Direct binding of hydroxylamine to the heme iron of Arthromyces ramosus peroxidase. Substrate analogue that inhibits compound I formation in a competetive manner

Kinetic Study of Coprinus cinereus Peroxidase-Catalyzed Oxidation of 2,2'-Dihydroxyazobenzene

Azo dyes are of concern due to their harmful effects on the environment and human health. The oxidation of 2,2'-dihydroxyazobenzene (DHAB) catalyzed with recombinant Coprinus cinereus (rCiP) peroxidase was investigated. The kinetic measurements were performed using the spectrophotometric and fluorimetric methods. The dependences of the initial reaction rates on enzyme, substrate and hydrogen peroxide concentrations during DHAB oxidation were established, and bimolecular constants of enzyme interaction with DHAB were calculated. This research demonstrated that the initial biocatalytic oxidation rates of DHAB depend on the pH and the estimated pKa values of the active forms of rCip. This study's findings thus contribute to a more comprehensive understanding of the biocatalytic oxidation of DHAB, providing valuable data for assessing the long-term toxicity, carcinogenesis and epigenetic effects of azo dyes in the environment.

Hydroxylamine Complexes of Cytochrome c': Influence of Heme Iron Redox State on Kinetic and Spectroscopic Properties

Hydroxylamine (NH₂OH or HA) is a redox-active nitrogen oxide that occurs as a toxic intermediate in the oxidation of ammonium by nitrifying and methanotrophic bacteria. Within ammonium containing environments, HA is generated by ammonia monooxygenase (nitrifiers) or methane monooxygenase (methanotrophs). Subsequent oxidation of HA is catalyzed by heme proteins, including cytochromes P460 and multiheme hydroxylamine oxidoreductases, the former contributing to emissions of N₂O, an ozone-depleting greenhouse gas. A heme-HA complex is also a proposed intermediate in the reduction of nitrite to ammonia by cytochrome c nitrite reductase. Despite the importance of heme-HA complexes within the biogeochemical nitrogen cycle, fundamental aspects of their coordination chemistry remain unknown, including the effect of the Fe redox state on heme-HA affinity, kinetics, and spectroscopy. Using stopped-flow UV-vis and resonance Raman spectroscopy, we investigated HA complexes of the L16G distal pocket variant of Alcaligenes xylosoxidans cytochrome c'-α (L16G AxCP-α), a pentacoordinate c-type cytochrome that we show binds HA in its Fe(III) (K_d ∼ 2.5 mM) and Fe(II) (K_d = 0.0345 mM) states. The ∼70-fold higher HA affinity of the Fe(II) state is due mostly to its lower k_off value (0.0994 s^-1 vs 11 s^-1), whereas k_on values for Fe(II) (2880 M^-1 s^-1) and Fe(III) (4300 M^-1 s^-1) redox states are relatively similar. A comparison of the HA and imidazole affinities of L16G AxCP-α was also used to predict the influence of Fe redox state on HA binding to other proteins. Although HA complexes of L16G AxCP-α decompose via redox reactions, the lifetime of the Fe(II)HA complex was prolonged in the presence of excess reductant. Spectroscopic parameters determined for the Fe(II)HA complex include the N-O stretching vibration of the NH₂OH ligand, ν(N-O) = 906 cm^-1. Overall, the kinetic trends and spectroscopic benchmarks from this study provide a foundation for future investigations of heme-HA reaction mechanisms.

Cytochrome c'β-Met Is a Variant in the P460 Superfamily Lacking the Heme-Lysyl Cross-Link: A Peroxidase Mimic Generating a Ferryl Intermediate

A defining characteristic of bacterial cytochromes (cyt's) in the P460 family is an unusual cross-link connecting the heme porphyrin to the side chain of a lysyl residue in the protein backbone. Here, via proteomics of the periplasmic fraction of the ammonia-oxidizing bacterium (AOB) Nitrosomonas europaea, we report the identification of a variant member of the P460 family that contains a methionyl residue in place of the cross-linking lysine. We formally designate this protein cytochrome "c'_β-Met" to distinguish it from other members bearing different residues at this position (e.g., cyt c'_β-Phe from the methane-oxidizing Methylococcus capsulatus Bath). As isolated, the monoheme cyt c'_β-Met is high-spin (S = ⁵/₂). Optical spectroscopy suggests that a cross-link is absent. Hydroxylamine, the substrate for the cross-linked cyt P460 from N. europaea, did not appreciably alter the optical spectrum of cyt c'_β with up to 1000-fold excess at pH 7.5. Cyt c'_β-Met did however bind 1 equiv of H₂O₂, and with a slight excess, Mössbauer spectroscopy indicated the formation of a semistable ferryl (Fe^IV═O) Compound II-like species. The corresponding electron paramagnetic resonance showed a very low intensity signal indicative of a radical at g = 2.0. Furthermore, cyt c'_β-Met exhibited guaiacol-dependent peroxidase activity (k_cat = 20.0 ± 1.2 s^-1; K_M = 2.6 ± 0.4 mM). Unlike cyt c'_β-Met, cyt P460 showed evidence of heme inactivation in the presence of 2 equiv of H₂O₂ with no appreciable guaiacol-dependent peroxidase activity. Mutagenesis of the cross-linking lysyl residue to an alanine in cyt P460, however, reversed this lack of activity.

Improving the synthesis of phenolic polymer using Coprinus cinereus peroxidase mutant Phe230Ala

The F230A mutant of Coprinus cinereus peroxidase (CiP), which has a high stability against radical-inactivation, was previously reported. In the present study, the radical-robust F230A mutant was applied to the oxidative polymerization of phenol. The F230A mutant exhibited better polymerization activities than the wild-type CiP in the presence of water-miscible alcohols i.e., methanol, ethanol, and isopropanol despite its lower stability against alcohols. In particular, the F230A mutant showed a higher consumption of phenol (40%) and yielded phenolic polymer of larger molecular weight (8850Da) in a 50% (v/v) isopropanol-buffer mixture compared with the wild-type CiP (2% and 1519Da, respectively). In addition, the wild-type CiP and F230A mutant had no significant differences in enzyme inactivation by physical adsorption on the polymeric products or by heat incubation, and showed comparable kinetic parameters. These results indicate that high radical stability of the F230A mutant and improved solubility of phenolic polymers in alcohol-water cosolvent systems may synergistically contribute to the production of the high molecular weight phenolic polymer.

Spectroscopic properties of rubber oxygenase RoxA from Xanthomonas sp., a new type of dihaem dioxygenase

Natural rubber [poly-(cis-1,4-isoprene)] is cleaved to 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD) by rubber oxygenase A (RoxA) isolated from Xanthomonas sp. RoxA has two c-type haem centres that show two distinct alpha-bands at 549 and 553 nm in the dithionite-reduced state. A well-resolved midpoint potential (E(0)') of -65 mV was determined for one haem by spectrophotometric titrations in the absence of dioxygen with dithionite and ferricyanide as reductant and oxidant, respectively. The midpoint potential of the second haem was not resolvable (E(0)' about -130 to -160 mV). One of the two haems was reduced by NADH (549 nm alpha-band), similar to bacterial dihaem peroxidases. Evidence for an electron transfer between the two haems was provided by slow reduction of the second haem (553 nm alpha-band) upon incubation of the partially reduced enzyme at room temperature. Addition of imidazole or related compounds to RoxA led to UV/vis spectral features similar to those observed for partially reduced RoxA. Notably, reduction of RoxA with dithionite or NADH, or binding of compounds such as imidazole, resulted in a reversible inactivation of the enzyme, unlike dihaem peroxidases. In line with this result, RoxA did not show any peroxidase activity. EPR spectra of RoxA as isolated showed two low-spin Fe(III) haem centres, with apparent g-values of 3.39, 3.09, 2.23, 1.92 and 1.50. A weak signal in the g=6 region resulting from a high-spin Fe(III) haem was also observed with a preparation-dependent intensity that disappeared in the presence of imidazole. Attempts to provide spectroscopic evidence for binding of the natural substrate (polyisoprene latex) to RoxA failed. However, experimental data are presented that RoxA is able to subtract redox equivalents from its substrate or from model compounds. In conclusion, RoxA is a novel type of dihaem dioxygenase with features clearly different from classical cytochrome c peroxidases.

Redox intermediates in the catalase cycle of catalase-peroxidases from Synechocystis PCC 6803, Burkholderia pseudomallei, and Mycobacterium tuberculosis

Monofunctional catalases (EC 1.11.1.6) and catalase-peroxidases (KatGs, EC 1.11.1.7) have neither sequence nor structural homology, but both catalyze the dismutation of hydrogen peroxide (2H2O2 --> 2H2O + O2). In monofunctional catalases, the catalatic mechanism is well-characterized with conventional compound I [oxoiron(IV) porphyrin pi-cation radical intermediate] being responsible for hydrogen peroxide oxidation. The reaction pathway in KatGs is not as clearly defined, and a comprehensive rapid kinetic and spectral analysis of the reactions of KatGs from three different sources (Synechocystis PCC 6803, Burkholderia pseudomallei, and Mycobacterium tuberculosis) with peroxoacetic acid and hydrogen peroxide has focused on the pathway. Independent of KatG, but dependent on pH, two low-spin forms dominated in the catalase cycle with absorbance maxima at 415, 545, and 580 nm at low pH and 418 and 520 nm at high pH. By contrast, oxidation of KatGs with peroxoacetic acid resulted in intermediates with different spectral features that also differed among the three KatGs. Following the rate of H2O2 degradation by stopped-flow allowed the linking of reaction intermediate species with substrate availability to confirm which species were actually present during the catalase cycle. Possible reaction intermediates involved in H2O2 dismutation by KatG are discussed.

Influence of the unusual covalent adduct on the kinetics and formation of radical intermediates in synechocystis catalase peroxidase: a stopped-flow and EPR characterization of the MET275, TYR249, and ARG439 variants

Catalase-peroxidases (KatGs) are heme peroxidases with a catalatic activity comparable to monofunctional catalases. They contain an unusual covalent distal side adduct with the side chains of Trp(122), Tyr(249), and Met(275) (Synechocysis KatG numbering). The known crystal structures suggest that Tyr(249) and Met(275) could be within hydrogen-bonding distance to Arg(439). To investigate the role of this peculiar adduct, the variants Y249F, M275I, R439A, and R439N were investigated by electronic absorption, steady-state and transient-state kinetic techniques and EPR spectroscopy combined with deuterium labeling. Exchange of these conserved residues exhibited dramatic consequences on the bifunctional activity of this peroxidase. The turnover numbers of catalase activity of M275I, Y249F, R439A, and R439N are 0.6, 0.17, 4.9, and 3.14% of wild-type activity, respectively. By contrast, the peroxidase activity was unaffected or even enhanced, in particular for the M275I variant. As shown by mass spectrometry and EPR spectra, the KatG typical adduct is intact in both Arg(439) variants, as is the case of the wild-type enzyme, whereas in the M275I variant the covalent link exists only between Tyr(249) and Trp(122). In the Y249F variant, the link is absent. EPR studies showed that the radical species formed upon reaction of the Y249F and R439A/N variants with peroxoacetic acid are the oxoferryl-porphyrin radical, the tryptophanyl and the tyrosyl radicals, as in the wild-type enzyme. The dramatic loss in catalase activity of the Y249F variant allowed the comparison of the radical species formed with hydrogen peroxide and peroxoacetic acid. The EPR data strongly suggest that the sequence of intermediates formed in the absence of a one electron donor substrate, is por(.-)(+) --> Trp(.-) (or Trp(.-)(+)) --> Tyr(.-). The M275I variant did not form the Trp(.-) species because of the dramatic changes on the heme distal side, most probably induced by the repositioning of the remaining Trp(122)-Tyr(249) adduct. The results are discussed with respect to the bifunctional activity of catalase-peroxidases.

Hydroxylamine and hydrazine bind directly to the heme iron of the heme–heme oxygenase-1 complex

We investigated whether or not hydroxylamine (HA) and hydrazine (HZ) interact with heme bound to heme oxygenase-1. Anaerobic addition of either HA or HZ to the ferric heme-enzyme complex produced a low-spin heme species. Titration studies at different pHs revealed that the neutral form of each of HA and HZ selectively binds to the heme with dissociation constants of 9.8 and 1.8 mM, respectively. Electron spin resonance analysis suggested that the nitrogen atom of each amine is coordinated to the ferric heme iron. With a concentrated solution of the heme-enzyme complex, however, another species of HA binding appeared, in which the oxygen atom of HA is coordinated to the iron. This species showed an unusual low-spin signal which is similar to that of the ferric hydroperoxide species in the heme oxygenase reaction.

New Insight into the Peroxidase−Hydroxamic Acid Interaction Revealed by the Combination of Spectroscopic and Crystallographic Studies

Aromatic hydroxamic acids, such as salicylhydroxamic (SHA) and benzohydroxamic (BHA) acids, are commonly used as probes for studying the active sites of peroxidases. In this paper, we have extended the study of the complexes of Arthromyces ramosus peroxidase (ARP/CIP) with BHA and SHA by analyzing their Raman spectra in solution and in single crystals. The experiments were carried out under various conditions to identify the best experimental conditions, and hence, avoid artifacts deriving from the preparation of the samples or collection of the spectra. The analysis of the data takes also into account the characteristic of the electronic absorption spectra in solution and the crystal structures of the complexes. The results showed small differences between the solution and the crystal phases even though the coordination state can be dramatically affected by the physical or chemical conditions. The greater sensitivity of the spectroscopic technique enabled us to establish the existence of multiple species upon complexation of the protein with the hydroxamic acids that could not be detected by ordinary X-ray crystallography. Furthermore, SHA titration experiments and singular value decomposition analysis of the absorption spectra indicated the presence of two binding sites in the protein, one with a high affinity (K(d) = 1.7 mM), which should correspond to the SHA bound protein as determined by X-ray, and the other with a very low affinity (K(d) > 80 mM) probably located in a non-heme site. This suggests that the heterogeneous titration line shape involves ligand binding to a non-heme site in competition with the canonical heme site. In contrast, the titration profile obtained with the BHA ligand is monophasic, in agreement with all the peroxidases so far studied.