenocysteine was found to have no effect at all on the properties of Cpd I (e.g., spin density on the chalcogen, Mössbauer parameters, etc.) and its relative stability to Cpd 0 or on the corresponding barrier for formation. This surprising finding shows that the polar CPO pocket applies a leveling effect that stabilizes the anionic forms of the proximal ligands (CysS(-) and CysSe(-)). This in turn means that the Se-Cpd I of the mutant CPO is observable.