Catalase of Neurospora crassa. 2. Electron paramagnetic resonance and chemical properties of the prosthetic group

A traffic light enzyme: acetate binding reversibly switches chlorite dismutase from a red- to a green-colored heme protein

Abstract

Chlorite dismutase is a unique heme enzyme that catalyzes the conversion of chlorite to chloride and molecular oxygen. The enzyme is highly specific for chlorite but has been known to bind several anionic and neutral ligands to the heme iron. In a pH study, the enzyme changed color from red to green in acetate buffer pH 5.0. The cause of this color change was uncovered using UV–visible and EPR spectroscopy. Chlorite dismutase in the presence of acetate showed a change of the UV–visible spectrum: a redshift and hyperchromicity of the Soret band from 391 to 404 nm and a blueshift of the charge transfer band CT1 from 647 to 626 nm. Equilibrium binding titrations with acetate resulted in a dissociation constant of circa 20 mM at pH 5.0 and 5.8. EPR spectroscopy showed that the acetate bound form of the enzyme remained high spin S = 5/2, however with an apparent change of the rhombicity and line broadening of the spectrum. Mutagenesis of the proximal arginine Arg183 to alanine resulted in the loss of the ability to bind acetate. Acetate was discovered as a novel ligand to chlorite dismutase, with evidence of direct binding to the heme iron. The green color is caused by a blueshift of the CT1 band that is characteristic of the high spin ferric state of the enzyme. Any weak field ligand that binds directly to the heme center may show the red to green color change, as was indeed the case for fluoride.

Graphic abstract

Electronic supplementary material

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Effect of axial ligands on electronic structure and O2 reduction by iron porphyrin complexes: Towards a quantitative understanding of the "push effect"

Axial ligands play a dominating role in determining the electronic structure and reactivity of iron porphyrin active sites and synthetic models. Several properties unique to the cysteine bound heme enzyme, cytochrome P450, is attributed to the "push effect" of the thiolate axial ligand. In this mini-review the ground state electronic structure of iron porphyrins with imidazole, phenolate and thiolate complexes, derived using a combination of spectroscopy and DFT calculations, are discussed. The differences in kinetics and selectivity of oxygen reduction reaction (ORR), catalyzed by these iron porphyrin complexes with different axial ligands, help elucidate the varying push effects of the different axial ligands on oxygen activation by ferrous porphyrin. The spectroscopic and kinetic data help to develop a quantitative understanding of the "push effect" and, in particular, the electrostatic and covalent contributions to it.

Unusual post-translational protein modifications: the benefits of sophistication

This review summarizes the “seemingly bizarre”, yet naturally occurring, covalent non-disulphide cross-links in enzymatic and scaffolding proteins and their functions.

Regulation and oxidation of two large monofunctional catalases

The two Neurospora crassa catalase genes cat-1 and cat-3 were shown to encode Cat-1 and Cat-3 large monofunctional catalases. cat-1 and cat-3 genes are regulated differentially during the asexual life cycle and under stress conditions. A stepwise increase in catalase activity occurs during conidiation. Conidia have 60 times more catalase activity than exponentially growing hyphae. Cat-1 activity was predominant in conidia, during germination and early exponential growth. It was induced during prestationary growth and by ethanol or heat shock. Cat-3 activity was predominant during late exponential growth and at the start of the conidiation process. It was induced under stress conditions, such as H(2)O(2), paraquat, cadmium, heat shock, uric acid, and nitrate treatment. In general, Cat-1 activity was associated with nongrowing cells and Cat-3 activity with growing cells. The Cat-3 N-terminus sequence indicates that this catalase is processed and presumably secreted. Paraquat caused modification and degradation of Cat-1. Under heat shock both Cat-1 and Cat-3 were modified and degraded and Cat-1 was resynthesized. Paraquat and heat shock effects were observed only in the presence of air and are probably related to in vivo generation of singlet oxygen. Purified Cat-3 was modified with a photosensitizing reaction in which singlet oxygen is produced.

Neurospora crassa catalases, singlet oxygen and cell differentiation

The morphogenetic transitions of the N. crassa asexual life cycle are responses to a hyperoxidant state in which probably singlet oxygen is generated. Induction of catalase activity and catalase oxidation by singlet oxygen are consequences of this recurrent hyperoxidant state. Here the biochemical properties and regulation of two large monofunctional catalases are reviewed, and a new catalase-peroxidase gene and activity is described. Catalase-3 is associated to growing and Catalase-1 to non-growing cells. Under stressful conditions one of these catalases is synthesized, depending on whether growth can be continued or a resistant cell has to be made. The catalase-peroxidase Catalase-2 was possibly derived from a bacterial enzyme. In contrast to the other catalases, Catalase-2 had catalase and peroxidase activity. Catalase-2 was expressed under conditions in which vacuolization of hyphae is observed. All three enzymes have a chlorin in its active site instead of ferroprotoheme IX and are resistant to molar concentrations of hydrogen peroxide. These and all other catalases tested so far are oxidized by singlet oxygen, probably at the heme moiety. The catalase activity is virtually unaffected by oxidation, but the enzymes are probably degraded more rapidly than the unmodified ones.

Molecular and kinetic study of catalase-1, a durable large catalase of Neurospora crassa

Catalase-1 (Cat-1), one of the two monofunctional catalases of Neurospora crassa, increases during asexual spore formation to constitute 0.6% of total protein in conidia. Cat-1 was purified 170-fold with a yield of 48% from conidiating cultures. Like most monofunctional catalases, Cat-1 is a homotetramer, resistant to inactivation by solvents, fully active over a pH range of 4-12, and inactivated by 3-amino-1,2,4-triazole. Unlike most monofunctional catalases, Cat-1 consists of 88 kDa monomers that are glycosylated with alpha-glucose and/or alpha-mannose, is unusually stable, and is not inactivated or inhibited by hydrogen peroxide. Cat-1 was more resistant than other catalases to heat inactivation and to high concentrations of salt and denaturants. Cat-1 exhibited unusual kinetics: at molar concentrations of hydrogen peroxide the apparent V was 10 times higher than at millimolar concentrations. Inactivation of Cat-1 activity with azide and hydroxylamine was according to first order kinetics, while cyanide at micromolar concentrations was a reversible competitive inhibitor.

Oxidation of catalase by singlet oxygen

Different bands of catalase activity in zymograms (Cat-1a-Cat-1e) appear during Neurospora crassa development and under stress conditions. Here we demonstrate that singlet oxygen modifies Cat-1a, giving rise to a sequential shift in electrophoretic mobility, similar to the one observed in vivo. Purified Cat-1a was modified with singlet oxygen generated from a photosensitization reaction; even when the reaction was separated from the enzyme by an air barrier, a condition in which only singlet oxygen can reach the enzyme by diffusion. Modification of Cat-1a was hindered when reducing agents or singlet oxygen scavengers were present in the photosensitization reaction. The sequential modification of the four monomers gave rise to five active catalase conformers with more acidic isoelectric points. The pI of purified Cat-1a-Cat-1e decreased progressively, and a similar shift in pI was observed as Cat-1a was modified by singlet oxygen. No further change was detected once Cat-1e was reached. Catalase modification was traced to a three-step reaction of the heme. The heme of Cat-1a gave rise to three additional heme peaks in a high performance liquid chromatography when modified to Cat-1c. Full oxidation to Cat-1e shifted all peaks into a single one. Absorbance spectra were consistent with an increase in asymmetry as heme was modified. Bacterial, fungal, plant, and animal catalases were all susceptible to modification by singlet oxygen, indicating that this is a general feature of the enzyme that could explain in part the variety of catalases seen in several organisms and the modifications observed in some catalases. Modification of catalases during development and under stress could indicate in vivo generation of singlet oxygen.

Structure of the heme d of Penicillium vitale and Escherichia coli catalases

A heme d prosthetic group with the configuration of a cis-hydroxychlorin gamma-spirolactone has been found in the crystal structures of Penicillium vitale catalase and Escherichia coli catalase hydroperoxidase II (HPII). The absolute stereochemistry of the two heme d chiral carbon atoms has been shown to be identical. For both catalases the heme d is rotated 180 degrees about the axis defined by the alpha-gamma-meso carbon atoms, with respect to the orientation found for heme b in beef liver catalase. Only six residues in the heme pocket, preserved in P. vitale and HPII, differ from those found in the bovine catalase. In the crystal structure of the inactive N201H variant of HPII catalase the prosthetic group remains as heme b, although its orientation is the same as in the wild type enzyme. These structural results confirm the observation that heme d is formed from protoheme in the interior of the catalase molecule through a self-catalyzed reaction.

Spectral characterization and chemical modification of catalase-peroxidase from Streptomyces sp

Catalase-peroxidase was purified to near homogeneity from Streptomyces sp. The enzyme was composed of two subunits with a molecular mass of 78 kDa and contained 1.05 mol of protoporphyrin IX/mol of dimeric protein. The absorption and resonance Raman spectra of the native and its cyano-enzyme were closely similar to those of other heme proteins with a histidine as the fifth ligand. However, the peak from tyrosine ring at approximately 1612 cm-1, which is unique in catalases, was not found in resonance Raman spectra of catalase-peroxidase. The electron paramagnetic resonance spectrum of the native enzyme revealed uniquely two sets of rhombic signals, which were converted to a single high spin, hexacoordinate species after the addition of sodium formate. Cyanide bound to the sixth coordination position of the heme iron, thereby converting the enzyme to a low spin, hexacoordinate species. The time-dependent inactivation of the enzyme with diethyl pyrocarbonate and its kinetic analysis strongly suggested the occurrence of histidine residue. From the above-mentioned spectroscopic results and chemical modification, it was deduced that the native enzyme is predominantly in the high spin, ferric form and has a histidine as the fifth ligand.

Purification and characterization of a catalase-peroxidase from the fungus Septoria tritici

Three classes of heme proteins, commonly designated hydroperoxidases, are involved in the metabolism of hydrogen peroxide: catalases, peroxidases, and catalase-peroxidases. While catalases and peroxidases are widely spread in animals, plants, and microorganisms, catalase-peroxidases were characterized only in prokaryotes. We report here, for the first time, on a catalase-peroxidase in a eukaryotic organism. The enzyme was purified from the fungal wheat pathogen Septoria tritici, and is one of three different hydroperoxidases synthesized by this organism. The S. tritici catalase-peroxidase, designated StCP, is similar to the enzymes previously isolated from the bacteria Rhodobacter capsulatus, Escherichia coli, and Klebsiella pneumoniae, although it is significantly more sensitive to denaturing conditions. In addition to its catalatic activity StCP catalyzes peroxidatic activity with o-dianisidine, diaminobenzidine, pyrogallol, NADH, and NADPH as electron donors. The enzyme is a tetramer with identical subunits of 61,000 Da molecular weight. StCP shows a typical high-spin ferric heme spectrum with a Soret band at 405 nm and a peak at 632 nm, and binding of cyanide causes a shift of the Soret band to 421 nm, the appearance of a peak at 537 nm, and abolition of the peak at 632 nm. Reduction with dithionite results in a decrease in the intensity of the Soret band and its shift to 436 nm, and in the appearance of a peak at 552 nm. The pH optimum is 6-6.5 and 5.4 for the catalatic and peroxidatic activities, respectively. Fifty percent of the apparent maximal activity is reached at 3.4 mM and 0.26 mM for the catalatic and peroxidatic activities, respectively. The enzyme is inactivated by ethanol/chloroform, and is inhibited by KCN and NaN3, but not by the typical catalase inhibitor 3-amino-1,2,4-triazole.

The active site structure of E. coli HPII catalase. Evidence favoring coordination of a tyrosinate proximal ligand to the chlorin iron

E. coli produces 2 catalases known as HPI and HPII. While the heme prosthetic group of the HPII catalase has been established to be a dihydroporphyrin or chlorin, the identity of the proximal ligand to the iron has not been addressed. The magnetic circular dichroism (MCD) spectrum of native ferric HPII catalase is very similar to those of a 5-coordinate phenolate-ligated ferric chlorin complex, a model for tyrosinate proximal ligation, as well as of chlorin-reconstituted ferric horseradish peroxidase, a model for 5-coordinate histidine ligation. However, further MCD comparisons of chlorin-reconstituted myoglobin with parallel ligand-bound adducts of the catalase clearly rule out histidine ligation in the latter, leaving tyrosinate as the best candidate for the proximal ligand.

Purification and characterization of a novel type of catalase from the bacterium Klebsiella pneumoniae

A novel type of catalase, designated KpA, was purified from the bacterium Klebsiella pneumoniae. The enzyme is unique in that it is a dimer with subunit molecular weight of 80,000, it bears a chlorine-type heme as prosthetic group, and is active over a very wide range of H+ concentrations, with a plateau from pH 2.8 to 11.8. Yet, some properties of KpA are characteristic of typical catalases: it is stable when treated with with ethanol/chloroform, cannot be reduced by dithionite and it is inhibited by 3-amino-1,2,4-triazole and by the conjugate acid forms of azide and cyanide. The protein of KpA is outstandingly resistant to denaturing conditions: it retains full activity when incubated with 8 M urea, at 30 degrees C for 4 days, it is stable for 1 h at 70 degrees C and at pH values 3.1 and 11.5 and, when dialyzed against 50 mM H2O2, it still retains 42% of its activity after 80 min.

Prosthetic group content and ligand binding properties of a spinach catalase

A recently discovered form of spinach catalase that contains both a novel heme and protoheme as prosthetic groups has been characterized using immunological and spectroscopic techniques. The enzyme appears to be a dimer of identical Mr 60,000 monomers. Extraction of the non-covalently bound prosthetic groups, followed by thin-layer chromatography of the extract, suggested that the novel heme contains four carboxylic acid side-chain groups. The resonance Raman spectrum of the resting enzyme indicates that the protoheme prosthetic group is five-coordinate and high-spin. The enzyme was shown to bind formate, azide and cyanide. Cyanide and azide binding to catalase are biphasic, suggesting the existence of two different binding sites for cyanide and azide in the enzyme. Results obtained from EPR and resonance Raman spectroscopies also support the hypothesis that two different ligand-binding sites are present in the enzyme. Western blots suggest that the Mr 60,000 peptide of the novel heme-containing catalase is similar or identical to that of a previously characterized, exclusively protoheme-containing, tetrameric catalase.

Resonance Raman spectra of bovine liver catalase: enhancement of proximal tyrosinate vibrations

Resonance Raman spectra of native bovine liver ferri-catalase have been obtained in the 200-1800 cm-1 region. Excitation at a series of wavelengths ranging from 406.7 to 514.5 nm has been used and gives rise to distinct sets of resonance Raman bands. Excitation within the Soret and Q-bands of the heme group produces the expected set of polarized and nonpolarized porphyrin modes, respectively. The frequencies of the porphyrin skeletal stretching bands in the 1450-1700 cm-1 region indicate that catalase contains only five-coordinate, high-spin heme groups. In addition to the porphyrin modes, bovine liver catalase exhibits bands near 1612 and 1520 cm-1 that are attributable to ring vibrations of the proximal tyrosinate that are enhanced via resonance with a proximal tyrosinate----Fe(III) change transfer transition centered near 490 nm. Similar bands have been observed in mutant hemoglobins that have tyrosinate axial ligands and in other Fe(III)-tyrosinate proteins. No resonance Raman bands have been observed that can be attributed to degraded hemes. The spectra are relatively insensitive to pH over the range of 5-10, and the same spectra are observed for catalase samples that do and do not contain tightly bound NADPH. Resonance Raman spectra of the fluoride complex exhibit porphyrin skeletal stretching modes that show it to be six coordinate, high spin, while the cyanide complex is six coordinate, low spin. Both the azide and thiocyanate complexes, however, are spin-state mixtures with the high-spin form predominant.

Three-dimensional structure of catalase from Penicillium vitale at 2.0 A resolution

The three-dimensional structure analysis of crystalline fungal catalase from Penicillium vitale has been extended to 2.0 A resolution. The crystals belong to space group P3(1)21, with the unit cell parameters of a = b = 144.4 A and c = 133.8 A. The asymmetric unit contains half a tetrameric molecule of 222 symmetry. Each subunit is a single polypeptide chain of approximately 670 amino acid residues and binds one heme group. The amino acid sequence has been tentatively determined by computer graphics model building (using the FRODO system) and comparison with the known sequence of beef liver catalase. The atomic model has been refined by the Hendrickson & Konnert (1981) restrained least-squares program against 68,000 reflections between 5 A and 2 A resolution. The final R-factor is 0.31 after 24 refinement cycles. The secondary and tertiary structure of the catalase has been analyzed.

Correlations among parameters that describe low-spin ferric heme complexes

The g values from low-spin ferric hemes can be related through the t2g hole model to rhombic (V/lambda) and tetragonal (delta/lambda) ligand field components and to the lowest Kramer's doublet energy (E/lambda). The latter is also a measure of unpaired electron sharing among the iron 3d (t2g) orbitals. For a series of ligands (X), there is a monotonic increase in myoglobin complex (Mb . X) [E/lambda] values with nonheme hexacoordinate metal complex (M . X6) [eg-t2gPg] orbital separations. As the aqueous solution pKa values of the sulfurous or nitrogenous ligands in model heme complexes increase, values of V/lambda and delta/lambda increase linearly, but those of [E/lambda] decrease linearly. The greater the electron-acceptor ability of the ligand, as suggested by its position in the spectrochemical series or its pKa, the more the unpaired electron sharing among the heme t2g orbitals increases. The rate of change of [E/lambda] with V/lambda and the pKa is different with sulfurous and nitrogenous ligands, and the magnitude of both rates increases with two sulfurs less than sulfur and nitrogen less than two nitrogens bound to the heme. The maximum magnitude of this rate with V/lambda for cytochrome P-450 is four times less than that for myoglobin, which may explain, in part, the differences in ligand binding between these two hemeproteins. The perturbation of [E/lambda], V/lambda, and delta/lambda induced by strain of iron-ligand bonds is quantitated for several hemeproteins and heme models. In addition, energy level comparisons suggest that the largest-magnitude g value falls approximately along the iron-chlorin ring normal. This suggestion implies that the electron distribution of the iron at the catalytic sites of cytochrome P-450 and certain chlorin-containing enzymes is in some way similar, but distinct from that at the transport site of myoglobin.