Substrate oxidation sites in versatile peroxidase and other basidiomycete peroxidases

Versatile peroxidase (VP) is defined by its capabilities to oxidize the typical substrates of other basidiomycete peroxidases: (i) Mn(2+), the manganese peroxidase (MnP) substrate (Mn(3+) being able to oxidize phenols and initiate lipid peroxidation reactions); (ii) veratryl alcohol (VA), the typical lignin peroxidase (LiP) substrate; and (iii) simple phenols, which are the substrates of Coprinopsis cinerea peroxidase (CIP). Crystallographic, spectroscopic, directed mutagenesis, and kinetic studies showed that these 'hybrid' properties are due to the coexistence in a single protein of different catalytic sites reminiscent of those present in the other basidiomycete peroxidase families. Crystal structures of wild and recombinant VP, and kinetics of mutated variants, revealed certain differences in its Mn-oxidation site compared with MnP. These result in efficient Mn(2+) oxidation in the presence of only two of the three acidic residues forming its binding site. On the other hand, a solvent-exposed tryptophan is the catalytically-active residue in VA oxidation, initiating an electron transfer pathway to haem (two other putative pathways were discarded by mutagenesis). Formation of a tryptophanyl radical after VP activation by peroxide was detected using electron paramagnetic resonance. This was the first time that a protein radical was directly demonstrated in a ligninolytic peroxidase. In contrast with LiP, the VP catalytic tryptophan is not beta-hydroxylated under hydrogen peroxide excess. It was also shown that the tryptophan environment affected catalysis, its modification introducing some LiP properties in VP. Moreover, some phenols and dyes are oxidized by VP at the edge of the main haem access channel, as found in CIP. Finally, the biotechnological interest of VP is discussed.     

Protein control of prosthetic heme reactivity. Reaction of substrates with the heme edge of horseradish peroxidase

Incubation of horseradish peroxidase with phenylhydrazine and H2O2 markedly depresses the catalytic activity and the intensity, but not position, of the Soret band. Approximately 11-13 mol of phenylhydrazine and 25 mol of H2O2 are required per mol of enzyme to minimize the chromophore intensity. The enzyme retains some activity after such treatment, but this activity is eliminated if the enzyme is isolated and reincubated with phenylhydrazine. The prosthetic heme of the enzyme does not react with phenylhydrazine to give a sigma-bonded phenyl-iron complex, as it does in other hemoproteins, but is converted instead to the delta-mesophenyl and 8-hydroxymethyl derivatives. The loss of activity is due more to protein than heme modification, however. The inactivated enzyme reacts with H2O2 to give a spectroscopically detectable Compound I. The results imply that substrates interact with the heme edge rather than with the activated oxygen of Compounds I and II and specifically identify the region around the delta-meso-carbon and 8-methyl group as the exposed sector of the heme. Horseradish peroxidase, in contrast to cytochrome P-450, generally does not catalyze oxygen-transfer reactions. The present results indicate that oxygen-transfer reactions do not occur because the activated oxygen and the substrate are physically separated by a protein-imposed barrier in horseradish peroxidase.     

Reaction of horseradish peroxidase with azide and some implications for the heme environmental structure. NMR and kinetic studies.

The azide complex of horseradish peroxidase was studied by high resolution 1H and 15N NMR spectroscopy and by the temperature-jump method. The heme peripheral methyl proton peaks and the ligand 15N resonance were resolved to show that binding of azide by horseradish peroxidase occurs only in acidic solution below pH 6.5. It was also found that the chemical exchange rate of azide with the ferric enzyme was much faster on the 1H and 15N NMR time scale. This was further substantiated by kinetics of azide binding by horseradish peroxidase where the chemical exchange rate was confirmed to be in the microseconds range at pH 5.0 and 23 degrees C. This rate is salient in usual ligand exchange reactions in hemoproteins so far reported. pH dependences of the first order association and dissociation rate constants were also studied by the temperature-jump method to suggest a strong linkage of the azide binding with a proton uptake of an amino acid residue on the enzyme. These results were compared with the case of horse metmyoglobin and were interpreted to indicate that a heme-linked ionizable group on the enzyme facilitates the fast entry of the ligand to the coordination site. A histidyl residue is a possible candidate for the ionizable group of the enzyme.     

Inhibition of lignin peroxidase H2 by sodium azide.

The oxidation of veratryl alcohol (3,4-dimethoxybenzyl alcohol) by lignin peroxidase H2 from Phanerochaete chrysosporium and H2O2 was strongly inhibited by sodium azide. Inhibition was competitive with respect to veratryl alcohol (Ki = 1-2 microM) and uncompetitive with respect to H2O2. In contrast, sodium azide bound to the native enzyme at pH 6.0 with an apparent dissociation constant (KD) of 126 mM. Formation of azidyl radicals was detected by ESR spin trapping techniques. The enzymes is nearly completely inactivated in four turnovers. The H2O2-activated enzyme intermediate (compound I) reacted with sodium azide to form a new species rather than be reduced to the enzyme intermediate compound II. The new species has absorption maxima at 418, 540, and 570 nm, suggesting the formation of a ferrous-lignin peroxidase-NO complex. Confirmation of this assignment was obtained by low-temperature ESR spectroscopy. An identical complex could be simulated by the addition of nitrite to the reduced enzyme. The enzyme intermediate compound II is readily reduced by sodium azide to native enzyme with essentially no loss of activity.     

The catalytic site of manganese peroxidase. Regiospecific addition of sodium azide and alkylhydrazines to the heme group.

Manganese peroxidase (MnP), which normally oxidizes Mn2+ to Mn3+, is rapidly and completely inactivated in an H2O2-dependent reaction by 2 equivalents of sodium azide. The inactivation is paralleled by formation of the azidyl radical and high yield conversion of the prosthetic heme into a meso-azido adduct. The meso-azido enzyme is oxidized by H2O2 to a Compound II-like species with the Soret band red-shifted 2 nm relative to that of native Compound II. The time-dependent decrease in this Compound II-like spectrum (t1/2 = 2.3 h) indicates that the delta-meso azido heme is more rapidly degraded by H2O2 than the prosthetic heme of control enzyme (t1/2 = 4.8 h). MnP is also inactivated by phenyl-, methyl-, and ethylhydrazine. The phenylhydrazine reaction is too rapid for kinetic analysis, but KI = 402 microM and kinact = 0.22/min for the slower inactivation by methylhydrazine. Reaction with phenylhydrazine at pH 4.5 does not yield iron-phenyl, N-phenyl, or meso-phenyl heme adducts. Ethylhydrazine inactivates the enzyme both at pH 4.5 and 7.0, but only detectably produces delta-meso-ethyl-heme at pH 7.0. Reconstitution of apo-MnP with hemin or delta-meso-ethylheme yields enzyme with, respectively, 50 and 5% of the native activity. The delta-meso-alkyl group thus suppresses most of the catalytic activity of the enzyme even though a Compound II-like species is still formed with H2O2. Finally, Co2+ inhibits the enzyme competitively with respect to Mn2+ but does not inhibit its inactivation by azide or the alkylhydrazines. The results argue that substrates interact with the heme edge in the vicinity of the delta-meso-carbon. They also suggest that Mn2+ and Co2+ bind to a common site close to the delta-meso-carbon without blocking the approach of small molecules to the heme edge. An active site model is proposed that accommodates these results.     

Optimization of extracellular fungal peroxidase production by 2 Coprinus species

Optimum culture conditions for the batch production of extracellular peroxidase by Coprinus cinereus UAMH 4103 and Coprinus sp. UAMH 10067 were explored using 2 statistical experimental designs, including 2-level, 7-factor fractional factorial design and 2-factor central composite design. Of the 7 factors examined in the screening study, the concentrations of carbon (glucose) and nitrogen (peptone or casitone) sources showed significant effects on the peroxidase production by Coprinus sp. UAMH 10067. The optimum glucose and peptone concentrations were determined as 2.7% and 0.8% for Coprinus sp. UAMH 10067, and 2.9% and 1.4% for C. cinereus UAMH 4103, respectively. Under the optimized culture condition the maximum peroxidase activity achieved in this study was 34.5 U x mL(-1) for Coprinus sp. UAMH 10067 and 68.0 U x mL(-1) for C. cinereus UAMH 4103, more than 2-fold higher than the results of previous studies.     

Inactivation of lignin peroxidase by phenylhydrazine and sodium azide

Lignin peroxidase (LiP) is rapidly inactivated in a concentration-dependent manner by H2O2 and either phenylhydrazine or sodium azide. Full inactivation of isozyme 2b (H8) requires approximately 50 eq of phenylhydrazine or 80 eq of sodium azide. Anaerobic incubation of isozyme 2b with [14C]phenylhydrazine and H2O2 results in 77% loss of catalytic activity and covalent binding of 0.45 mol radiolabel/mol of enzyme. Comparable but not identical results are obtained with an isozyme mixture. A lag period is observed before the peroxidative activity can be measured when an aliquot of an incubation with sodium azide is diluted into the mixture used to assay residual catalytic activity. This lag is associated with reversible accumulation of a catalytically inert species with a Compound III-like spectrum. No meso-phenyl, iron-phenyl, or N-phenyl adducts are formed with phenylhydrazine but a low yield of what appears to be delta-meso-azidoheme is obtained with sodium azide. LiP is thus less susceptible to meso heme additions and more susceptible to oxidative heme degradation than horseradish peroxidase. The data suggest that the active of LiP resembles the closed structure of horseradish peroxidase more than it does the open structure of the globins, catalase, chloroperoxidase, or cytochrome P450.     

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.     

Divergent evolutionary lines of fungal cytochrome c peroxidases belonging to the superfamily of bacterial, fungal and plant heme peroxidases

Novel open reading frames coding for cytochrome c peroxidase (CcP) belonging to the superfamily of bacterial, fungal, and plant heme peroxidases were analyzed in the available fungal genomes. Multiple sequence alignment of 71 selected peroxidase genes revealed the presence of three conserved regions essential for their function: one on the distal and two on the proximal side of the prosthetic heme group. Conserved sequence motifs on the proximal heme side are peculiar for CcPs and are responsible for their reactivity. Phylogenetic analysis performed with the distance method as well as with the maximum likelihood method revealed the existence of three distinct subfamilies of fungal CcP and their relationship to other members of the peroxidase superfamily. These divergent CcP evolutionary lines apparently evolved from a single primordial heme peroxidase gene in parallel with the evolution of ascorbate peroxidase genes. Analyzed CcPs differ significantly in their N-terminal sequences. Only subfamily I did not exhibit a presence of any signal sequence. Subfamily II members possess a well defined signal sequence allowing processing and release into mitochondrion and also in subfamily III a signal sequence was detected. Several here analyzed peroxidase genes mainly from Candida albicans and from Rhizopus oryzae can be considered interesting for the investigation of the structure-function relationship of novel CcPs revealing differences to the well documented properties of cytochrome c peroxidase from Saccharomyces cerevisiae.     

Purification and Identification of the Fruiting-Inducing Substances in Coprinus macrorhizus

Substances which are effective in inducing fruiting bodies in monokaryotic mycelia of the fis(+) strain of Coprinus macrorhizus were purified and characterized. The active components of fruiting-inducing substances were identified as adenosine-3'-monophosphate, adenosine 3',5'-cyclic monophosphate (cyclic AMP), and a protein which is bound with the cyclic AMP. Cyclic AMP was synthesized from adenine within mycelia of the mutant strains which form monokaryotic fruiting bodies without the addition of fruiting-inducing substances, but not in those of the strains which do not form monokaryotic fruiting bodies. The proteins which bind with cyclic AMP were detected in crude extracts of mycelia of those strains which form monokaryotic fruiting bodies and of the dikaryon, but not in those of the strains which do not form monokaryotic fruiting bodies.     

Mechanism-based inactivation of horseradish peroxidase by sodium azide. Formation of meso-azidoprotoporphyrin IX

Catalytic turnover of sodium azide by horseradish peroxidase, which produces the azidyl radical, results in inactivation of the enzyme with KI = 1.47 mM and kinact = 0.69 min-1. Inactivation of 80% of the enzyme requires approximately 60 equiv each of NaN3 and H2O2. The enzyme is completely inactivated by higher concentrations of these two agents. meso-Azidoheme as well as some residual heme are obtained when the prosthetic group of the partially inactivated enzyme is isolated and characterized. Reconstitution of horseradish peroxidase with meso-azidoheme yields an enzyme without detectable catalytic activity even though reconstitution with heme itself gives fully active enzyme. The finding that catalytically generated nitrogen radicals add to the meso carbon of heme shows that biological meso additions are not restricted to carbon radicals. The analogous addition of oxygen radicals may trigger the normal and/or pathological degradation of heme.     

Substrate oxidation by dye-decolorizing peroxidases (DyPs) from wood- and litter-degrading agaricomycetes compared to other fungal and plant heme-peroxidases

Catalytic and physicochemical properties of representative fungal dye-decolorizing peroxidases (DyPs) of wood- (WRF) and litter-decomposing white-rot fungi (LDF) are summarized and compared, including one recombinant Mycetinis scorodonius DyP (rMscDyP; LDF), the wild-type Auricularia auricula-judae DyP (AauDyP; WRF), and two new DyPs secreted by the jelly fungi Exidia glandulosa (EglDyP; WRF) and Mycena epipterygia (MepDyP; LDF). Homogeneous preparations of these DyPs were obtained after different steps of fast protein liquid chromatography, and they increase the total number of characterized fungal DyP proteins to eight. The peptide sequences of AauDyP, MepDyP, and EglDyP showed highest homologies (52–56 %) to the DyPs of M. scorodonius. Five out of the eight characterized fungal DyPs were used to evaluate their catalytic properties compared to classic fungal and plant heme peroxidases, namely lignin peroxidase of Phanerochaete chrysosporium (PchLiP; WRF), versatile peroxidase of Bjerkandera adusta (BadVP; WRF), and generic peroxidases of Coprinopsis cinerea (CiP) and Glycine max (soybean peroxidase?=?SBP). All DyPs tested possess unique properties regarding the stability at low pH values: 50–90 % enzymatic activity remained after 4-h exposition at pH?2.5, and the oxidation of nonphenolic aromatic substrates (lignin model compounds) was optimal below pH?3. Furthermore, all DyPs efficiently oxidized recalcitrant dyes (e.g., Azure B) as well as the phenolic substrate 2,6-dimethoxyphenol. Thus, DyPs combine features of different peroxidases on the functional level and may be part of the biocatalytic system secreted by fungi for the oxidation of lignin and/or toxic aromatic compounds.     

Topology of the chloroperoxidase active site: regiospecificity of heme modification by phenylhydrazine and sodium azide.

Chloroperoxidase (CLP) from Caldariomyces fumago is rapidly and irreversibly inactivated by phenylhydrazine and H2O2 but not by H2O2 alone. Inactivation is characterized by a phenylhydrazine-to-CLP partition ratio of approximately 15, formation of trans-azobenzene, and formation of a sigma-bonded phenyl-iron heme complex with a characteristic absorption maximum of 472 nm. Anaerobic extraction of the heme complex from the protein, followed by exposure to dioxygen under acidic conditions, shifts the phenyl group from the iron to the porphyrin nitrogens and yields the four possible N-phenylprotoporphyrin IX regioisomers. Oxidation of the iron-phenyl complex within the intact protein by ferricyanide or high peroxide concentrations results in protein-directed phenyl migration to give exclusively the N-phenylprotoporphyrin IX regioisomers with the phenyl group on pyrrole rings A and C. CLP also catalyzes the H2O2-dependent oxidation of azide to the azidyl radical and is inactivated by azide in the presence of H2O2. Inactivation of CLP by azide and H2O2 results in loss of heme Soret absorbance and formation of delta-meso-azidoheme. These results suggest a topological model for the CLP active site and indicate that the tertiary structure of the enzyme permits substrates to interact with both the delta-meso heme edge and catalytic ferryl (FeIV = O) species, in agreement with the fact that CLP catalyzes both H2O2-dependent peroxidation and monooxygenation reactions.     

Magnetic resonance spectral characterization of the heme active site of Coprinus cinereus peroxidase

Examination of the peroxidase isolated from the inkcap Basidiomycete Coprinus cinereus shows that the 42,000-dalton enzyme contains a protoheme IX prosthetic group. Reactivity assays and the electronic absorption spectra of native Coprinus peroxidase and several of its ligand complexes indicate that this enzyme has characteristics similar to those reported for horseradish peroxidase. In this paper, we characterize the H2O2-oxidized forms of Coprinus peroxidase compounds I, II, and III by electronic absorption and magnetic resonance spectroscopies. Electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) studies of this Coprinus peroxidase indicate the presence of high-spin Fe(III) in the native protein and a number of differences between the heme site of Coprinus peroxidase and horseradish peroxidase. Carbon-13 (of the ferrous CO adduct) and nitrogen-15 (of the cyanide complex) NMR studies together with proton NMR studies of the native and cyanide-complexed Coprinus peroxidase are consistent with coordination of a proximal histidine ligand. The EPR spectrum of the ferrous NO complex is also reported. Protein reconstitution with deuterated hemin has facilitated the assignment of the heme methyl resonances in the proton NMR spectrum.     

Effects of 2,4-substituents of deuteroheme upon peroxidase functions. II. Reactions of peroxidases and metmyoglobin with azide, cyanide and fluoride

Artificial horseradish peroxidases and metmyoglobins were reconstituted from their apoproteins and the following unnatural hemes: mesoheme, deuteroheme, hematoheme, chlorocruoroheme, and diacetyldeuteroheme. The electron-withdrawing effects of the 2,4-substituents upon affinities of these hemoproteins for azide, cyanide, and fluoride were investigated. Peroxidase preparations used were acidic (A₁ + A₂) and neutral (B + C) enzymes.The electron withdrawal of the substituents increased the strength of ligaud binding. Plotting the logaritms of dissociation constants for the hemoprotein-ligand complexes against pK₃, a measure of relative basicities for metal-free porphyrins, the Hammett relationship was found to be applicable to this case except for a few. The affinities of deuterohemoproteins for ligands were definitely higher than those expected from the above relationship.The constant ρ, slope of the Hammett equation, varied with the ligand. For any particular ligand, the two peroxidase preparations gave the same ρ value, but it was different from the value for metmyoglobin.     

Fine-tuning of the binding and dissociation of CO by the amino acids of the heme pocket of Coprinus cinereus peroxidase

Resonance Raman and infrared spectra and the CO dissociation rates (k(off)) were measured in Coprinus cinereus peroxidase (CIP) and several mutants in the heme binding pocket. These mutants included the Asp245Asn, Arg51Leu, Arg51Gln, Arg51Asn, Arg51Lys, Phe54Trp, and Phe54Val mutants. Binding of CO to CIP produced different CO adducts at pH 6 and 10. At pH 6, the bound CO is H-bonded to the protonated distal His55 residue, whereas at alkaline pH, the vibrational signatures and the rate of CO dissociation indicate a distal side which is more open or flexible than in other plant peroxidases. The distal Arg51 residue is important in determining the rate of dissociation in the acid form, increasing by 8-17-fold in the Arg51 mutants compared to that for the wild-type protein. Replacement of the distal Phe with Trp created a new acid form characterized by vibrational frequencies and k(off) values very similar to those of cytochrome c peroxidase.     

The quantum mixed-spin heme state of barley peroxidase: A paradigm for class III peroxidases.

Electronic absorption and resonance Raman (RR) spectra of the ferric form of barley grain peroxidase (BP 1) at various pH values, at both room temperature and 20 K, are reported, together with electron paramagnetic resonance spectra at 10 K. The ferrous forms and the ferric complex with fluoride have also been studied. A quantum mechanically mixed-spin (QS) state has been identified. The QS heme species coexists with 6- and 5-cHS hemes; the relative populations of these three spin states are found to be dependent on pH and temperature. However, the QS species remains in all cases the dominant heme spin species. Barley peroxidase appears to be further characterized by a splitting of the two vinyl stretching modes, indicating that the vinyl groups are differently conjugated with the porphyrin. An analysis of the currently available spectroscopic data for proteins from all three peroxidase classes suggests that the simultaneous occurrence of the QS heme state as well as the splitting of the two vinyl stretching modes is confined to class III enzymes. The former point is discussed in terms of the possible influences of heme deformations on heme spin state. It is found that moderate saddling alone is probably not enough to cause the QS state, although some saddling may be necessary for the QS state.     

Relationship between deficiency of phosphoglucose isomerase in Coprinus macrorhizus and fruiting body formation.

A mutant (pgi) of Coprinus macrorhizus deficient in phosphoglucose isomerase did not grow on fructose and grew poorly on glucose. The pgi mutation inhibited the formation of monokaryotic and dikaryotic fruiting bodies.     

Reaction intermediates and single turnover rate constants for the oxidation of heme by human heme oxygenase-1

Heme oxygenase converts heme to biliverdin, iron, and CO in a reaction with two established intermediates, alpha-meso-hydroxyheme and verdoheme. Transient kinetic studies show that the conversion of Fe(3+)-heme to Fe(3+)-verdoheme is biphasic. Electron transfer to the heme (0.11 s(-1) at 4 degrees C and 0.49 s(-1) at 25 degrees C) followed by rapid O(2) binding yields the ferrous dioxy complex. Transfer of an electron (0.056 s(-1) at 4 degrees C and 0.21 s(-1) at 25 degrees C) to this complex triggers the formation of alpha-meso-hydroxyheme and its subsequent O(2)-dependent fragmentation to Fe(3+)-verdoheme. The conversion of Fe(3+)-verdoheme to Fe(3+)-biliverdin is also biphasic. Thus, reduction of Fe(3+) to Fe(2+)-verdoheme (0.15 s(-1) at 4 degrees C and 0.55 s(-1) at 25 degrees C) followed by O(2) binding and an electron transfer produces Fe(3+)-biliverdin (0.025 s(-1) at 4 degrees C and 0.10 s(-1) at 25 degrees C). The conversion of Fe(3+)-biliverdin to free biliverdin is triphasic. Reduction of Fe(3+)-biliverdin (0.035 s(-1) at 4 degrees C and 0.15 s(-1) at 25 degrees C), followed by rapid release of Fe(2+) (0.19 s(-1) at 4 degrees C and 0.39 s(-1) at 25 degrees C), yields the biliverdin-enzyme complex from which biliverdin slowly dissociates (0.007 s(-1) at 4 degrees C and 0.03 s(-1) at 25 degrees C). The rate of Fe(2+) release agrees with the rate of Fe(3+)-biliverdin reduction. Fe(2+) release clearly precedes biliverdin dissociation. In the absence of biliverdin reductase, biliverdin release is the rate-limiting step, but in its presence biliverdin release is accelerated and the overall rate of heme degradation is limited by the conversion of Fe(2+)-verdoheme to the Fe(3+)-biliverdin.