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

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.

Spectroscopic and Computational Comparisons of Thiolate-Ligated Ferric Nonheme Complexes to Cysteine Dioxygenase: Second-Sphere Effects on Substrate (Analogue) Positioning

Parallel spectroscopic and computational studies of iron(III) cysteine dioxygenase (CDO) and synthetic models are presented. The synthetic complexes utilize the ligand tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (^Ph2TIP), which mimics the facial three-histidine triad of CDO and other thiol dioxygenases. In addition to the previously reported [Fe^II(CysOEt)(^Ph2TIP)]BPh₄ (1; CysOEt is the ethyl ester of anionic l-cysteine), the formation and crystallographic characterization of [Fe^II(2-MTS)(^Ph2TIP)]BPh₄ (2) is reported, where the methyl 2-thiosalicylate anion (2-MTS) resembles the substrate of 3-mercaptopropionate dioxygenase (MDO). One-electron chemical oxidation of 1 and 2 yields ferric species that bind cyanide and azide anions, which have been used as spectroscopic probes of O₂ binding in prior studies of Fe^III-CDO. The six-coordinate Fe^III-CN and Fe^III-N₃ adducts are examined with UV-vis absorption, electron paramagnetic resonance (EPR), and resonance Raman (rRaman) spectroscopies. In addition, UV-vis and rRaman studies of cysteine- and cyanide-bound Fe^III-CDO are reported for both the wild-type (WT) enzyme and C93G variant, which lacks the Cys-Tyr cross-link that is present in the second coordination sphere of the WT active site. Density functional theory (DFT) and ab initio calculations are employed to provide geometric and electronic structure descriptions of the synthetic and enzymatic Fe^III adducts. In particular, it is shown that the complete active space self-consistent field (CASSCF) method, in tandem with n-electron valence state second-order perturbation theory (NEVPT2), is capable of elucidating the structural basis of subtle shifts in EPR g values for low-spin Fe^III species.

Synthesis and Speciation-Dependent Properties of a Multimetallic Model Complex of NiSOD That Exhibits Unique Hydrogen-Bonding

The complex Na₃[{Ni^II(nmp)}₃S₃BTA^alk)] (1) (nmp^2- = deprotonated form of N-(2-mercaptoethyl)picolinamide; H₃S₃BTA^alk = N¹,N³,N⁵-tris(2-mercaptoethyl)benzene-1,3,5-tricarboxamide, where H = dissociable protons), supported by the thiolate-benzenetricarboxamide scaffold (S₃BTA^alk), has been synthesized as a trimetallic model of nickel-containing superoxide dismutase (NiSOD). X-ray absorption spectroscopy (XAS) and ¹H NMR measurements on 1 indicate that the Ni^II centers are square-planar with N₂S₂ coordination, and Ni-N and Ni-S distances of 1.95 and 2.16 Å, respectively. Additional evidence from IR indicates the presence of H-bonds in 1 from the approximately -200 cm^-1 shift in ν_NH from free ligand. The presence of H-bonds allows for speciation that is temperature-, concentration-, and solvent-dependent. In unbuffered water and at low temperature, a dimeric complex (1^A; λ = 410 nm) that aggregates through intermolecular NH···O═C bonds of BTA units is observed. Dissolution of 1 in pH 7.4 buffer or in unbuffered water at temperatures above 50 °C results in monomeric complex (1^M; λ = 367 nm) linked through intramolecular NH···S bonds. DFT computations indicate a low energy barrier between 1^A and 1^M with nearly identical frontier MOs and Ni-ligand metrics. Notably, 1^A and 1^M exhibit remarkable stability in protic solvents such as MeOH and H₂O, in stark contrast to monometallic [Ni^II(nmp)(SR)]^- complexes. The reactivity of 1 with excess O₂, H₂O₂, and O₂^•- is species-dependent. IR and UV-vis reveal that 1^A in MeOH reacts with excess O₂ to yield an S-bound sulfinate, but does not react with O₂^•-. In contrast, 1^M is stable to O₂ in pH 7.4 buffer, but reacts with O₂^•- to yield a putative [Ni^II(nmp)(O₂)]^- complex from release of the BTA-thiolate based on EPR.

Single turnover of substrate-bound ferric cysteine dioxygenase with superoxide anion: enzymatic reactivation, product formation, and a transient intermediate

Cysteine dioxygenase (CDO) is a non-heme mononuclear iron enzyme that catalyzes the O(2)-dependent oxidation of L-cysteine (Cys) to produce cysteine sulfinic acid (CSA). In this study we demonstrate that the catalytic cycle of CDO can be "primed" by one electron through chemical oxidation to produce CDO with ferric iron in the active site (Fe(III)-CDO, termed 2). While catalytically inactive, the substrate-bound form of Fe(III)-CDO (2a) is more amenable to interrogation by UV-vis and EPR spectroscopy than the 'as-isolated' Fe(II)-CDO enzyme (1). Chemical-rescue experiments were performed in which superoxide (O(2)(•-)) anions were introduced to 2a to explore the possibility that a Fe(III)-superoxide species represents the first intermediate within the catalytic pathway of CDO. In principle, O(2)(•-) can serve as a suitable acceptor for the remaining 3-electrons necessary for CSA formation and regeneration of the active Fe(II)-CDO enzyme (1). Indeed, addition of O(2)(•-) to 2a resulted in the rapid formation of a transient species (termed 3a) observable at 565 nm by UV-vis spectroscopy. The subsequent decay of 3a is kinetically matched to CSA formation. Moreover, a signal attributed to 3a was also identified using parallel mode X-band EPR spectroscopy (g ~ 11). Spectroscopic simulations, observed temperature dependence, and the microwave power saturation behavior of 3a are consistent with a ground state S = 3 from a ferromagnetically coupled (J ~ -8 cm(-1)) high-spin ferric iron (S(A) = 5/2) with a bound radical (S(B) = 1/2), presumably O(2)(•-). Following treatment with O(2)(•-), the specific activity of recovered CDO increased to ~60% relative to untreated enzyme.

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.

Methanoferrodoxin represents a new class of superoxide reductase containing an iron-sulfur cluster

Protein MM0632 from the methanogenic archaeon Methanosarcina mazei showed strong superoxide reductase activity and rapidly decomposed superoxide radicals to peroxides. The superoxide reductase activity of the heterologously produced enzyme was determined by a cytochrome c assay and in a test system with NADPH, ferredoxin:NADP(+) reductase, and rubredoxin. Furthermore, EPR spectroscopy showed that MM0632 is the first superoxide reductase that possesses an iron-sulfur cluster instead of a second mononuclear iron center. We propose the name methanoferrodoxin for this new class of superoxide reductase with an [Fe(NHis)(4)(SCys)] site as the catalytic center and a [4Fe-4S] cluster as second prosthetic group that is probably involved in electron transfer to the catalytic center. Methanosarcina mazei grows only under anaerobic conditions, but is one of the most aerotolerant methanogens. It is tempting to speculate that methanoferrodoxin contributes to the protection of cells from oxygen radicals formed by flavoproteins during periodic exposure to oxygen in natural environments.

Reductive elimination of superoxide: Structure and mechanism of superoxide reductases

Superoxide anion is among the deleterious reactive oxygen species, towards which all organisms have specialized detoxifying enzymes. For quite a long time, superoxide elimination was thought to occur through its dismutation, catalyzed by Fe, Cu, and Mn or, as more recently discovered, by Ni-containing enzymes. However, during the last decade, a novel type of enzyme was established that eliminates superoxide through its reduction: the superoxide reductases, which are spread among anaerobic and facultative microorganisms, from the three life kingdoms. These enzymes share the same unique catalytic site, an iron ion bound to four histidines and a cysteine that, in its reduced form, reacts with superoxide anion with a diffusion-limited second order rate constant of approximately 10(9) M(-1) s(-1). In this review, the properties of these enzymes will be thoroughly discussed.

Analysis of the nitric oxide-sensing non-heme iron center in the NorR regulatory protein

The NorR regulatory protein senses nitric oxide (NO) to activate genes required for NO detoxification under anaerobic and microaerobic conditions in Escherichia coli. NorR belongs to the sigma(54)-dependent family of transcriptional activators and contains an N-terminal regulatory GAF (cGMP phosphodiesterase, adenylate cyclase, FhlA) domain that controls the ATPase activity of the central AAA+ domain to regulate productive interactions with sigma(54). Binding of NO to a non-heme iron center in the GAF domain results in the formation of a mononitrosyl-iron complex and releases intramolecular repression of the AAA+ domain to enable activation of transcription. In this study, we have further characterized NorR spectroscopically and substituted conserved residues in the GAF domain. This analysis, in combination with structural modeling of the GAF domain, has identified five candidate ligands to the non-heme iron and suggests a model in which the metal ion is coordinated in a pseudo-octahedral environment by three aspartate residues, an arginine, and a cysteine.

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).

High unique diversity of sulfate-reducing prokaryotes characterized in a depth gradient in an acidic fen

The dissimilatory reduction of sulfate contributes to the retention of sulfur in acidic mineratrophic peatlands. Novel sulfate-reducing prokaryotes (SRPs) colonize these low-sulfate fens. This study assessed the community structures of SRPs in a depth gradient (0-50 cm) in a fen, located in the Fichtelgebirge (Spruce Mountains), Germany. Detection of SRPs with multiplex (terminal-) restriction fragment length polymorphism analysis of amplified dissimilatory (bi)sulfite reductase genes (dsrAB) separated three subgroups derived from (i) the upper 5 and 10 cm, (ii) 15-25 cm, and (iii) 30-50 cm depth. Biogeochemical parameters measured in the soil solution from July 2001 to July 2004 documented that the upper 5-10 cm were exposed to drying and oxygenation prior to sampling. Periodic oxygenation reached a maximum depth of 25 cm in the water-saturated fen and was concomitant with relative high concentrations of nitrate (120 microM) and sulfate (up to 310 microM). The fen soil was permanently anoxic below 30 cm depth with average concentrations of sulfate below 40 microM and maximum concentrations of methane. Cloning of dsrAB PCR products from 5, 20 and 40 cm depth yielded a total of 84 unique dsrAB restriction patterns. Partial sequencing of 61 distinct clones resulted in 59 unique partial protein sequences that mainly clustered with DsrA sequences of uncultivated sulfate reducers. Syntrophobacter fumaroxidans- and Syntrophobacter wolinii-related bacteria appeared to be present only in 40 cm depth. Differences in the SRP community structures suggested that SRPs present in the upper fen soil have to tolerate O(2) and even drying, whereas SRPs present in deep anoxic zones may act as syntrophic fermentors in cooperation with H(2)-utilizing methanogens.

Superoxide reduction by Archaeoglobus fulgidus desulfoferrodoxin: comparison with neelaredoxin

Superoxide reductases (SORs) are non-heme iron-containing enzymes that remove superoxide by reducing it to hydrogen peroxide. The active center of SORs consists of a ferrous ion coordinated by four histidines and one cysteine in a square-pyramidal geometry. In the 2Fe-SOR, a distinct family of SORs, there is an additional desulforedoxin-like site that does not appear to be involved in SOR activity. Our previous studies on recombinant Archaeoglobus fulgidus neelaredoxin (1Fe-SOR) have shown that the reaction with superoxide involves the formation of a transient ferric form that, upon protonation, decays to yield an Fe(3+)-OH species, followed by binding of glutamate to the ferric ion via replacement of hydroxide (Rodrigues et al. in Biochemistry 45:9266-9278, 2006). Here, we report the characterization of recombinant desulfoferrodoxin from the same organism, which is a member of the 2Fe-SOR family, and show that the steps involved in the superoxide reduction are similar in both families of SOR. The electron donation to the SOR from its redox partner, rubredoxin, is also presented here.

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.

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.

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.

Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion upon X-Ray-Induced Photo-Reduction

Some sulfate-reducing and microaerophilic bacteria rely on the enzyme superoxide reductase (SOR) to eliminate the toxic superoxide anion radical (O2*-). SOR catalyses the one-electron reduction of O2*- to hydrogen peroxide at a nonheme ferrous iron center. The structures of Desulfoarculus baarsii SOR (mutant E47A) alone and in complex with ferrocyanide were solved to 1.15 and 1.7 A resolution, respectively. The latter structure, the first ever reported of a complex between ferrocyanide and a protein, reveals that this organo-metallic compound entirely plugs the SOR active site, coordinating the active iron through a bent cyano bridge. The subtle structural differences between the mixed-valence and the fully reduced SOR-ferrocyanide adducts were investigated by taking advantage of the photoelectrons induced by X-rays. The results reveal that photo-reduction from Fe(III) to Fe(II) of the iron center, a very rapid process under a powerful synchrotron beam, induces an expansion of the SOR active site.