Spectroscopic description of an unusual protonated ferryl species in the catalase from Proteus mirabilis and density functional theory calculations on related models. Consequences for the ferryl protonation state in catalase, peroxidase and chloroperoxidase.

The catalase from Proteus mirabilis peroxide-resistant bacteria is one of the most efficient heme-containing catalases. It forms a relatively stable compound II. We were able to prepare samples of compound II from P. mirabilis catalase enriched in (57)Fe and to study them by spectroscopic methods. Two different forms of compound II, namely, low-pH compound II (LpH II) and high-pH compound II (HpH II), have been characterized by Mössbauer, extended X-ray absorption fine structure (EXAFS) and UV-vis absorption spectroscopies. The proportions of the two forms are pH-dependent and the pH conversion between HpH II and LpH II is irreversible. Considering (1) the Mössbauer parameters evaluated for four related models by density functional theory methods, (2) the existence of two different Fe-O(ferryl) bond lengths (1.80 and 1.66 A) compatible with our EXAFS data and (3) the pH dependence of the alpha band to beta band intensity ratio in the absorption spectra, we attribute the LpH II compound to a protonated ferryl Fe(IV)-OH complex (Fe-O approximately 1.80 A), whereas the HpH II compound corresponds to the classic ferryl Fe(IV)=O complex (Fe=O approximately 1.66 A). The large quadrupole splitting value of LpH II (measured 2.29 mm s(-1) vs. computed 2.15 mm s(-1)) compared with that of HpH II (measured 1.47 mm s(-1) vs. computed 1.46 mm s(-1)) reflects the protonation of the ferryl group. The relevancy and involvement of such (Fe(IV)=O/Fe(IV)-OH) species in the reactivity of catalase, peroxidase and chloroperoxidase are discussed.

Mössbauer identification of a protonated ferryl species in catalase from Proteus mirabilis: density functional calculations on related models.

The Proteus mirabilis catalase is one of the most efficient heme-containing catalase and forms a relatively stable compound II. Samples of compound II were prepared from PMC enriched in (57)Fe. For the first time, two different forms of compound II, namely low pH compound II (LpH II) (43%) and high pH compound II (HpH II) (25%), have been characterized by Mössbauer spectroscopy at pH 8.3. The ratio LpH II/HpH II increases irreversibly with decreasing pH. The large quadrupole splitting value of LpH II (DeltaE(Q)=2.29 (2) mm/s, with delta(/Fe)=0.03 (2) mm/s), compared to that of HpH II (DeltaE(Q)=1.47 (2) mm/s, with delta(/Fe)=0.07 (2) mm/s), reflects the protonation of the ferryl group. Quadrupole splitting values of 1.46 and 2.15mm/s have been computed by DFT for optimized models of the ferryl compound II (model 1) and the protonated ferryl compound II (model 2), respectively, starting from the Fe(IV)O model initially published by Rovira and Fita [C. Rovira, I. Fita, J. Phys. Chem. B 107 (2003) 5300-5305]. Therefore, we attribute the LpH II compound to a protonated ferryl Fe(IV)-OH complex, whereas the HpH II compound corresponds to the classical ferryl Fe(IV)O complex.

Formation of a tyrosyl radical intermediate in Proteus mirabilis catalase by directed mutagenesis and consequences for nucleotide reactivity.

Proteus mirabilis catalase (PMC) belongs to the family of NADPH binding catalases. The function of NADPH in these enzymes is still a matter of debate. This study presents the effects of two independent phenylalanine mutations (F194 and F215), located between NADPH and heme in the PMC structure. The phenylalanines were replaced with tyrosines which we predicted could carry radicals in a NADPH-heme electron transfer. The X-ray crystal structures of the two mutants indicated that neither the binding site of NADPH nor the immediate environment of the residues was affected by the mutations. Measurements using H2O2 as a substrate confirmed that the variants were as active as the native enzyme. With equivalent amounts of peroxoacetic acid, wild-type PMC, F215Y PMC, and beef liver catalase (BLC) formed a stable compound I, while the F194Y PMC variant produced a compound I which was rapidly transformed into compound II and a tyrosyl radical. EPR studies showed that this radical, generated by the oxidation of Y194, was not related to the previously observed radical in BLC, located on Y369. In the presence of excess NADPH, compound I was reduced to a resting enzyme (k(obs) = 1.7 min(-1)) in a two-electron process. This was independent of the enzyme's origin and did not require any thus far identified tyrosyl radicals. Conversely, the presence of a tyrosyl radical in F194Y PMC greatly enhanced the oxidation of reduced beta-nicotinamide mononucleotide under a steady-state H2O2 flow with observable compound II. This process could involve a one-electron reduction of compound I via Y194.

Ligand diffusion in the catalase from Proteus mirabilis: a molecular dynamics study.

The role of the channels and cavities present in the catalase from Proteus mirabilis (PMC) was investigated using molecular dynamics (MD) simulations. The reactant and products of the reaction, H(2)O(2) -->1/2 O(2) + H(2)O, catalyzed by the enzyme were allowed to diffuse to and from the active site. Dynamic fluctuations in the structure are found necessary for the opening of the major channel, identified in the X-ray model, which allows access to the active site. This channel is the only pathway to the active site observed during the dynamics, and both the products and reactant use it. H(2)O and O(2) are also detected in a cavity defined by the heme and Ser196, which could play an important role during the reaction. Free energy profiles of the ligands diffusing through the major channel indicate that the barriers to ligand diffusion are less than 20 kJ mol(-1) for each of the species. It is not clear from our study that minor channels play a role for access to the protein active site or to the protein surface.

EPR investigation of compound I in Proteus mirabilis and bovine liver catalases: formation of porphyrin and tyrosyl radical intermediates.

Compound I of Proteus mirabilis and bovine liver catalases (PMC and BLC, respectively) were studied combining EPR spectroscopy and the rapid-mix freeze-quench techniques. Both enzymes, when treated with peroxyacetic acid, form a catalytic intermediate which consists of an oxoferryl porphyrin pi-cation radical. In PMC this intermediate is semistable, and an unexpected reversible equilibrium under pH influence takes place between two forms of compound I with different coupling between the oxoferryl and the porphyrin pi-cation radical. At acid pH, one form has a ferromagnetic character as in Micrococcus luteus compound I. At neutral pH, another form with a much smaller coupling, reminiscent of the horse radish peroxidase compound I, is detected. The approximate midpoint, estimated for these changes in the range 5.3 < pH < 6.0, approaches the pKa value of an histidyl residue. The residues possibly involved in the transformation are discussed in terms of the known structure of PMC compound I. The EPR spectrum of BLC compound I (pH 5.6), obtained in the millisecond time scale (40 ms), also showed a mixture of two forms which, most probably, correspond to two different magnetic exchange interactions, as in the case of PMC. Taken together, the low-temperature electronic absorption and the EPR spectra of BLC compound I formed in the 0.04-15 s range show that the porphyrin pi-cation radical disappears and, instead, a tyrosyl radical is formed. ENDOR experiments confirm our previously estimated hyperfine couplings to the C2,6 and C3,5 ring protons and the beta-methylene protons of the purported tyrosyl radical. Candidates for such a tyrosyl radical are discussed in connection with the possible electron transfer pathways between the heme active site and the NADPH cofactor.

Structural analysis of compound I in hemoproteins: study on Proteus mirabilis catalase.

Ferryl catalysis has attracted considerable interest, because a diverse variety of enzymes use ferryl intermediates to perform difficult chemistry. The structure of the reactional intermediate compound I of Proteus mirabilis catalase (PMC) has been solved using time-resolved X-ray diffraction techniques and single crystal microspectrophotometry. Formation of compound I is characterized by significant changes in the absorbance spectrum, and the creation of an oxoferryl group on the distal side of the heme. This group is clearly visible in the X-ray electron density maps. An unidentified electron density, likely to be an anion because of the nature of its environment, appears during the reaction, in a site distant from the heme. The structure of compound I in PMC is compared with that of compound I in cytochrome c peroxidase (CCP).

Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy.

Various enzymes use semi-stable ferryl intermediates and free radicals during their catalytic cycle, amongst them haem catalases. Structures for two transient intermediates (compounds I and II) of the NADPH-dependent catalase from Proteus mirabilis (PMC) have been determined by time-resolved X-ray crystallography and single crystal microspectrophotometry. The results show the formation and transformation of the ferryl group in the haem, and the unexpected binding of an anion during this reaction at a site distant from the haem.

Simulations of electron transfer in the NADPH-bound catalase from Proteus mirabilis PR.

Catalase-bound NADPH both prevents and reverses the accumulation of compound II, an inactive form of catalase that is generated from the normal active intermediate form (compound I) when catalase is exposed to a steady flow of hydrogen peroxide. The mechanism for the regeneration reaction is unknown although NADPH could act either as a one-electron or a two-electron donor. Recently, a reaction scheme has been proposed in which the formation of compound II from compound I generates a neighboring radical species within the protein. NADPH would then donate two electrons, one to compound II for reduction of the iron and the other to the protein free radical. In this paper, we report calculations to find the dominant electron tunneling pathways between NADPH and the heme iron in the catalase from the peroxide-resistant mutant of Proteus mirabilis. Two major tunneling pathways are found which fuse together on Ser-196. It is suggested that the sequence Gly-Ser of the loop that divides the beta 5-strand is the key element for shielding a radical amino acid.

Crystal structure of Proteus mirabilis PR catalase with and without bound NADPH.

A catalase from a peroxide resistant mutant of Proteus mirabilis binds NADPH tightly. Interestingly, this enzyme can be stripped of NADPH without loss of the catalatic activity. It is the only known non-mammalian catalase able to bind NADPH. The structure without cofactor was solved by molecular replacement using the structure of beef liver catalase as a model. The structure was refined to an R-factor of 19.3% in the range 8 to 2.2 A resolution. According to the sequence, a methionine sulphone was positioned in the haem active site. This oxidized form of methionine is particular to Proteus mirabilis catalase and likely to produce some steric hindrance in the active site. Two important water molecules are positioned in the haem distal site. These two water molecules are not located in the structure of beef liver catalase, but are supposed to account for the catalytic mechanism. The liganded form was obtained by soaking crystals of the unliganded form into an NADPH solution. The structure was refined to an R-factor of 15.9% in the range of 8 to 3.1 A resolution using the unliganded structure as a model. The NADPH was clearly located in the electron density map with the same conformation as in beef liver catalase. The NADPH binding induces slight structural changes. However, the imidazole ring of a histidine residue (His284) rotates about 50 degrees to accommodate the cofactor. The electron transfer from NADPH to the haem molecule was examined and several pathways are proposed.

Complete amino acid sequence of Proteus mirabilis PR catalase. Occurrence of a methionine sulfone in the close proximity of the active site.

The catalase of Proteus mirabilis PR, a peroxide-resistant (PR) mutant of Proteus mirabilis, binds strongly NADPH, which is a unique property among known bacterial catalases. The enzyme subunit consists of 484 amino acid residues for a mass of 55,647 daltons. The complete amino acid sequence was resolved through the combination of protein sequencing, mass spectrometry, and nucleotide sequencing of a PCR fragment. The sequence obtained was compared with that of other known catalases. Amino acids of the active site are all conserved as well as essential residues involved in NADPH binding. Among the amino acids interacting with the heme, a methionine sulfone was found at position 53, in place of a valine in most other catalases. The origin of oxidation of this methionine is unknown, but the presence of this modification could change iron accessibility by large substrates or inhibitors. This posttranslational modification was also demonstrated in the wild-type P. mirabilis catalase.

Purification and properties of a halophilic catalase-peroxidase from Haloarcula marismortui.

A heme protein, hCP, from the extreme halophile, Haloarcula marismortui, showing both peroxidatic and catalatic activity has been purified and characterized as a catalase-peroxidase. Catalatic activity is enhanced by molar concentrations of NaCl or (NH4)2SO4, while peroxidase activity decreases with increasing salt concentration. Optimal pH values are 6.0 for peroxidatic activity assayed in absence of NaCl and 7.5 for catalatic activity assayed in molar concentrations of NaCl. The two activities present saturation behaviour with increasing H2O2 concentration with apparent Km values of 0.5 and 2.5 mM for the peroxidatic and catalatic activities, respectively. A molecular mass of 81,292 +/- 9 Da was measured for the polypeptide by mass spectroscopy. One heme group (protoporphyrin IX with an iron atom in the ferric state) is associated with one molecule of hCP. Its amino-acid composition shows hCP to contain a high proportion of acidic residues. The EPR spectrum of the NO-compound of reduced (ferrous) hCP strongly suggests that the proximal ligand of the heme is the imidazole group of a histidine residue.

Crystallization and crystal packing of Proteus mirabilis PR catalase.

The tetrameric catalase from Proteus mirabilis PR (EC 1.11.1.6), known to bind NADPH, has been crystallized by the hanging-drop method in a form apparently depleted in dinucleotide. The crystals belong to the hexagonal space group P6(2)22 with a = b = 111.7 A, c = 248.8 A. There is one subunit in the asymmetric unit. Data were collected to 2.9 A at the L.U.R.E. (Orsay) synchrotron radiation facility. The tetramers have been located in the crystal, centered on the site (1/2, 0, 0) with 222 symmetry.

Interaction between pyridine adenine dinucleotides and bovine liver catalase: a chromatographic and spectral study.

Two different fractions were present in crystalline bovine liver catalase, and could be resolved using dye-ligand affinity chromatography with Red-A Matrex gel containing Procion HE 3B. The major part (alpha) was not adsorbed on this gel. The second fraction (beta) was firmly adsorbed to the gel, and could be eluted either by high salt or by NADPH in the micromolar range. Elution of catalase beta was also obtained with NADH, NADP+, and ADP at higher concentration. Fractions alpha and beta displayed no detectable difference in specific activity, stability to heat, and light absorption data. It is suggested that the difference in behavior between alpha and beta is related to the binding of NADPH to the mammalian catalase [H. N. Kirkman and G. F. Gaetani (1984) Proc. Natl. Acad. Sci. USA 81, 4343-4347], and that the beta fraction corresponds to the enzyme molecules that have at least one free site for NADPH binding. Modifications of catalase molecules in the presence of dithioerythritol (DTE) were examined using light absorption and EPR data. Thiol induced changes that corresponded to the formation of catalase complex II. They were partially reversed by NADPH at very low level, and the dinucleotide appeared to be oxidized in this process. DTE-treated bovine catalase was totally adsorbed on the Red-A Matrex columns, and could be eluted as fraction beta. Similar spectral changes in the presence of DTE and NADPH were displayed by a bacterial catalase from Proteus mirabilis. This enzyme was also able to oxidize NADPH, but was not adsorbed by Red-A Matrex. This work suggests that dye-affinity chromatography provides a very convenient tool for isolating dinucleotide-depleted catalase from bovine liver, facilitating further study of the physiological function of this cofactor within the enzyme.

Characterization and spectral properties of Proteus mirabilis PR catalase.

Purified catalase from a peroxide-resistant mutant (PR) of Proteus mirabilis displayed great similarities with the bovine liver catalase on the basis of its amino acid composition, content in prosthetic groups, and spectroscopic data. The bacterial enzyme was found to have 2.6 +/- 0.2 mol of protoheme IX per tetramer, with an equivalent amount of titrable iron atoms. The optical absorption of P. mirabilis PR catalase in the presence of various anionic species (cyanide, azide, formate) was examined. The dissociation constant of the formate-enzyme complex was determined as 60 +/- 2 mM at pH 7.5. Inhibition and spectral shifts induced by some thiol compounds were very similar to those reported with mammalian catalase. The electron paramagnetic resonance (EPR) spectra (at 9 GHz and 6 K) of bacterial catalase and its various complexes were reported. Two major different rhombic high-spin ferric signals could be seen in the g = 6 region, using either the pure enzyme or the cell crude extract. The balance between the two rhombic forms was reversibly altered by pH. Various changes in rhombicity were also observed after binding with anionic ligands. The EPR spectrum (at 40 K) of nitrosyl ferrous catalase was very similar to reported data with horse liver catalase.

Properties of a catalase from a peroxide-resistant mutant of Proteus mirabilis.

A catalase (EC 1.11.1.6) from Proteus mirabilis PR, a mutant with strong resistance to hydrogen peroxide, was purified to homogeneity and compared with catalase from wild-type P. mirabilis. In crude extracts from the mutant, catalase was present as two different entities called A and B, that could be resolved by ion-exchange chromatography. The B form was transformed into A. The pure catalase preparation contained the A form only. This catalase was not found to be different from the wild-type enzyme, considering its molecular weight, subunit composition, isoelectric pH, and reactivity to specific antibodies. Partial proteolytic cleavage of the two bacterial enzymes with four different proteases proceeded at the same rate and produced identical patterns. However, pure catalase from the mutant had a specific activity against H2O2 of 2.7 X 10(7) M-1 X s-1, and its purity index (A406/A280) was 1.12. These values were higher than previously determined for the wild-type enzyme. Furthermore, the mutant catalase was more stable to heat. The results suggest that the purified catalase (A form) differs from the wild-type enzyme and appears to be a more efficient catalase against H2O2. Both enzymes were found to be much more resistant than beef liver catalase to the classically used catalase inhibitor 3-amino-1,2,4-triazole.

Purification and properties of the Proteus mirabilis catalase.

The purification of catalase from Proteus mirabilis has been described. The protein had four subunits of equal apparent molecular weight (MW 62 000). The enzyme was found to be slightly heterogenous after electrofocusing, the main fraction having an isoelectric pH 4.8. No detectable peroxidatic activity was observed in physiological conditions. The absorbance spectrum and the effects of pH and temperature on catalase have also been described.

Generation of hydrogen peroxide during the oxidation of L-phenylalanine by Proteus mirabilis isolated membranes.

In the process of L-phenylalanine oxidation by Proteus mirabilis cytoplasmic membrane, hydrogen peroxide was produced at a rate corresponding to 1-3 per cent of the total electron flow (30-110 nmoles min-1mg-1). Peroxide was estimated using a fluorimetric assay with horseradish peroxidase, or by anodic oxidation on a platinum electrode. When using the former method, superoxide dismutase decreased the apparent yield of peroxide, a fact suggesting that H2O2 was in part the dismutation product of superoxide radicals. However the superoxide dismutase effect could be an artefact due to the generation of some superoxide during the peroxidatic reaction in the assay. Adrenaline was the reagent used for the detection of superoxide. There was no significant emergence of superoxide as the result of phenylalanine oxidation by the membrane (specific activity lower than 1-2 nmoles min-1mg-1). Thus it seemed that superoxide was not an intermediate for the bulk of H2O2 formed in this system. According to the results, peroxide was probably formed at a stage of electron transport earlier than the cytochrome level. The membrane phenylalanine dehydrogenase could be a site where peroxide was evolved in these experiments.