On the two iron centers of desulfoferrodoxin

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

Linear nitramines (R-N(R')NO2; R' = H or alkyl) are toxic compounds, some with environmental relevance, while others are rare natural product nitramines. One of these natural product nitramines is N-nitroglycine (NNG), which is produced by some Streptomyces strains and exhibits antibiotic activity towards Gram-negative bacteria. An NNG degrading heme enzyme, called NnlA, has recently been discovered in the genome of Variovorax sp. strain JS1663 (Vs NnlA). Evidence is presented that NnlA and therefore, NNG degradation activity is widespread. To achieve this objective, we characterized and tested the NNG degradation activity of five Vs NnlA homologs originating from bacteria spanning several classes and isolated from geographically distinct locations. E. coli transformants containing all five homologs converted NNG to nitrite. Four of these five homologs were isolated and characterized. Each isolated homolog exhibited similar oligomerization and heme occupancy as Vs NnlA. Reduction of this heme was shown to be required for NnlA activity in each homolog, and each homolog degraded NNG to glyoxylate, NO2- and NH4+ in accordance with observations of Vs NnlA. It was also shown that NnlA cannot degrade the NNG analog 2-nitroaminoethanol. The combined data strongly suggest that NnlA enzymes specifically degrade NNG and are found in diverse bacteria and environments. These results imply that NNG is also produced in diverse environments and NnlA may act as a detoxification enzyme to protect bacteria from exposure to NNG.

New spectroscopic and electrochemical insights on a class I superoxide reductase: evidence for an intramolecular electron-transfer pathway

SORs (superoxide reductases) are enzymes involved in bacterial resistance to reactive oxygen species, catalysing the reduction of superoxide anions to hydrogen peroxide. So far three structural classes have been identified. Class I enzymes have two iron-centre-containing domains. Most studies have focused on the catalytic iron site (centre II), yet the role of centre I is poorly understood. The possible roles of this iron site were approached by an integrated study using both classical and fast kinetic measurements, as well as direct electrochemistry. A new heterometallic form of the protein with a zinc-substituted centre I, maintaining the iron active-site centre II, was obtained, resulting in a stable derivative useful for comparison with the native all-iron from. Second-order rate constants for the electron transfer between reduced rubredoxin and the different SOR forms were determined to be 2.8×107 M−1·s−1 and 1.3×106 M−1·s−1 for SORFe(IIII)-Fe(II) and for SORFe(IIII)-Fe(III) forms respectively, and 3.2×106 M−1·s−1 for the SORZn(II)-Fe(III) form. The results obtained seem to indicate that centre I transfers electrons from the putative physiological donor rubredoxin to the catalytic active iron site (intramolecular process). In addition, electrochemical results show that conformational changes are associated with the redox state of centre I, which may enable a faster catalytic response towards superoxide anion. The apparent rate constants calculated for the SOR-mediated electron transfer also support this observation.

Kinetics studies of the superoxide-mediated electron transfer reactions between rubredoxin-type proteins and superoxide reductases

In this work we present a kinetic study of the superoxide-mediated electron transfer reactions between rubredoxin-type proteins and members of the three different classes of superoxide reductases (SORs). SORs from the sulfate-reducing bacteria Desulfovibrio vulgaris (Dv) and D. gigas (Dg) were chosen as prototypes of classes I and II, respectively, while SOR from the syphilis spirochete Treponema pallidum (Tp) was representative of class III. Our results show evidence for different behaviors of SORs toward electron acceptance, with a trend to specificity for the electron donor and acceptor from the same organism. Comparison of the different kapp values, 176.9+/-25.0 min(-1) in the case of the Tp/Tp electron transfer, 31.8+/-3.6 min(-1) for the Dg/Dg electron transfer, and 6.9+/-1.3 min(-1) for Dv/Dv, could suggest an adaptation of the superoxide-mediated electron transfer efficiency to various environmental conditions. We also demonstrate that, in Dg, another iron-sulfur protein, a desulforedoxin, is able to transfer electrons to SOR more efficiently than rubredoxin, with a kapp value of 108.8+/-12.0 min(-1), and was then assigned as the potential physiological electron donor in this organism.

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.

EPR spectroscopy as a probe of metal centres in biological systems

Molecular paramagnetism pervades the bioinorganic chemistry of V, Mn, Fe, Co, Ni, Cu, Mo, W, and of a number of non-biological transition elements. To date we can look back at half a century of fruitful EPR studies on metalloproteins, and against this background evaluate the significance of modern EPR spectroscopy from the perspective of a biochemist, making a distinction between conventional continuous wave X-band spectroscopy as a reliable work horse with broad, established applicability even on crude preparations, vs. a diffuse set of "advanced EPR" technologies whose practical application typically calls for narrowly focused research hypotheses and very high quality samples. The type of knowledge on metalloproteins that is readily obtainable with EPR spectroscopy, is explained with illustrative examples, as is the relation between experimental complexity and the spin value of the system.

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.

Spectroscopic characterization of the [Fe(His)(4)(Cys)] site in 2Fe-superoxide reductase from Desulfovibrio vulgaris

The electronic and vibrational properties of the [Fe(His)(4)(Cys)] site (Center II) responsible for catalysis of superoxide reduction in the two-iron superoxide reductase (2Fe-SOR) from Desulfovibrio vulgaris have been investigated using the combination of EPR, resonance Raman, UV/visible/near-IR absorption, CD, and VTMCD spectroscopies. Deconvolution of the spectral contributions of Center II from those of the [Fe(Cys)(4)] site (Center I) has been achieved by parallel investigations of the C13S variant, which does not contain Center I. The resonance Raman spectrum of ferric Center II has been assigned based on isotope shifts for (34)S and (15)N globally labeled proteins. As for the [Fe(His)(4)(Cys)] active site in 1Fe-SOR from Pyrococcus furiosus, the spectroscopic properties of ferric and ferrous Center II in D. vulgaris 2Fe-SOR are indicative of distorted octahedral and square-pyramidal coordination geometries, respectively. Differences in the properties of the ferric [Fe(His)(4)(Cys)] sites in 1Fe- and 2Fe-SORs are apparent in the rhombicity of the S=5/2 ground state ( E/ D=0.06 and 0.28 in 1Fe- and 2Fe-SORs, respectively), the energy of the CysS(-)(p(pi))-->Fe(3+)(d(pi)) CT transition (15150+/-150 cm(-1) and 15600+/-150 cm(-1) in 1Fe- and 2Fe-SORs, respectively) and in changes in the Fe-S stretching region of the resonance Raman spectrum indicative of a weaker Fe-S(Cys) bond in 2Fe-SORs. These differences are interpreted in terms of small structural perturbations in the Fe coordination sphere with changes in the Fe-S(Cys) bond strength resulting from differences in the peptide N-H.S(Cys) hydrogen bonding within a tetrapeptide bidentate "chelate". Observation of the characteristic intervalence charge transfer transition of a cyano-bridged [Fe(III)-NC-Fe(II)(CN)(5)] unit in the near-IR VTMCD spectra of ferricyanide-oxidized samples of both P. furiosus 1Fe-SOR and D. vulgaris 2Fe-SOR has confirmed the existence of novel ferrocyanide adducts of the ferric [Fe(His)(4)(Cys)] sites in both 1Fe- and 2Fe-SORs.

An engineered two-iron superoxide reductase lacking the [Fe(SCys)4] site retains its catalytic properties in vitro and in vivo

Superoxide reductases (SORs) contain a characteristic square-pyramidal [Fe(NHis)(4)(SCys)] active site that catalyzes reduction of superoxide to hydrogen peroxide in several anaerobic bacteria and archaea. Some SORs, referred to as two-iron SORs (2Fe-SORs), also contain a lower-potential [Fe(SCys)(4)] site that is presumed to have an electron transfer function. However, the intra- and inter-subunit distances between [Fe(SCys)(4)] and [Fe(NHis)(4)(SCys)] iron centers within the 2Fe-SOR homodimer seem too long for efficient electron transfer between these sites. The possible role of the [Fe(SCys)(4)] site in 2Fe-SORs was addressed in this work by examination of an engineered Desulfovibrio vulgaris 2Fe-SOR variant, C13S, in which one ligand residue of the [Fe(SCys)(4)] site, cysteine 13, was changed to serine. This single amino acid residue change destroyed the native [Fe(SCys)(4)] site with complete loss of its iron, but left the [Fe(NHis)(4)(SCys)] site and the protein homodimer intact. The spectroscopic, redox and superoxide reactivity properties of the [Fe(NHis)(4)(SCys)] site in the C13S variant were nearly indistinguishable from those of the wild-type 2Fe-SOR. Aerobic growth complementation of a superoxide dismutase (SOD)-deficient Escherichia coli strain showed that the presence of the [Fe(NHis)(4)(SCys)] site in C13S 2Fe-SOR was apparently sufficient to catalyze reduction of the intracellular superoxide to nonlethal levels. As is the case for the wild-type protein, C13S 2Fe-SOR did not show any detectable SOD activity, i.e., destruction of the [Fe(SCys)(4)] site did not unmask latent SOD activity of the [Fe(NHis)(4)(SCys)] site. Possible alternative roles for the [Fe(SCys)(4)] site in 2Fe-SORs are considered.

Superoxide reductase activities of neelaredoxin and desulfoferrodoxin metalloproteins

Superoxide reductases have now been well characterized from several organisms. Unique biochemical features include the ability of the reduced enzyme to react with O2- but not dioxygen (reduced SORs are stable in an aerobic atmosphere for hours). Future biochemical assays that measure the reaction of SOR with O2- should take into account the difficulties of assaying O2- directly and the myriad of redox reactions that can take place between components in the assay, for example, direct electron transfer between cytochrome c and Dfx. Future prospects include further delineation of the reaction mechanisms, characterization of the putative (hydro)peroxo intermediate, and studies that uncover the components between reduced pyridine nucleotides and SOR in the metabolic pathway responsible for O2- detoxification.

A role for rubredoxin in oxidative stress protection in Desulfovibrio vulgaris: catalytic electron transfer to rubrerythrin and two-iron superoxide reductase

Desulfovibrio vulgaris rubredoxin, which contains a single [Fe(SCys)4] site, is shown to be a catalytically competent electron donor to two enzymes from the same organism, namely, rubrerythrin and two-iron superoxide reductase (a.k.a. rubredoxin oxidoreductase or desulfoferrodoxin). These two enzymes have been implicated in catalytic reduction of hydrogen peroxide and superoxide, respectively, during periods of oxidative stress in D. vulgaris, but their proximal electron donors had not been characterized. We further demonstrate the incorrectness of a previous report that rubredoxin is not an electron donor to the superoxide reductase and describe convenient assays for demonstrating the catalytic competence of all three proteins in their respective functions. Rubrerythrin is shown to be an efficient rubredoxin peroxidase in which the rubedoxin:hydrogen peroxide redox stoichiometry is 2:1 mol:mol. Using spinach ferredoxin-NADP+ oxidoreductase (FNR) as an artificial, but proficient, NADPH:rubredoxin reductase, rubredoxin was further found to catalyze rapid and complete reduction of all Fe3+ to Fe2+ in rubrerythrin by NADPH under anaerobic conditions. The combined system, FNR/rubredoxin/rubrerythrin, was shown to function as a catalytically competent NADPH peroxidase. Another small rubredoxin-like D. vulgaris protein, Rdl, could not substitute for rubredoxin as a peroxidase substrate of rubrerythrin. Similarly, D. vulgaris rubredoxin was demonstrated to efficiently catalyze reduction of D. vulgaris two-iron superoxide reductase and, when combined with FNR, to function as an NADPH:superoxide oxidoreductase. We suggest that, during periods of oxidative stress, rubredoxin could divert electron flow from the electron transport chain of D. vulgaris to rubrerythrin and superoxide reductase, thereby simultaneously protecting autoxidizable redox enzymes and lowering intracellular hydrogen peroxide and superoxide levels.

Equilibrium unfolding of dimeric desulfoferrodoxin involves a monomeric intermediate: iron cofactors dissociate after polypeptide unfolding

Here we report the conformational stability of homodimeric desulfoferrodoxin (dfx) from Desulfovibrio desulfuricans (ATCC 27774). The dimer is formed by two dfx monomers linked through beta-strand interactions in two domains; in addition, each monomer contains two different iron centers: one Fe-(S-Cys)(4) center and one Fe-[S-Cys+(N-His)(4)] center. The dissociation constant for dfx was determined to be 1 microM (DeltaG = 34 kJ/mol of dimer) from the concentration dependence of aromatic residue emission. Upon addition of the chemical denaturant guanidine hydrochloride (GuHCl) to dfx, a reversible fluorescence change occurred at 2-3 M GuHCl. This transition was dependent upon protein concentration, in accord with a dimer to monomer reaction [DeltaG(H(2)O) = 46 kJ/mol of dimer]. The secondary structure did not disappear, according to far-UV circular dichroism (CD), until 6 M GuHCl was added; this transition was reversible (for incubation times of < 1 h) and independent of dfx concentration [DeltaG(H(2)O) = 50 kJ/mol of monomer]. Thus, dfx equilibrium unfolding is at least three-state, involving a monomeric intermediate with native-like secondary structure. Only after complete polypeptide unfolding (and incubation times of > 1 h) did the iron centers dissociate, as monitored by disappearance of ligand-to-metal charge transfer absorption, fluorescence of an iron indicator, and reactivity of cysteines to Ellman's reagent. Iron dissociation took place over several hours and resulted in an irreversibly denatured dfx. It appears as if the presence of the iron centers, the amino acid composition, and, to a lesser extent, the dimeric structure are factors that aid in facilitating dfx's unusually high thermodynamic stability for a mesophilic protein.

Reaction of the desulfoferrodoxin from Desulfoarculus baarsii with superoxide anion. Evidence for a superoxide reductase activity

Desulfoferrodoxin is a small protein found in sulfate-reducing bacteria that contains two independent mononuclear iron centers, one ferric and one ferrous. Expression of desulfoferrodoxin from Desulfoarculus baarsii has been reported to functionally complement a superoxide dismutase deficient Escherichia coli strain. To elucidate by which mechanism desulfoferrodoxin could substitute for superoxide dismutase in E. coli, we have purified the recombinant protein and studied its reactivity toward O-(2). Desulfoferrodoxin exhibited only a weak superoxide dismutase activity (20 units mg(-1)) that could hardly account for its antioxidant properties. UV-visible and electron paramagnetic resonance spectroscopy studies revealed that the ferrous center of desulfoferrodoxin could specifically and efficiently reduce O-(2), with a rate constant of 6-7 x 10(8) M(-1) s(-1). In addition, we showed that membrane and cytoplasmic E. coli protein extracts, using NADH and NADPH as electron donors, could reduce the O-(2) oxidized form of desulfoferrodoxin. Taken together, these results strongly suggest that desulfoferrodoxin behaves as a superoxide reductase enzyme and thus provide new insights into the biological mechanisms designed for protection from oxidative stresses.

The superoxide dismutase activity of desulfoferrodoxin from Desulfovibrio desulfuricans ATCC 27774

Desulfoferrodoxin (Dfx), a small iron protein containing two mononuclear iron centres (designated centre I and II), was shown to complement superoxide dismutase (SOD) deficient mutants of Escherichia coli [Pianzzola, M.J., Soubes M. & Touati, D. (1996) J. Bacteriol. 178, 6736-6742]. Furthermore, neelaredoxin, a protein from Desulfovibrio gigas containing an iron site similar to centre II of Dfx, was recently shown to have a significant SOD activity [Silva, G., Oliveira, S., Gomes, C.M., Pacheco, I., Liu, M.Y., Xavier, A.V., Teixeira, M., Le Gall, J. & Rodrigues-Pousada, C. (1999) Eur. J. Biochem. 259, 235-243]. Thus, the SOD activity of Dfx isolated from the sulphate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 was studied. The protein exhibits a SOD activity of 70 U x mg-1, which increases approximately 2.5-fold upon incubation with cyanide. Cyanide binds specifically to Dfx centre II, yielding a low-spin iron species with g-values at 2.27 (g perpendicular) and 1.96 (g parallel). Upon reaction of fully oxidized Dfx with the superoxide generating system xanthine/xanthine oxidase, Dfx centres I and II become partially reduced, suggesting that Dfx operates by a redox cycling mechanism, similar to those proposed for other SODs. Evidence for another SOD in D. desulfuricans is also presented - this enzyme is inhibited by cyanide, and N-terminal sequence data strongly indicates that it is an analogue to Cu,Zn-SODs isolated from other sources. This is the first indication that a Cu-containing protein may be present in a sulphate-reducing bacterium.

Cloning and expression of the rubredoxin gene from Desulfovibrio vulgaris (Miyazaki F)--comparison of the primary structure of desulfoferrodoxin

A gene encoding rubredoxin from Desulfovibrio vulgaris (Miyazaki F) was cloned and overexpressed in Escherichia coli. A 1.1-kilobase pair DNA fragment, isolated from D. vulgaris (Miyazaki F) by double digestion with SmaI and SalI, contained two genes, the rubredoxin gene (rub) and the desulfoferrodoxin gene (rbo) which was situated upstream of rub. The deduced amino acid sequence of desulfoferrodoxin was homologous to those from other strains and Cys residues that are responsible to bind irons were also conserved. The expression system for rub was constructed under the control of the T7 promoter in E. coli. The purified protein was soluble and had a characteristic visible absorption spectrum. Inductively coupled plasma-atomic emission analysis and electron paramagnetic resonance analysis of the recombinant rubredoxin revealed the presence of an iron ion in a distorted tetrahedral geometry that was the same as native D. vulgaris rubredoxin. In vitro NADH reduction analysis indicated that recombinant rubredoxin was active, and its redox potential was determined as -5 mV.

Primary structure of desulfoferrodoxin from Desulfovibrio desulfuricans ATCC 27774, a new class of non-heme iron proteins

The primary structure of desulfoferrodoxin from Desulfovibrio desulfuricans ATCC 27774, a redox protein with two mononuclear iron sites, was determined by automatic Edman degradation and mass spectrometry of the composing peptides. It contains 125 amino acid residues of which five are cysteines. The first four, Cys-9, Cys-12, Cys-28 and Cys-29, are responsible for the binding of Center I which has a distorted tetrahedral sulfur coordination similar to that found in desulforedoxin from D. gigas. The remaining Cys-115 is proposed to be involved in the coordination of Center II, which is probably octahedrally coordinated with predominantly nitrogen/oxygen containing ligands as previously suggested by Mössbauer and Raman spectroscopy.

Expression of Desulfovibrio gigas desulforedoxin in Escherichia coli. Purification and characterization of mixed metal isoforms

The dsr gene from Desulfovibrio gigas encoding the nonheme iron protein desulforedoxin was cloned using the polymerase chain reaction, expressed in Escherichia coli, and purified to homogeneity. The physical and spectroscopic properties of the recombinant protein resemble those observed for the native protein isolated from D. gigas. These include an alpha 2 tertiary structure, the presence of bound iron, and absorbance maxima at 370 and 506 nm in the UV/visible spectrum due to ligand-to-iron charge transfer bands. Low temperature electron paramagnetic resonance studies confirm the presence of a high-spin ferric ion with g values of 7.7, 5.7, 4.1, and 1.8. Interestingly, E. coli produced two forms of desulforedoxin containing iron. One form was identified as a dimer with the metal-binding sites of both subunits occupied by iron while the second form contained equivalent amounts of iron and zinc and represents a dimer with one subunit occupied by iron and the second with zinc.

A blue non-heme iron protein from Desulfovibrio gigas

A novel iron-containing blue protein, named neelaredoxin, was isolated from the sulfate-reducing bacterium Desulfovibrio gigas. It is a monomeric protein with a molecular mass of 15 kDa containing two iron atoms/molecule. The N-terminal sequence of neelaredoxin has similarity to the second domain of desulfoferrodoxin, a protein purified from Desulfovibrio vulgaris Hildenborough. This finding supports the hypothesis that the gene coding for desulfoferrodoxin (rbo) might have arisen from a gene fusion [Brumlik, M. J., Leroy, G., Bruschi, M. & Voordouw, G. (1990) J. Bacteriol. 172, 7289-7292]. The visible spectrum exhibits a single band at 666 nm, responsible for the blue color of the protein, which is completely bleached upon reduction with sodium ascorbate. In the oxidized state the EPR spectrum is complex, exhibiting well-resolved features at g = 7.6, 7.0, 5.9, and 5.8 which are assigned to two high-spin (S = 5/2) mononuclear-iron (III) centers with different rhombic distortions (E/D approximately 0.05 and approximately 0.08). The two iron atoms contribute identically to the visible spectrum as judged from visible redox titrations, from which a reduction potential of +190 mV was determined for both iron sites at pH 7.5. At high pH the visible and the EPR spectra become pH-dependent with a pKa above 9: the 666-nm band shifts to 590 nm and the EPR signals are converted into a signal with gmax approximately 4.7. Neelaredoxin is readily reduced both by H2/hydrogenase/cytochrome c3 and by NADH/NADH-rubredoxin oxidoreductase.