The catalytic cycle of catechol oxidase

Monophenolase and catecholase activity of Aspergillus oryzae catechol oxidase: insights from hybrid QM/MM calculations

Catechol oxidase from Aspergillus oryzae (AoCO4) can not only catalyze oxidation of o-diphenols to o-quinones, but can also catalyze monooxygenation of small phenolics. To gain insight into the catecholase and monophenolase activities of AoCO4, the reaction mechanism of catechol oxidation was investigated by means of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations. The oxy-form of AoCO4 was found to be a μ-η2:η2 side-on peroxo dicopper(ii) complex, which can undergo a proton coupled electron transfer from the substrate rather than a proton transfer from the nearby Ser302 residue to generate a hydroperoxide. The μ-1,1-OOH Cu2(i,ii) complex is thermodynamically more stable than the μ-η1:η2 hydroperoxide. Moreover, the cleavage of the O-O bond in the μ-1,1-OOH Cu2(i,ii) intermediate has a much lower barrier than that in the μ-η1:η2 hydroperoxide species. In both cases, the O-O bond cleavage is the rate-limiting step, generating the reactive (μ-O˙)(μ-OH) dicopper(ii) complex. In addition, our results demonstrated that the oxidation of catechol to quinone is much more preferred than the hydroxylation reaction. These findings may provide useful information for understanding the reactivity of the Cu2O2 active site of coupled binuclear copper enzymes.

Energetics for the Mechanism of Nickel-Containing Carbon Monoxide Dehydrogenase

Nickel-containing carbon monoxide (CO) dehydrogenase is an enzyme that catalyzes the important reversible carbon dioxide reduction. Several high-resolution structures have been determined at various stages of the reduction, which can be used as good starting points for the present computational study. The cluster model is used in combination with a systematic application of the density functional theory as recently described. The results are in very good agreement with experimental evidence. There are a few important results. To explain why the X-ray structure for the reduced C_red1 state has an empty site on nickel, it is here suggested that the cluster has been over-reduced by X-rays and is therefore not the desired reduced state, which instead contains a bound CO on nickel. After an additional reduction, a hydride bound to nickel is suggested to play a role. In order to obtain energetics in agreement with experiments, it is concluded that one sulfide bridge in the Ni-Fe cluster should be protonated. The best test of the accuracy obtained is to compare the computed rate for reduction using -0.6 V with that for oxidation using -0.3 V, where good agreement was obtained. Obtaining a mechanism that is easily reversible is another demanding aspect of the modeling. Nickel oscillates between nickel(II) and nickel(I), while nickel(0) never comes in.

Copper-Promoted Functionalization of Organic Molecules: from Biologically Relevant Cu/O2 Model Systems to Organometallic Transformations

Copper is one of the most abundant and less toxic transition metals. Nature takes advantage of the bioavailability and rich redox chemistry of Cu to carry out oxygenase and oxidase organic transformations using O₂ (or H₂O₂) as oxidant. Inspired by the reactivity of these Cu-dependent metalloenzymes, chemists have developed synthetic protocols to functionalize organic molecules under enviormentally benign conditions. Copper also promotes other transformations usually catalyzed by 4d and 5d transition metals (Pd, Pt, Rh, etc.) such as nitrene insertions or C-C and C-heteroatom coupling reactions. In this review, we summarized the most relevant research in which copper promotes or catalyzes the functionalization of organic molecules, including biological catalysis, bioinspired model systems, and organometallic reactivity. The reaction mechanisms by which these processes take place are discussed in detail.

Artificial Metalloproteins for Binding and Stabilization of a Semiquinone Radical

The interaction of a number of first-row transition-metal ions with a 2,2′-bipyridyl alanine (bpyA) unit incorporated into the lactococcal multidrug resistance regulator (LmrR) scaffold is reported. The composition of the active site is shown to influence binding affinities. In the case of Fe(II), we demonstrate the need of additional ligating residues, in particular those containing carboxylate groups, in the vicinity of the binding site. Moreover, stabilization of di-tert-butylsemiquinone radical (DTB-SQ) in water was achieved by binding to the designed metalloproteins, which resulted in the radical being shielded from the aqueous environment. This allowed the first characterization of the radical semiquinone in water by resonance Raman spectroscopy.

A coordination study of first-row transition-metal ions to bipyridine alanine (bpyA) incorporated into the lactococcal multidrug resistance regulator (LmrR) scaffold is reported. The designed metalloproteins were shown to bind and stabilize the di-tert-butylsemiquinone radical (DTB-SQ) in water, allowing for the first resonance Raman characterization of this radical species in water.

Competitive coordination aggregation for V-shaped [Co3] and disc-like [Co7] complexes: synthesis, magnetic properties and catechol oxidase activity

The synthetic procedures, magnetic properties and catecholase-like activity of a V-shaped [CoII3L₄] and planar disc-like [CoII7L₆] complexes have been discussed.

Spectroscopic, thermodynamic, kinetic studies and oxidase/antioxidant biomimetic catalytic activities of tris(3,5-dimethylpyrazolyl)borate Cu(II) complexes

A series of copper(ii) complexes, viz. [Tp(MeMe)Cu(Cl)(H2O)] (), [Tp(MeMe)Cu(OAc)(H2O)] (), [Tp(MeMe)Cu(NO3)] () and [Tp(MeMe)Cu(ClO4)] () containing tris(3,5-dimethylpyrazolyl)borate (KTp(MeMe)), have been synthesized and fully characterized. The substitution reaction of with thiourea was studied under pseudo-first-order conditions as a function of concentration, temperature and pressure in methanol and acetonitrile as solvents. Two reaction steps that both depended on the nucleophile concentration were observed for both solvents. Substitution of coordinated methanol is about 40 times faster than the substitution of chloride. In acetonitrile, the rate constant for the displacement of coordinated acetonitrile was more than 20 times faster than the substitution of chloride. The reported activation parameters indicate that both reaction steps follow a dissociative mechanism in both solvents. On going from methanol to acetonitrile, the rate constant for the displacement of the solvent becomes more than 200 times faster due to the more labile acetonitrile, but the substitution mechanism remained to have a dissociative character. The antioxidant activities of were evaluated for superoxide dismutase (SOD), glutathione-s-transferase (GST0 and glutathione reduced (GSH-Rd) activity. and were found to show (p < 0.05) the highest antioxidant activity in comparison to and , which can be ascribed to the geometric configuration as well as the nature of the co-ligand. showed catechol oxidase activity with turnover numbers of 20 min(-1) and a coordination affinity for 3,5-DTBC of K1, = 31 mM(-1). K1 is rather large and seems to be typical for faster biomimetic models, and also for the enzyme itself (25 mM(-1)). The reaction rate depended linearly on the complex concentration, indicating a first-order dependence on the catalyst concentration.

The synthesis, characterization and catecholase activity of dinuclear cobalt(ii/iii) complexes of an O-donor rich Schiff base ligand

A dinuclear Co^III complex oxidizes 3,5-di-tert-butylcatechol by binding to two molecules of the substrate simultaneously during oxidation along with the formation of H₂O₂.

The crystal structure of an extracellular catechol oxidase from the ascomycete fungus Aspergillus oryzae

Catechol oxidases (EC 1.10.3.1) catalyse the oxidation of o-diphenols to their corresponding o-quinones. These oxidases contain two copper ions (CuA and CuB) within the so-called coupled type 3 copper site as found in tyrosinases (EC 1.14.18.1) and haemocyanins. The crystal structures of a limited number of bacterial and fungal tyrosinases and plant catechol oxidases have been solved. In this study, we present the first crystal structure of a fungal catechol oxidase from Aspergillus oryzae (AoCO4) at 2.5-Å resolution. AoCO4 belongs to the newly discovered family of short-tyrosinases, which are distinct from other tyrosinases and catechol oxidases because of their lack of the conserved C-terminal domain and differences in the histidine pattern for CuA. The sequence identity of AoCO4 with other structurally known enzymes is low (less than 30 %), and the crystal structure of AoCO4 diverges from that of enzymes belonging to the conventional tyrosinase family in several ways, particularly around the central α-helical core region. A diatomic oxygen moiety was identified as a bridging molecule between the two copper ions CuA and CuB separated by a distance of 4.2-4.3 Å. The UV/vis absorption spectrum of AoCO4 exhibits a distinct maximum of absorbance at 350 nm, which has been reported to be typical of the oxy form of type 3 copper enzymes.

Theoretical study on the degradation of ADP-ribose polymer catalyzed by poly(ADP-ribose) glycohydrolase

Poly(ADP-ribose) glycohydrolase (PARG) is the only enzyme responsible for the degradation of ADP-ribose polymers. Very recently, the first crystal structure of PARG was reported (Dea Slade, et al., Nature 477 (2011) 616), and a possible SN1-type-like mechanism was proposed. In this work, we present a computational study on the hydrolysis of glycosidic ribose-ribose bond catalyzed by PARG using hybrid density functional theory (DFT) methods. Based on the crystal structure of PARG, three models of the active site were constructed. The calculation results suggest that the degradation of poly(ADP-ribose) follows an SN2 mechanism, and the oxocarbenium expected by Dea Slade is a possible transition state but not an intermediate. The calculated reaction pathway agrees with the proposed mechanism. According to the computational models with different sizes, the roles of key residues are elucidated. Our results may provide useful information for the subsequent experimental and theoretical studies on the structure and functional relationships of PARG.

A short review on the structure-function relationship of artificial catecholase/tyrosinase and nuclease activities of Cu-complexes

The synthesis of metal complexes has vastly increased the scope of research for many scientists during the two last decades. Among these compounds, artificial tyrosinases, catecholases, proteases, and nucleases are some of the most studied due to their importance as modern tools in the fields of medicine, scientific research, and industry. Transition metals such as Zn(2+), Cu(2+), Fe(3+), Co(3+), Ni(2+), and lanthanide ions are the most commonly used. Among these ions, copper complexes have been the focus of the majority of studies thanks to their significant activity in comparison with other ions. Studies of copper-based tyrosinases, catecholases, and nucleases have revealed some of the overarching factors affecting reactions of all three types, which has led to improved activity and efficiency for all. Key factors include proper core-core distance, (Cu⋯Cu distance 2.90-2.99 Å), suitable solvent, and ligands with proper hydrophobic structure and geometry. In the present investigation, we review and introduce the proposed mechanisms and the kinetically effective factors of natural catecholase, tyrosinase, and nuclease and their Cu-based synthetic mimics.

The oxygenase-peroxidase theory of Bach and Chodat and its modern equivalents: change and permanence in scientific thinking as shown by our understanding of the roles of water, peroxide, and oxygen in the functioning of redox enzymes

Alexander Bach was both revolutionary politician and biochemist. His earliest significant publication, "Tsar-golod" ("The Tsar of Hunger"), introduced Marxist thought to Russian workers. In exile for 30 years, he moved to study the dialectic of the oxidases. When his theory of oxidases as combinations of oxygenases and peroxidases was developed (circa 1900) the enzyme concept was not fully formulated, and the enzyme/substrate distinction not yet made. Peroxides however were then and remain now significant intermediates, when either free or bound, in oxidase catalyses. The aerobic dehydrogenase/peroxidase/catalase coupled systems which were studied slightly later clarified the Bach model and briefly became an oxidase paradigm. Identification of peroxidase as a metalloprotein, a key step in understanding oxidase and peroxidase mechanisms, postdated Bach's major work. Currently we recognize catalytic organic peroxides in flavoprotein oxygenases; such organic peroxides are also involved in lipid oxidation and tryptophan radical decay. But most physiologically important peroxides are now known to be bound to transition metals (either Fe or Cu) and formed both directly and indirectly (from oxygen). The typical stable metalloprotein peroxide product is the ferryl state. When both peroxide oxidizing equivalents are retained the second equivalent is held as a protein or porphyrin radical. True metal peroxide complexes are unstable. But often water molecules mark the spot where the original peroxide decayed. The cytochrome c oxidase Fe-Cu center can react with either peroxide or oxygen to form the intermediate higher oxidation states P and F. In its resting state water molecules and hydroxyl ions can be seen marking the original location of the oxygen or peroxide molecule.

Theoretical study of the catalytic mechanism of catechol oxidase

The mechanism for the oxidation of catechol by catechol oxidase has been studied using B3LYP hybrid density functional theory. On the basis of the X-ray structure of the enzyme, the molecular system investigated includes the first-shell protein ligands of the two metal centers as well as the second-shell ligand Cys92. The cycle starts out with the oxidized, open-shell singlet complex with oxidation states Cu(2)(II,II) with a mu-eta(2):eta(2) bridging peroxide, as suggested experimentally, which is obtained from the oxidation of Cu(2)(I,I) by dioxygen. The substrate of each half-reaction is a catechol molecule approaching the dicopper complex: the first half-reaction involves Cu(I) oxidation by peroxide and the second one Cu(II) reduction. The quantitative potential energy profile of the reaction is discussed in connection with experimental data. Since no protons leave or enter the active site during the catalytic cycle, no external base is required. Unlike the previous density functional theory study, the dicopper complex has a charge of +2.

Mechanistic Insight into the Activity of Tyrosinase from Variable-Temperature Studies in an Aqueous/Organic Solvent

The activity of mushroom tyrosinase towards a representative series of phenolic and diphenolic substrates structurally related to tyrosine has been investigated in a mixed solvent of 34.4% methanol-glycerol (7:1, v/v) and 65.6% (v/v) aqueous 50 mM Hepes buffer at pH 6.8 at various temperatures. The kinetic activation parameters controlling the enzymatic reactions and the thermodynamic parameters associated with the process of substrate binding to the enzyme active species have been deduced from the temperature variation of the kcat and KM parameters. The activation free energy is dominated by the enthalpic term, the value of which lies in the relatively narrow range of 61+/-9 kJ mol(-1) irrespective of substrate or reaction type (monophenolase or diphenolase). The activation entropies are small and generally negative and contribute no more than 10% to the activation free energy. The substrate binding parameters are characterized by large and negative enthalpy and entropy contributions, which are typically dictated by polar protein-substrate interactions. The substrate 4-hydroxyphenylpropionic acid exhibits a strikingly anomalous temperature dependence of the enzymatic oxidation rate, with deltaH(double dagger) approximately = 150 kJ mol(-1) and deltaS(double dagger) approximately = 280 J K(-1) mol(-1), due to the fact that it can competitively bind to the enzyme through the phenol group, like the other substrates, or the carboxylate group, like carboxylic acid inhibitors. A kinetic model that takes into account the dual substrate/inhibitor nature of this compound enables rationalization of this anomalous behavior.

Synthetic models of the active site of catechol oxidase: mechanistic studies

The ability of copper proteins to process dioxygen at ambient conditions has inspired numerous research groups to study their structural, spectroscopic and catalytic properties. Catechol oxidase is a type-3 copper enzyme usually encountered in plant tissues and in some insects and crustaceans. It catalyzes the conversion of a large number of catechols into the respective o-benzoquinones, which subsequently auto-polymerize, resulting in the formation of melanin, a dark pigment thought to protect a damaged tissue from pathogens. After the report of the X-ray crystal structure of catechol oxidase a few years earlier, a large number of publications devoted to the biomimetic modeling of its active site appeared in the literature. This critical review (citing 114 references) extensively discusses the synthetic models of this enzyme, with a particular emphasis on the different approaches used in the literature to study the mechanism of the catalytic oxidation of the substrate (catechol) by these compounds. These are the studies on the substrate binding to the model complexes, the structure-activity relationship, the kinetic studies of the catalytic oxidation of the substrate and finally the substrate interaction with (per)oxo-dicopper adducts. The general overview of the recognized types of copper proteins and the detailed description of the crystal structure of catechol oxidase, as well as the proposed mechanisms of the enzymatic cycle are also presented.

A Novel o-Aminophenol Oxidase Responsible for Formation of the Phenoxazinone Chromophore of Grixazone

Grixazone contains a phenoxazinone chromophore and is a secondary metabolite produced by Streptomyces griseus. In the grixazone biosynthesis gene cluster, griF (encoding a tyrosinase homolog) and griE (encoding a protein similar to copper chaperons for tyrosinases) are encoded. An expression study of GriE and GriF in Escherichia coli showed that GriE activated GriF by transferring copper ions to GriF, as has been observed for a Streptomyces melanogenesis system in which the MelC1 copper chaperon transfers copper ions to MelC2 tyrosinase. In contrast with tyrosinases, GriF showed no monophenolase activity, although it oxidized various o-aminophenols as preferable substrates rather than catechol-type substrates. Deletion of the griEF locus on the chromosome resulted in accumulation of 3-amino-4-hydroxybenzaldehyde (3,4-AHBAL) and its acetylated compound, 3-acetylamino-4-hydroxybenzaldehyde. GriF oxidized 3,4-AHBAL to yield an o-quinone imine derivative, which was then non-enzymatically coupled with another molecule of the o-quinone imine to form a phenoxazinone. The coexistence of N-acetylcysteine in the in vitro oxidation of 3,4-AH-BAL by GriF resulted in the formation of grixazone A, suggesting that the -SH group of N-acetylcysteine is conjugated to the o-quinone imine formed from 3,4-AHBAL and that the conjugate is presumably coupled with another molecule of the o-quinone imine. GriF is thus a novel o-aminophenol oxidase that is responsible for the formation of the phenoxazinone chromophore in the grixazone biosynthetic pathway.

Urea decomposition facilitated by a urease model complex: a theoretical investigation

Density functional theory calculations were used to examine the role of the urease model complex [Ni2(bdptz)(micro-OH)(micro-H2O)(H2O)2](OTs)3(bdptz=1,4-bis(2,2'-dipyridylmethyl)-phthalazine; OTs=tosylate) in the degradation of urea. An elimination mechanism that converts urea to ammonium cyanate was investigated in detail. The lowest energy pathway involves urea coordination through the oxygen atom to a Ni center followed by protonation of a urea NH2 group by the bridging water ligand. Subsequent rotation of the protonated urea, followed by deprotonation of the NH2 by a bridging OH ligand generates the bound, disproportionated urea substrate, HNCONH3, from which ammonium cyanate was produced.