Mössbauer Characterization of an Unusual High-Spin Side-On Peroxo−Fe3+ Species in the Active Site of Superoxide Reductase from Desulfoarculus baarsii. Density Functional Calculations on Related Models

Conformational H-bonding modulation of the iron active site cysteine ligand of superoxide reductase: absorption and resonance Raman studies

Superoxide reductases (SORs) are mononuclear non-heme iron enzymes involved in superoxide radical detoxification in some microorganisms. Their atypical active site is made of an iron atom pentacoordinated by four equatorial nitrogen atoms from histidine residues and one axial sulfur atom from a cysteinate residue, which plays a central role in catalysis. In most SORs, the residue immediately following the cysteinate ligand is an asparagine, which belongs to the second coordination sphere and is expected to have a critical influence on the properties of the active site. In this work, in order to investigate the role of this asparagine residue in the Desulfoarculus baarsii enzyme (Asn117), we carried out, in comparison with the wild-type enzyme, absorption and resonance Raman (RR) studies on a SOR mutant in which Asn117 was changed into an alanine. RR analysis was developed in order to assign the different bands using excitation in the (Cys116)-S^-→ Fe³⁺ charge transfer band. By investigating the correlation between the (Cys116)-S^-→ Fe³⁺ charge transfer band maximum with the frequency of each RR band in different SOR forms, we assessed the contribution of the ν(Fe-S) vibration among the different RR bands. The data showed that Asn117, by making hydrogen bond interactions with Lys74 and Tyr76, allows a rigidification of the backbone of the Cys116 ligand, as well as that of the neighboring residues Ile118 and His119. Such a structural role of Asn117 has a deep impact on the S-Fe bond. It results in a tight control of the H-bond distance between the Ile118 and His119 NH peptidic moiety with the cysteine sulfur ligand, which in turn enables fine-tuning of the S-Fe bond strength, an essential property for the SOR active site. This study illustrates the intricate roles of second coordination sphere residues to adjust the ligand to metal bond properties in the active site of metalloenzymes.

Rational redox tuning of transition metal sites: learning from superoxide reductase

Using superoxide reductase as a model system, a computational approach reveals how histidine tautomerism tunes the redox properties of metalloenzymes to enable their catalytic function. Inspired by these experimentally inaccessible insights, non-canonical histidine congeners are introduced as new versatile tools for the rational engineering of biological transition metal sites.

Multiconfigurational and DFT analyses of the electromeric formulation and UV-vis absorption spectra of the superoxide adduct of ferrous superoxide reductase

The putative initial adduct of ferrous superoxide reductase (SOR) with superoxide has been alternatively formulated as ferric-peroxo or ferrous-superoxo. The ~600-nm UV-vis absorption band proposed to be assigned to this adduct (either as sole intermediate in the SOR catalytic cycle, or as one of the two intermediates) has recently been interpreted as due to a ligand-to-metal charge transfer, involving thiolate and superoxide in a ferrous complex, contrary to an alternative assignment as a predominantly cysteine thiolate-to-ferric charge transfer in a ferric-peroxo electromer. In an attempt to clarify the electromeric formulation of this adduct, we report a computational study using a multiconfigurational complete active space self-consistent field (MC-CASSCF) wave function approach as well as modelling the UV-vis absorption spectra with time-dependent density functional theory (TD-DFT). The MC-CASSCF calculations disclose a weak interaction between iron and the dioxygenic ligand and a dominant configuration with an essentially ferrous-superoxo character. The computed UV-vis absorption spectra reveal a marked dependence on the choice of density functional - both in terms of location of bands and in terms of orbital contributors. For the main band in the visible region, besides the recently reported thiolate-to-superoxide charge transfer, a more salient, and less functional-dependent, feature is a thiolate-to-ferric iron charge transfer, consistent with a ferric-peroxo electromer. By contrast, the computed UV-vis spectra of a ferric-hydroperoxo SOR model match distinctly better (and with no qualitative dependence on the DFT methodology) the 600-nm band as due to a mainly thiolate-to-ferric character - supporting the assignment of the SOR "600-nm intermediate" as a S=5/2 ferric-hydroperoxo species.

Iron-doped nickel oxide nanocrystals as highly efficient electrocatalysts for alkaline water splitting

Efficient electrochemical water splitting to hydrogen and oxygen is considered a promising technology to overcome our dependency on fossil fuels. Searching for novel catalytic materials for electrochemical oxygen generation is essential for improving the total efficiency of water splitting processes. We report the synthesis, structural characterization, and electrochemical performance in the oxygen evolution reaction of Fe-doped NiO nanocrystals. The facile solvothermal synthesis in tert-butanol leads to the formation of ultrasmall crystalline and highly dispersible FexNi1-xO nanoparticles with dopant concentrations of up to 20%. The increase in Fe content is accompanied by a decrease in particle size, resulting in nonagglomerated nanocrystals of 1.5-3.8 nm in size. The Fe content and composition of the nanoparticles are determined by X-ray photoelectron spectroscopy and energy-dispersive X-ray spectroscopy measurements, while Mössbauer and extended X-ray absorption fine structure analyses reveal a substitutional incorporation of Fe(III) into the NiO rock salt structure. The excellent dispersibility of the nanoparticles in ethanol allows for the preparation of homogeneous ca. 8 nm thin films with a smooth surface on various substrates. The turnover frequencies (TOF) of these films could be precisely calculated using a quartz crystal microbalance. Fe0.1Ni0.9O was found to have the highest electrocatalytic water oxidation activity in basic media with a TOF of 1.9 s(-1) at the overpotential of 300 mV. The current density of 10 mA cm(-2) is reached at an overpotential of 297 mV with a Tafel slope of 37 mV dec(-1). The extremely high catalytic activity, facile preparation, and low cost of the single crystalline FexNi1-xO nanoparticles make them very promising catalysts for the oxygen evolution reaction.

Redesigning the blue copper azurin into a redox-active mononuclear nonheme iron protein: preparation and study of Fe(II)-M121E azurin

Much progress has been made in designing heme and dinuclear nonheme iron enzymes. In contrast, engineering mononuclear nonheme iron enzymes is lagging, even though these enzymes belong to a large class that catalyzes quite diverse reactions. Herein we report spectroscopic and X-ray crystallographic studies of Fe(II)-M121E azurin (Az), by replacing the axial Met121 and Cu(II) in wild-type azurin (wtAz) with Glu and Fe(II), respectively. In contrast to the redox inactive Fe(II)-wtAz, the Fe(II)-M121EAz mutant can be readily oxidized by Na2IrCl6, and interestingly, the protein exhibits superoxide scavenging activity. Mössbauer and EPR spectroscopies, along with X-ray structural comparisons, revealed similarities and differences between Fe(II)-M121EAz, Fe(II)-wtAz, and superoxide reductase (SOR) and allowed design of the second generation mutant, Fe(II)-M121EM44KAz, that exhibits increased superoxide scavenging activity by 2 orders of magnitude. This finding demonstrates the importance of noncovalent secondary coordination sphere interactions in fine-tuning enzymatic activity.

Non-heme iron hydroperoxo species in superoxide reductase as a catalyst for oxidation reactions

The non-heme high-spin ferric iron hydroperoxo species formed in superoxide reductase can act both as a nucleophile and as an electrophile to catalyze oxidation reactions.

SORGOdb: Superoxide Reductase Gene Ontology curated DataBase

BACKGROUND

Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many sor remain anonymous or mis-annotated.

DESCRIPTION

SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010).

CONCLUSIONS

SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze sor in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at http://sorgo.genouest.org/index.php.

X-ray absorption spectroscopy and reactivity of thiolate-ligated Fe(III)-OOR complexes

The reaction of a series of thiolate-ligated iron(II) complexes [Fe(II)([15]aneN(4))(SC(6)H(5))]BF(4) (1), [Fe(II)([15]aneN(4))(SC(6)H(4)-p-Cl)]BF(4) (2), and [Fe(II)([15]aneN(4))(SC(6)H(4)-p-NO(2))]BF(4) (3) with alkylhydroperoxides at low temperature (-78 °C or -40 °C) leads to the metastable alkylperoxo-iron(III) species [Fe(III)([15]aneN(4))(SC(6)H(5))(OOtBu)]BF(4) (1a), [Fe(III)([15]aneN(4))(SC(6)H(4)-p-Cl)(OOtBu)]BF(4) (2a), and [Fe(III)([15]aneN(4))(SC(6)H(4)-p-NO(2))(OOtBu)]BF(4) (3a), respectively. X-ray absorption spectroscopy (XAS) studies were conducted on the Fe(III)-OOR complexes and their iron(II) precursors. The edge energy for the iron(II) complexes (∼7118 eV) shifts to higher energy upon oxidation by ROOH, and the resulting edge energies for the Fe(III)-OOR species range from 7121-7125 eV and correlate with the nature of the thiolate donor. Extended X-ray absorption fine structure (EXAFS) analysis of the iron(II) complexes 1-3 in CH(2)Cl(2) show that their solid state structures remain intact in solution. The EXAFS data on 1a-3a confirm their proposed structures as mononuclear, 6-coordinate Fe(III)-OOR complexes with 4N and 1S donors completing the coordination sphere. The Fe-O bond distances obtained from EXAFS for 1a-3a are 1.82-1.85 Å, significantly longer than other low-spin Fe(III)-OOR complexes. The Fe-O distances correlate with the nature of the thiolate donor, in agreement with the previous trends observed for ν(Fe-O) from resonance Raman (RR) spectroscopy, and supported by optimized geometries obtained from density functional theory (DFT) calculations. Reactivity and kinetic studies on 1a- 3a show an important influence of the thiolate donor.

Influence of the nitrogen donors on nonheme iron models of superoxide reductase: high-spin Fe(III)-OOR complexes

A new five-coordinate, (N(4)S(thiolate))Fe(II) complex, containing tertiary amine donors, [Fe(II)(Me(4)[15]aneN(4))(SPh)]BPh(4) (2), was synthesized and structurally characterized as a model of the reduced active site of superoxide reductase (SOR). Reaction of 2 with tert-butyl hydroperoxide (tBuOOH) at -78 degrees C led to the generation of the alkylperoxo-iron(III) complex [Fe(III)(Me(4)[15]aneN(4))(SPh)(OOtBu)](+) (2a). The nonthiolate-ligated complex, [Fe(II)(Me(4)[15]aneN(4))(OTf)(2)] (3), was also reacted with tBuOOH and yielded the corresponding alkylperoxo complex [Fe(III)(Me(4)[15]aneN(4))(OTf)(OOtBu)](+) (3a) at an elevated temperature of -23 degrees C. These species were characterized by low-temperature UV-vis, EPR, and resonance Raman spectroscopies. Complexes 2a and 3a exhibit distinctly different spectroscopic signatures than the analogous alkylperoxo complexes [Fe(III)([15]aneN(4))(SAr)(OOR)](+), which contain secondary amine donors. Importantly, alkylation at nitrogen leads to a change from low-spin (S = 1/2) to high-spin (S = 5/2) of the iron(III) center. The resonance Raman data reveal that this change in spin state has a large effect on the nu(Fe-O) and nu(O-O) vibrations, and a comparison between 2a and the nonthiolate-ligated complex 3a shows that axial ligation has an additional significant impact on these vibrations. To our knowledge this study is the first in which the influence of a ligand trans to a peroxo moiety has been evaluated for a structurally equivalent pair of high-spin/low-spin peroxo-iron(III) complexes. The implications of spin state and thiolate ligation are discussed with regard to the functioning of SOR.

Rational tuning of the thiolate donor in model complexes of superoxide reductase: direct evidence for a trans influence in Fe(III)-OOR complexes

Iron peroxide species have been identified as important intermediates in a number of nonheme iron as well as heme-containing enzymes, yet there are only a few examples of such species either synthetic or biological that have been well characterized. We describe the synthesis and structural characterization of a new series of five-coordinate (N4S(thiolate))Fe(II) complexes that react with tert-butyl hydroperoxide ((t)BuOOH) or cumenyl hydroperoxide (CmOOH) to give metastable alkylperoxo-iron(III) species (N4S(thiolate)Fe(III)-OOR) at low temperature. These complexes were designed specifically to mimic the nonheme iron active site of superoxide reductase, which contains a five-coordinate iron(II) center bound by one Cys and four His residues in the active form of the protein. The structures of the Fe(II) complexes are analyzed by X-ray crystallography, and their electrochemical properties are assessed by cyclic voltammetry. For the Fe(III)-OOR species, low-temperature UV-vis spectra reveal intense peaks between 500-550 nm that are typical of peroxide to iron(III) ligand-to-metal charge-transfer (LMCT) transitions, and EPR spectroscopy shows that these alkylperoxo species are all low-spin iron(III) complexes. Identification of the vibrational modes of the Fe(III)-OOR unit comes from resonance Raman (RR) spectroscopy, which shows nu(Fe-O) modes between 600-635 cm(-1) and nu(O-O) bands near 800 cm(-1). These Fe-O stretching frequencies are significantly lower than those found in other low-spin Fe(III)-OOR complexes. Trends in the data conclusively show that this weakening of the Fe-O bond arises from a trans influence of the thiolate donor, and density functional theory (DFT) calculations support these findings. These results suggest a role for the cysteine ligand in SOR, and are discussed in light of the recent assessments of the function of the cysteine ligand in this enzyme.

Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity

Superoxide reductase (SOR) is a non-heme iron enzyme that reduces superoxide to peroxide at a diffusion-controlled rate. Sulfur K-edge X-ray absorption spectroscopy (XAS) is used to investigate the ground-state electronic structure of the resting high-spin and CN- bound low-spin FeIII forms of the 1Fe SOR from Pyrococcus furiosus. A computational model with constrained imidazole rings (necessary for reproducing spin states), H-bonding interaction to the thiolate (necessary for reproducing Fe-S bond covalency of the high-spin and low-spin forms), and H-bonding to the exchangeable axial ligand (necessary to reproduce the ground state of the low-spin form) was developed and then used to investigate the enzymatic reaction mechanism. Reaction of the resting ferrous site with superoxide and protonation leading to a high-spin FeIII-OOH species and its subsequent protonation resulting in H2O2 release is calculated to be the most energetically favorable reaction pathway. Our results suggest that the thiolate acts as a covalent anionic ligand. Replacing the thiolate with a neutral noncovalent ligand makes protonation very endothermic and greatly raises the reduction potential. The covalent nature of the thiolate weakens the FeIII bond to the proximal oxygen of this hydroperoxo species, which raises its pKa by an additional 5 log units relative to the pKa of a primarily anionic ligand, facilitating its protonation. A comparison with cytochrome P450 indicates that the stronger equatorial ligand field from the porphyrin results in a low-spin FeIII-OOH species that would not be capable of efficient H2O2 release due to a spin-crossing barrier associated with formation of a high-spin 5C FeIII product. Additionally, the presence of the dianionic porphyrin pi ring in cytochrome P450 allows O-O heterolysis, forming an FeIV-oxo porphyrin radical species, which is calculated to be extremely unfavorable for the non-heme SOR ligand environment. Finally, the 5C FeIII site that results from the product release at the end of the O2- reduction cycle is calculated to be capable of reacting with a second O2-, resulting in superoxide dismutase (SOD) activity. However, in contrast to FeSOD, the 5C FeIII site of SOR, which is more positively charged, is calculated to have a high affinity for binding a sixth anionic ligand, which would inhibit its SOD activity.

Assessing the role of the active-site cysteine ligand in the superoxide reductase from Desulfoarculus baarsii

Superoxide reductase is a novel class of non-heme iron proteins that catalyzes the one-electron reduction of O(2)(.) to H(2)O(2), providing an antioxidant defense in some bacteria. Its active site consists of an unusual non-heme Fe(2+) center in a [His(4) Cys(1)] square pyramidal pentacoordination. In this class of enzyme, the cysteine axial ligand has been hypothesized to be an essential feature in the reactivity of the enzyme. Previous Fourier transform infrared spectroscopy studies on the enzyme from Desulfoarculus baarsii revealed that a protonated carboxylate group, proposed to be the side chain of Glu(114), is in interaction with the cysteine ligand. In this work, using pulse radiolysis, Fourier transform infrared, and resonance Raman spectroscopies, we have investigated to what extent the presence of this Glu(114) carboxylic lateral chain affects the strength of the S-Fe bond and the reaction of the iron active site with superoxide. The E114A mutant shows significantly modified pulse radiolysis kinetics for the protonation process of the first reaction intermediate. Resonance Raman spectroscopy demonstrates that the E114A mutation results in both a strengthening of the S-Fe bond and an increase in the extent of freeze-trapping of a Fe-peroxo species after treatment with H(2)O(2) by a specific strengthening of the Fe-O bond. A fine tuning of the strength of the S-Fe bond by the presence of Glu(114) appears to be an essential factor for both the strength of the Fe-O bond and the pK(a) value of the Fe(3+)-peroxo intermediate species to form the reaction product H(2)O(2).

Iron(III) Complex of a Crown Ether−Porphyrin Conjugate and Reversible Binding of Superoxide to Its Iron(II) Form

The synthesis and characterization of the Fe(III) complex of a novel crown ether-porphyrin conjugate, 52-N-(4-aza-18-crown-6)methyl-54,104,154,204-tetra-tert-butyl-56-methyl-5,10,15,20-tetraphenylporphyrin (H2Porph), as well as the corresponding hydroxo, dimeric, Fe(II), and peroxo species are reported. The crystal structure of [FeIII(Porph)Cl].H3O+.FeCl4-.C6H6.EtOH is also reported. [FeIII(Porph)(DMSO)2]+ and K[FeIII(Porph)(O22-)] are high-spin species (Mössbauer data: delta = 0.38 mm s(-1), DeltaEq = 0.83 mm s(-1) and delta = 0.41 mm s(-1), DeltaEq = 0.51 mm s(-1), respectively), whereas in a solution of reduced [FeIII(Porph)(DMSO)2]+ complex the low-spin [FeII(Porph)(DMSO)2] (delta = 0.44 mm s(-1), DeltaEq = 1.32 mm s(-1)) and high-spin [FeII(Porph)(DMSO)] (delta = 1.27 mm s(-1), DeltaEq = 3.13 mm s(-1)) iron(II) species are observed. The reaction of [FeIII(Porph)(DMSO)2]+ with KO2 in DMSO has been investigated. The first reaction step, involving reduction to [FeII(Porph)(DMSO)2], was not investigated in detail because of parallel formation of an Fe(III)-hydroxo species. The kinetics and thermodynamics of the second reaction step, reversible binding of superoxide to the Fe(II) complex and formation of an Fe(III)-peroxo species, were studied in detail (by stopped-flow time-resolved UV/vis measurements in DMSO at 25 degrees C), resulting in kon = 36 500 +/- 500 M(-1) s(-1), koff = 0.21 +/- 0.01 s(-1) (direct measurements using an acid as a superoxide scavenger), and KO2- = (1.7 +/- 0.2) x 10(5) (superoxide binding constant kinetically obtained as kon/koff), (1.4 +/- 0.1) x 10(5), and (9.0 +/- 0.1) x 10(4) M(-1) (thermodynamically obtained in the absence and in the presence of 0.1 M NBu4PF6, respectively). Temperature-dependent kinetic measurements for kon (-40 to 25 degrees C in 3:7 DMSO/CH3CN mixture) yielded the activation parameters DeltaH = 61.2 +/- 0.9 kJ mol(-1) and DeltaS = +48 +/- 3 J K(-1) mol(-1). The observed reversible binding of superoxide to the metal center and the obtained kinetic and thermodynamic parameters are unique. The finding that fine-tuning of the proton concentration can cause the Fe(III)-peroxo species to release O2- and form an Fe(II) species is of biological interest, since this process might occur under very specific physiological conditions.

Comparing the electronic properties of the low-spin cyano-ferric [Fe(N4)(Cys)] active sites of superoxide reductase and p450cam using ENDOR spectroscopy and DFT calculations

Superoxide reductase (SOR) and P450 enzymes contain similar [Fe(N)4(SCys)] active sites and, although they catalyze very different reactions, are proposed to involve analogous low-spin (hydro)peroxo-Fe(III) intermediates in their respective mechanisms that can be modeled by cyanide binding. The equatorial FeN4 ligation by four histidine ligands in CN-SOR and the heme in CN-P450cam is directly compared by 14N ENDOR, while the axial Fe-CN and Fe-S bonding is probed by 13C ENDOR of the cyanide ligand and 1Hbeta ENDOR measurements to determine the spin density delocalization onto the cysteine sulfur. There are small, but notable, differences in the bonding between Fe(III) and its ligands in the two enzymes. The ENDOR measurements are complemented by DFT computations that support the semiempirical equation used to compute spin densities on metal-coordinated cysteinyl and shed light on bonding changes as the Fe-C-N linkage bends. They further indicate that H bonds to the cysteinyl thiolate sulfur ligand reduce the spin density on the sulfur in both active sites to a degree that exceeds the difference induced by the alternative sets of "in-plane" nitrogen ligands.

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.

A functional model for the cysteinate-ligated non-heme iron enzyme superoxide reductase (SOR)

Superoxide reductases (SORs) are cysteine-ligated, non-heme iron enzymes that reduce toxic superoxide radicals (O2-). The functional role of the trans cysteinate, as well as the mechanism by which SOR reduces O2-, is unknown. Herein is described a rare example of a functional metalloenzyme analogue, which catalytically reduces superoxide in a proton-dependent mechanism, via a trans thiolate-ligated iron-peroxo intermediate, the first example of its type. Acetic-acid-promoted H2O2 release, followed by Cp2Co reduction, regenerates the active Fe(II) catalyst. The thiolate ligand and its trans positioning relative to the substrate are shown to contribute significantly to the catalyst's function, by lowering the redox potential, changing the spin state, and dramatically lowering the nuFe-O stretching frequency well-below that of any other reported iron-peroxo, while leaving nuO-O high, so as to favor superoxide reduction and Fe-O, as opposed to O-O, bond cleavage. Thus we provide critical insight into the relationship between the SOR structure and its function, as well as important benchmark parameters for characterizing highly unstable thiolate-ligated iron-peroxo intermediates.

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.

Avoiding high-valent iron intermediates: superoxide reductase and rubrerythrin

The Fenton or Fenton-type reaction between aqueous ferrous ion and hydrogen peroxide generates a highly oxidizing species, most often formulated as hydroxyl radical or ferryl ([Fe(IV)O](2+)). Intracellular Fenton-type chemistry can be lethal if not controlled. Nature has, therefore, evolved enzymes to scavenge superoxide and hydrogen peroxide, the reduced dioxygen species that initiate intracellular Fenton-type chemistry. Two such enzymes found predominantly in air-sensitive bacteria and archaea, superoxide reductase (SOR) and rubrerythrin (Rbr), functioning as a peroxidase (hydrogen peroxide reductase), contain non-heme iron. The iron coordination spheres in these enzymes contain five or six protein ligands from His and Glu residues, and, in the case of SOR, a Cys residue. SOR contains a mononuclear active site that is designed to protonate and rapidly expel peroxide generated as a product of the enzymatic reaction. The ferrous SOR reacts adventitiously but relatively slowly (several seconds to a few minutes) with exogenous hydrogen peroxide, presumably in a Fenton-type reaction. The diferrous active site of Rbr reacts more rapidly with hydrogen peroxide but can divert Fenton-type reactions towards the two-electron reduction of hydrogen peroxide to water. Proximal aromatic residues may function as radical sinks for Fenton-generated oxidants. Fenton-initiated damage to these iron active sites may become apparent only under extremely oxidizing intracellular conditions.

Geometries and electronic structures of cyanide adducts of the non-heme iron active site of superoxide reductases: vibrational and ENDOR studies

We have added cyanide to oxidized 1Fe and 2Fe superoxide reductase (SOR) as a surrogate for the putative ferric-(hydro)peroxo intermediate in the reaction of the enzymes with superoxide and have used vibrational and ENDOR spectroscopies to study the properties of the active site paramagnetic iron center. Addition of cyanide changes the active site iron center in oxidized SOR from rhombic high-spin ferric (S = 5/2) to axial-like low-spin ferric (S = 1/2). Low-temperature resonance Raman and ENDOR data show that the bound cyanide adopts three distinct conformations in Fe(III)-CN SOR. On the basis of 13CN, C15N, and 13C15N isotope shifts of the Fe-CN stretching/Fe-C-N bending modes, resonance Raman studies of 1Fe-SOR indicate one near-linear conformation (Fe-C-N angle approximately 175 degrees) and two distinct bent conformations (Fe-C-N angles <140 degrees). FTIR studies of 1Fe-SOR at ambient temperatures reveals three bound C-N stretching frequencies in the oxidized (ferric) state and one in the reduced (ferrous) state, indicating that the conformational heterogeneity in cyanide binding is a characteristic of the ferric state and is not caused by freezing-in of conformational substates at low temperature. 13C-ENDOR spectra for the 13CN-bound ferric active sites in both 1Fe- and 2Fe-SORs also show three well-resolved Fe-C-N conformations. Analysis of the 13C hyperfine tensors for the three substates of the 2Fe-SOR within a simple heuristic model for the Fe-C bonding gives values for the Fe-C-N angles in the three substates of ca. 123 degrees (C3) and 133 degrees (C2), taking a reference value from vibrational studies of 175 degrees (C1 species). Resonance Raman and ENDOR studies of SOR variants, in which the conserved glutamate and lysine residues in a flexible loop above the substrate binding pocket have been individually replaced by alanine, indicate that the side chains of these two residues are not involved in direct interaction with bound cyanide. The implications of these results for understanding the mechanism of SOR are discussed.

Fe3+–η2–peroxo species in superoxide reductase from Treponema pallidum. Comparison with Desulfoarculus baarsii

Superoxide reductases (SORs) are superoxide (O2-)-detoxifying enzymes that catalyse the reduction of O2- into hydrogen peroxide. Three different classes of SOR have been reported on the basis of the presence or not of an additional N-terminal domain. They all share a similar active site, with an unusual non-heme Fe atom coordinated by four equatorial histidines and one axial cysteine residues. Crucial catalytic reaction intermediates of SOR are purported to be Fe(3+)-(hydro)peroxo species. Using resonance Raman spectroscopy, we compared the vibrational properties of the Fe3+ active site of two different classes of SOR, from Desulfoarculus baarsii and Treponema pallidum, along with their ferrocyanide and their peroxo complexes. In both species, rapid treatment with H2O2 results in the stabilization of a side-on high spin Fe(3+)-(eta(2)-OO) peroxo species. Comparison of these two peroxo species reveals significant differences in vibrational frequencies and bond strengths of the Fe-O2 (weaker) and O-O (stronger) bonds for the T. pallidum enzyme. Thus, the two peroxo adducts in these two SORs have different stabilities which are also seen to be correlated with differences in the Fe-S coordination strengths as gauged by the Fe-S vibrational frequencies. This was interpreted from structural variations in the two active sites, resulting in differences in the electron donating properties of the trans cysteine ligand. Our results suggest that the structural differences observed in the active site of different classes of SORs should be a determining factor for the rate of release of the iron-peroxo intermediate during enzymatic turnover.

Fe3+-Hydroxide Ligation in the Superoxide Reductase from Desulfoarculus baarsii Is Associated with pH Dependent Spectral Changes

Superoxide reductase (SOR) catalyzes the reduction of O2*- to H2O2. Its active site consists of a non-heme Fe2+ center in an unusual square-pyramidal [His4 Cys] coordination. Like many SORs, the electronic absorption band corresponding to the oxidized active site of the SOR from Desulfoarculus baarsii exhibits a pH-dependent alkaline transition changing from ca. 644 to 560 nm as the pH increases and with an apparent pKa of 9.0. Variants in which the conserved amino acids glutamate 47 and lysine 48 were replaced by the neutral residues alanine (E47A) and isoleucine (K48I), respectively, exhibited the same alkaline transition but at lower apparent pKa values of 6.7 and 7.6, respectively. Previous work [Nivière, V.; Asso, M.; Weill, C. O.; Lombard, M.; Guigliarelli, B.; Favaudon, V.; Houée-Levin, C. Biochemistry 2004, 43, 808-818] has shown that this alkaline transition is associated with the protonation/deprotonation of an unidentified base, B-, which is neither E47 nor K48. In this work, we show by resonance Raman spectroscopy that at basic pH a high-spin Fe3+-OH species is formed at the active site. The presence of the HO- ligand was directly associated with an absorption band maximum at 560 nm, whereas upon protonation, the band shifts to 644 nm. With respect to our previous work, B- can be identified with this high-spin Fe3+-OH species, which upon protonation results in a water molecule at the active site. Implications for the SOR catalytic cycle are proposed.

Microbial detoxification of superoxide: the non-heme iron reductive paradigm for combating oxidative stress

A reductive paradigm has emerged in recent years for detoxification of superoxide and other redox active diatomic molecules in air-sensitive bacteria and archaea. Adventitiously generated superoxide in many anaerobic or microaerophilic bacteria and archaea is scavenged by superoxide reductase (SOR) rather than the classical superoxide dismutases characteristic of aerobic microbes. SORs contain a novel five-coordinate, square-pyramidal [Fe(His)4(Cys)] ferrous active site, which adds a sixth glutamate ligand upon oxidation. This Account summarizes the recently elucidated structural and mechanistic features of SORs. The non-heme iron reductive scavenging paradigm in these air-sensitive microbes also extends to recently characterized enzymes that scavenge hydrogen peroxide and nitric oxide and to oxygen sensing proteins.