EPR and Mössbauer studies of protocatechuate 4,5-dioxygenase. Characterization of a new Fe2+ environment

Crystal structure and mutagenic analysis of GDOsp, a gentisate 1,2-dioxygenase from Silicibacter pomeroyi

Dioxygenases catalyze dioxygen incorporation into various organic compounds and play a key role in the complex degradation pathway of mono- and polycyclic aromatic and hetero-aromatic compounds. Here we report the crystal structure of gentisate 1,2-dioxygenase from Silicibacter pomeroyi (GDOsp) at a 2.8 A resolution. The enzyme possessed a conserved three-dimensional structure of the bicupin family, forming a homotetramerization. However, each subunit of GDOsp unusually contained two ferrous centers that were located in its two homologous cupin domains, respectively. Further mutagenic analysis indicated that the enzyme activity of GDOsp depends on the microenvironment in both metal-binding sites. Moreover, homologous structural comparison and functional study on GDOsp variants unveiled a group of functionally essential residues and suggested that the active site of the enzyme is located in the amino-terminal domain, but could be influenced by changes in the carboxyl domain. Therefore, GDOsp may provide a working model for studying long-distance communication within a protein (or its complex).

Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases

Hydroquinone 1,2-dioxygenase (HQDO), an enzyme involved in the catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB, was purified to apparent homogeneity. Ligandation with 4-hydroxybenzoate prevented the enzyme from irreversible inactivation. HQDO was activated by iron(II) ions and catalyzed the ring fission of a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes. HQDO was inactivated by 2,2'-dipyridyl, o-phenanthroline, and hydrogen peroxide and inhibited by phenolic compounds. The inhibition with 4-hydroxybenzoate (K(i) = 14 microM) was competitive with hydroquinone. Online size-exclusion chromatography-mass spectrometry revealed that HQDO is an alpha2beta2 heterotetramer of 112.4 kDa, which is composed of an alpha-subunit of 17.8 kDa and a beta-subunit of 38.3 kDa. Each beta-subunit binds one molecule of 4-hydroxybenzoate and one iron(II) ion. N-terminal sequencing and peptide mapping and sequencing based on matrix-assisted laser desorption ionization--two-stage time of flight analysis established that the HQDO subunits are encoded by neighboring open reading frames (hapC and hapD) of a gene cluster, implicated to be involved in 4-hydroxyacetophenone degradation. HQDO is a novel member of the family of nonheme-iron(II)-dependent dioxygenases. The enzyme shows insignificant sequence identity with known dioxygenases.

Determination of the substrate binding mode to the active site iron of (S)-2-hydroxypropylphosphonic acid epoxidase using 17O-enriched substrates and substrate analogues

(S)-2-Hydroxypropylphosphonic acid epoxidase (HppE) is an O2-dependent, nonheme Fe(II)-containing oxidase that converts (S)-2-hydroxypropylphosphonic acid ((S)-HPP) to the regio- and enantiomerically specific epoxide, fosfomycin. Use of (R)-2-hydroxypropylphosphonic acid ((R)-HPP) yields the 2-keto-adduct rather than the epoxide. Here we report the chemical synthesis of a range of HPP analogues designed to probe the basis for this specificity. In past studies, NO has been used as an O2 surrogate to provide an EPR probe of the Fe(II) environment. These studies suggest that O2 binds to the iron, and substrates bind in a single orientation that strongly perturbs the iron environment. Recently, the X-ray crystal structure showed direct binding of the substrate to the iron, but both monodentate (via the phosphonate) and chelated (via the hydroxyl and phosphonate) orientations were observed. In the current study, hyperfine broadening of the homogeneous S = 3/2 EPR spectrum of the HppE-NO-HPP complex was observed when either the hydroxyl or the phosphonate group of HPP was enriched with 17O (I = 5/2). These results indicate that both functional groups of HPP bind to Fe(II) ion at the same time as NO, suggesting that the chelated substrate binding mode dominates in solution. (R)- and (S)-analogue compounds that maintained the core structure of HPP but added bulky terminal groups were turned over to give products analogous to those from (R)- and (S)-HPP, respectively. In contrast, substrate analogues lacking either the phosphonate or hydroxyl group were not turned over. Elongation of the carbon chain between the hydroxyl and phosphonate allowed binding to the iron in a variety of orientations to give keto and diol products at positions determined by the hydroxyl substituent, but no stable epoxide was formed. These studies show the importance of the Fe(II)-substrate chelate structure to active antibiotic formation. This fixed orientation may align the substrate next to the iron-bound activated oxygen species thought to mediate hydrogen atom abstraction from the nearest substrate carbon.

Two-pronged survival strategy for the major cystic fibrosis pathogen, Pseudomonas aeruginosa, lacking the capacity to degrade nitric oxide during anaerobic respiration

Protection from NO gas, a toxic byproduct of anaerobic respiration in Pseudomonas aeruginosa, is mediated by nitric oxide (NO) reductase (NOR), the norCB gene product. Nevertheless, a norCB mutant that accumulated approximately 13.6 microM NO paradoxically survived anaerobic growth. Transcription of genes encoding nitrate and nitrite reductases, the enzymes responsible for NO production, was reduced >50- and 2.5-fold in the norCB mutant. This was due, in part, to a predicted compromise of the [4Fe-4S](2+) cluster in the anaerobic regulator ANR by physiological NO levels, resulting in an inability to bind to its cognate promoter DNA sequences. Remarkably, two O(2)-dependent dioxygenases, homogentisate-1,2-dioxygenase (HmgA) and 4-hydroxyphenylpyruvate dioxygenase (Hpd), were derepressed in the norCB mutant. Electron paramagnetic resonance studies showed that HmgA and Hpd bound NO avidly, and helped protect the norCB mutant in anaerobic biofilms. These data suggest that protection of a P. aeruginosa norCB mutant against anaerobic NO toxicity occurs by both control of NO supply and reassignment of metabolic enzymes to the task of NO sequestration.

VTVH-MCD and DFT studies of thiolate bonding to [FeNO]7/[FeO2]8 complexes of isopenicillin N synthase: substrate determination of oxidase versus oxygenase activity in nonheme Fe enzymes

Isopenicillin N synthase (IPNS) is a unique mononuclear nonheme Fe enzyme that catalyzes the four-electron oxidative double ring closure of its substrate ACV. A combination of spectroscopic techniques including EPR, absorbance, circular dichroism (CD), magnetic CD, and variable-temperature, variable-field MCD (VTVH-MCD) were used to evaluate the geometric and electronic structure of the [FeNO]7 complex of IPNS coordinated with the ACV thiolate ligand. Density Function Theory (DFT) calculations correlated to the spectroscopic data were used to generate an experimentally calibrated bonding description of the Fe-IPNS-ACV-NO complex. New spectroscopic features introduced by the binding of the ACV thiolate at 13 100 and 19 800 cm-1 are assigned as the NO pi*(ip) --> Fe dx2-y2 and S pi--> Fe dx2-y2 charge transfer (CT) transitions, respectively. Configuration interaction mixes S CT character into the NO pi*(ip) --> Fe dx2-y2 CT transition, which is observed experimentally from the VTVH-MCD data from this transition. Calculations on the hypothetical {FeO2}8 complex of Fe-IPNS-ACV reveal that the configuration interaction present in the [FeNO]7 complex results in an unoccupied frontier molecular orbital (FMO) with correct orientation and distal O character for H-atom abstraction from the ACV substrate. The energetics of NO/O2 binding to Fe-IPNS-ACV were evaluated and demonstrate that charge donation from the ACV thiolate ligand renders the formation of the FeIII-superoxide complex energetically favorable, driving the reaction at the Fe center. This single center reaction allows IPNS to avoid the O2 bridged binding generally invoked in other nonheme Fe enzymes that leads to oxygen insertion (i.e., oxygenase function) and determines the oxidase activity of IPNS.

Spectroscopic and electronic structure studies of 2,3-dihydroxybiphenyl 1,2-dioxygenase: O2 reactivity of the non-heme ferrous site in extradiol dioxygenases

The extradiol dioxygenase, 2,3-dihydroxybiphenyl 1,2-dioxygenase (DHBD, EC 1.13.11.39), has been studied using magnetic circular dichroism (MCD), variable-temperature variable-field (VTVH) MCD, X-ray absorption (XAS) pre-edge, and extended X-ray absorption fine structure (EXAFS) spectroscopies, which are analogous to methods used in earlier studies on the extradiol dioxygenase catechol 2,3-dioxygenase [Mabrouk et al. J. Am. Chem Soc. 1991, 113, 4053-4061]. For DHBD, the spectroscopic data can be correlated to the results of crystallography and with the results from density functional calculations to obtain detailed geometric and electronic structure descriptions of the resting and substrate (DHB) bound forms of the enzyme. The geometry of the active site of the resting enzyme, square pyramidal with a strong Fe-glutamate bond in the equatorial plane, localizes the redox active orbital in an orientation appropriate for O(2) binding. However, the O(2) reaction is not favorable, as it would produce a ferric superoxide intermediate with a weak Fe-O bond. Substrate binding leads to a new square pyramidal structure with the strong Fe-glutamate bond in the axial direction as indicated by a decrease in the (5)E(g) and increase in the (5)T(2g) splitting. Electronic structure calculations provide insight into the relative lack of dioxygen reactivity for the resting enzyme and its activation upon substrate binding.

A non-haem iron centre in the transcription factor NorR senses nitric oxide

Nitric oxide (NO), synthesized in eukaryotes by the NO synthases, has multiple roles in signalling pathways and in protection against pathogens. Pathogenic microorganisms have apparently evolved defence mechanisms that counteract the effects of NO and related reactive nitrogen species. Regulatory proteins that sense NO mediate the primary response to NO and nitrosative stress. The only regulatory protein in enteric bacteria known to serve exclusively as an NO-responsive transcription factor is the enhancer binding protein NorR (refs 9, 10-11). In Escherichia coli, NorR activates the transcription of the norVW genes encoding a flavorubredoxin (FlRd) and an associated flavoprotein, respectively, which together have NADH-dependent NO reductase activity. The NO-responsive activity of NorR raises important questions concerning the mechanism of NO sensing. Here we show that the regulatory domain of NorR contains a mononuclear non-haem iron centre, which reversibly binds NO. Binding of NO stimulates the ATPase activity of NorR, enabling the activation of transcription by RNA polymerase. The mechanism of NorR reveals an unprecedented biological role for a non-haem mononitrosyl-iron complex in NO sensing.

ENDOR Studies of the Ligation and Structure of the Non-Heme Iron Site in ACC Oxidase

Ethylene is a plant hormone involved in all stages of growth and development, including regulation of germination, responses to environmental stress, and fruit ripening. The final step in ethylene biosynthesis, oxidation of 1-aminocyclopropane-1-carboxylic acid (ACC) to yield ethylene, is catalyzed by ACC oxidase (ACCO). In a previous EPR and ENDOR study of the EPR-active Fe(II)-nitrosyl, [FeNO],(7) complex of ACCO, we demonstrated that both the amino and the carboxyl moieties of the inhibitor d,l-alanine, and the substrate ACC by analogy, coordinate to the Fe(II) ion in the Fe(II)-NO-ACC ternary complex. In this report, we use 35 GHz pulsed and CW ENDOR spectroscopy to examine the coordination of Fe by ACCO in more detail. ENDOR data for selectively (15)N-labeled derivatives of substrate-free ACCO-NO (E-NO) and substrate/inhibitor-bound ACCO-NO (E-NO-S) have identified two histidines as protein-derived ligands to Fe; (1,2)H and (17)O ENDOR of samples in D(2)O and H(2)(17)O solvent have confirmed the presence of water in the substrate-free Fe(II) coordination sphere (E-NO). Analysis of orientation-selective (14,15)N and (17)O ENDOR data is interpreted in terms of a structural model of the ACCO active site, both in the presence (E-NO-S) and in the absence (E-NO) of substrate. Evidence is also given that substrate binding dictates the orientation of bound O(2).

Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases

Comamonas testosteroni T-2 degraded at least eight aromatic compounds via protocatechuate (PCA), whose extradiol ring cleavage to 2-hydroxy-4-carboxymuconate semialdehyde (HCMS) was catalysed by PCA 4,5-dioxygenase (PmdAB). This inducible, heteromultimeric enzyme was purified. It contained two subunits, alpha (PmdA) and beta (PmdB), and the molecular masses of the denatured proteins were 18 kDa and 31 kDa, respectively. PCA was converted stoichiometrically to HCMS with an apparent K(m) of 55 muM and at a maximum velocity of 1.5 mukat. Structure-activity-relationship analysis by testing 16 related compounds as substrate for purified PmdAB revealed an absolute requirement for the vicinal diol and for the carboxylate group of PCA. Besides PCA, only 5'-hydroxy-PCA (gallate) induced oxygen uptake. The N-terminal amino acid sequence of each subunit was identical to the corresponding sequences in C. testosteroni BR6020, which facilitated sequencing of the pmdAB genes in strain T-2. Small differences in the amino acid sequence had significant effects on enzyme stability. Several homologues of pmdAB were found in sequence databases. Residues involved in substrate binding are highly conserved among the homologues. Their sequences grouped within the class III extradiol dioxygenases. Based on our biochemical and genetic analyses, we propose a new branch of the heteromultimeric enzymes within that class.

Biophysical analyses of designed and selected mutants of protocatechuate 3,4-dioxygenase1

The catechol dioxygenases allow a wide variety of bacteria to use aromatic compounds as carbon sources by catalyzing the key ring-opening step. These enzymes use specifically either catechol or protocatechuate (2,3-dihydroxybenozate) as their substrates; they use a bare metal ion as the sole cofactor. To learn how this family of metalloenzymes functions, a structural analysis of designed and selected mutants of these enzymes has been undertaken. Here we review the results of this analysis on the nonheme ferric iron intradiol dioxygenase protocatechuate 3,4-dioxygenase.

Rates of the phthalate dioxygenase reaction with oxygen are dramatically increased by interactions with phthalate and phthalate oxygenase reductase

The phthalate dioxygenase system, which catalyzes the dihydroxylation of phthalate to form its cis-dihydrodiol (DHD), has two components: phthalate dioxygenase (PDO), a multimer with one Rieske-type [2Fe-2S] and one Fe(II) center per monomer, and phthalate dioxygenase reductase (PDR), which contains flavin mononucleotide (FMN) and a plant-like ferredoxin [2Fe-2S] center. PDR is responsible for transferring electrons from NADH to the Rieske center of PDO, and the Rieske center supplies electrons to the mononuclear center for the oxygenation of substrate. Reduced PDO (PDO(red)) that lacks Fe(II) at the mononuclear metal site (PDO-APO) reacts slowly with O(2) (1.4 x 10(-3) s(-1) at 125 microM O(2) and 22 degrees C), presumably in a direct reaction with the Rieske center. Binding of phthalate and/or PDR(ox) to reduced PDO-APO increases the reactivity of the Rieske center with O(2). When no PDR or phthalate is present, the oxidation of the Rieske center in native PDO(red) [which contains Fe(II) at the mononuclear site] occurs in two phases (approximately 1 and 0.1 s(-1) at 125 mM O(2), 23 degrees C), both much faster than in the absence of Fe(II), presumably because in this case O(2) reacts at the mononuclear Fe(II). Addition of PDR(ox) to native PDO(red) resulted in a large fraction of the Rieske center being oxidized at 5 s(-1), and the addition of phthalate resulted in about 70% of the reaction proceeding at 42 s(-1). With both PDR(ox) and phthalate present, most of the PDO(red) (approximately 80-85%) oxidizes at 42 s(-1), with the remaining oxidizing at approximately 5 s(-1). Thus, the binding of phthalate or PDR(ox) to PDO(red) each results in greater reactivity of PDO with O(2). The presence of both the substrate and PDR was synergistic, making PDO fully catalytically active. A model that explains the observed effects is presented and discussed in terms of PDO subunit cooperativity. It is proposed that, during oxidation of reduced PDO, each of two Rieske centers on separate subunits transfers an electron to the Fe(II) mononuclear center on a third subunit. This explanation is consistent with the observed multiphasic kinetics of the oxidation of the Rieske center and is being further tested by product analysis experiments.

Spectroscopic description of the two nitrosyl-iron complexes responsible for fur inhibition by nitric oxide

Ferric uptake regulation protein (Fur) is a global regulator, ubiquitous in Gram negative bacteria, that acts as a transcriptional repressor when it binds ferrous ion. Fur is involved in responses to several types of stress related to iron metabolism, such as stress induced by nitric oxide (NO) generated by macrophages against bacterial invasion. NO was recently shown to react with Fe(2+) ions in FeFur (iron substituted Fur protein) leading to an Fur bound iron-nitrosyl complex, unable to bind DNA, and characterized by a g = 2.03 EPR signal, associated with an S = (1)/(2) ground state. This electronic configuration could arise from either a mononitrosyl-iron [Fe(NO)](7) or a dinitrosyl-iron [Fe(NO)(2)](9) complex. The use of several spectroscopic tools such as EPR, ENDOR, FTIR, Mössbauer, and UV-visible spectroscopies as well as mass spectrometry analysis was necessary to characterize the iron-nitrosyl species in Fur. Furthermore, changes of C132 and C137 into glycines by site directed mutagenesis reveal that neither of the two cysteines is required for the formation of the g = 2.03 signal. Altogether, we found that two species are responsible for Fur inhibition in NO stress conditions: the major species, S(1/2), is an [Fe(NO)(2)](9) (S = (1)/(2)) complex without bound thiolate and the minor species is probably a diamagnetic [Fe(NO)(2)](8) (S = 0) complex. This is the first characterization of these physiologically relevant species potentially linking iron metabolism and the response to NO toxicity in bacteria.

Evidence for a new metal in a known active site: purification and characterization of an iron-containing quercetin 2,3-dioxygenase from Bacillus subtilis

The protein YxaG from Bacillus subtilis, of previously unknown function, was found to have quercetin 2,3-dioxygenase activity when overexpressed in Escherichia coli. The enzyme converts the flavonol quercetin to 2-protocatechuoylphloroglucinol carboxylic acid and carbon monoxide, indicating that it performs the same reaction and yields the same products as the well-characterized copper-containing quercetin 2,3-dioxygenase from Aspergillus. In contrast to the Aspergillus protein, YxaG contains iron, and the enzyme is sensitive to strong Fe(II) chelators, similar to the extensively studied catechol dioxygenases. The active site metal was probed by EPR spectroscopy using the label nitric oxide to confirm the presence of an Fe(II) atom. The kinetic parameters and pH activity profiles are also markedly different from those of the copper-containing quercetin 2,3-dioxygenases from Aspergillus. YxaG represents the first example of a prokaryotic quercetin 2,3-dioxygenase.

Mechanism for Catechol Ring-Cleavage by Non-Heme Iron Extradiol Dioxygenases

The catalytic mechanism of the non-heme iron extradiol dioxygenases has been studied using hybrid density functional theory. These enzymes cleave a C-C bond outside the two hydroxyl groups of catechols, in contrast to the intradiol enzymes which cleave the C-C bond between these two groups. The chemical models used comprise about 70 atoms and include the first-shell ligands, two histidines, one glutamate, and one water, as well as some second-shell ligands, two histidines, one aspartate, and one tyrosine. Catechol is found to bind as a monoanion in agreement with experiments, while dioxygen is found to replace the water ligand. A spin-transition from the initial septet to a quintet state prepares the system for formation of a bridging peroxide with the catechol substrate. When the O-O bond is cleaved in the suggested rate-limiting step, a key substrate intermediate with partly radical and partly anionic character is formed. The partly anionic character is found to determine the selectivity of the enzyme. The results are compared to available experimental information and to previous studies.

Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases

The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn2+ and Fe2+, respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four betaalphabetabetabeta modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214NE1 and E267OE1; one axial ligand, H155NE1; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 A), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O2. The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.

Biochemical and spectroscopic studies on (S)-2-hydroxypropylphosphonic acid epoxidase: a novel mononuclear non-heme iron enzyme

The last step of the biosynthesis of fosfomycin, a clinically useful antibiotic, is the conversion of (S)-2-hydroxypropylphosphonic acid (HPP) to fosfomycin. Since the ring oxygen in fosfomycin has been shown in earlier feeding experiments to be derived from the hydroxyl group of HPP, this oxirane formation reaction is effectively a dehydrogenation process. To study this unique C-O bond formation step, we have overexpressed and purified the desired HPP epoxidase. Results reported herein provided initial biochemical evidence revealing that HPP epoxidase is an iron-dependent enzyme and that both NAD(P)H and a flavin or flavoprotein reductase are required for its activity. The 2 K EPR spectrum of oxidized iron-reconstituted fosfomycin epoxidase reveals resonances typical of S = (5)/(2) Fe(III) centers in at least two environments. Addition of HPP causes a redistribution with the appearance of at least two additional species, showing that the iron environment is perturbed. Exposure of this sample to NO elicits no changes, showing that the iron is nearly all in the Fe(III) state. However, addition of NO to the Fe(II) reconstituted enzyme that has not been exposed to O(2) yields an intense EPR spectrum typical of an S = (3)/(2) Fe(II)-NO complex. This complex is also heterogeneous, but addition of substrate converts it to a single, homogeneous S = (3)/(2) species with a new EPR spectrum, suggesting that substrate binds to or near the iron, thereby organizing the center. The fact that NO binds to the ferrous center suggests O(2) can also bind at this site as part of the catalytic cycle. Using purified epoxidase and (18)O isotopic labeled HPP, the retention of the hydroxyl oxygen of HPP in fosfomycin was demonstrated. While ether ring formation as a result of dehydrogenation of a secondary alcohol has precedence in the literature, these catalyses require alpha-ketoglutarate for activity. In contrast, HPP epoxidase is alpha-ketoglutarate independent. Thus, the cyclization of HPP to fosfomycin clearly represents an intriguing conversion beyond the scope entailed by common biological epoxidation and C-O bond formation.

Conversion of extradiol aromatic ring-cleaving homoprotocatechuate 2,3-dioxygenase into an intradiol cleaving enzyme

The intra- and extradiol subfamilies of catechol-adduct ring-cleaving dioxygenases each exhibit nearly absolute fidelity for the ring cleavage position. This is often attributed to the fact that the oxygen activation mechanism of intradiol dioxygenases utilizes Fe3+ while that of the extradiol enzymes employs Fe2+, but the subfamilies also differ in primary sequence, structural fold, iron ligands, and second sphere active site amino acid residues. Here, we examine the effects of the second sphere residue H200 in the active site of homoprotocatechuate 2,3-dioxygenase (2,3-HPCD), an extradiol-cleaving enzyme. It is shown that the H200F mutant enzyme catalyzes extradiol cleavage of the normal substrate, homoprotocatechuate (HPCA), but intradiol cleavage of the alternative substrate 2,3-dihydroxybenzoate (2,3-DHB) while in the Fe2+ oxidation state. Wild-type 2,3-HPCD catalyzes extradiol cleavage of both substrates. This is the first report of intradiol cleavage by an extradiol dioxygenase. It suggests that intradiol cleavage can occur with the iron in the Fe2+ state, with the iron ligand set characteristic of extradiol dioxygenases, and through a mechanism in which oxygen is activated by binding to the iron rather than directly attacking the substrate as in true intradiol dioxygenases. This indicates that substrate binding geometry and acid/base chemistry of second sphere residues play important roles in determining the course of the dioxygenase reaction.

Spectroscopic and computational study of a non-heme iron [Fe-NO]7 system: exploring the geometric and electronic structures of the nitrosyl adduct of iron superoxide dismutase

Like many non-heme iron enzymes, reduced iron superoxide dismutase (Fe(2+)SOD) reacts with nitric oxide (NO) to yield an [Fe-NO]7 system. Electron paramagnetic resonance (EPR) data obtained for this Fe-NO adduct of FeSOD (NO-FeSOD) exhibit two rhombic S = 3/2 signals of comparable population; E/D = 0.128 (42%) and 0.154 (58%). While similar results were previously reported for NO-FeSOD [Niederhoffer, E. C.; Fee, J. A.; Papaefthymiou, V.; Münck, E. Magnetic Resonance Studies Involving Iron Superoxide Dismutase from Escherichia coli. Isotope and Nuclear Chemistry Division Annual Report; Los Alamos National Laboratory: Los Alamos, NM, 1987], detailed geometric and electronic structure descriptions of these [Fe-NO]7 systems had not yet been developed. Therefore, in addition to EPR spectroscopy, we have used electronic absorption, magnetic circular dichroism (MCD), variable-temperature, variable-field MCD, and resonance Raman spectroscopies to determine ground-state spin Hamiltonian parameters, electronic transition energies, oscillator strengths, and transition polarizations for NO-FeSOD. These spectroscopic parameters have been used in conjunction with density functional theory (DFT) and semiempirical INDO/S-CI calculations to generate an experimentally calibrated active site model for NO-FeSOD. Our studies indicate that NO binds to the active site of Fe(2+)SOD to form a six-coordinate [Fe-NO]7 system with an Fe-N-O angle of approximately 145 degrees. DFT computations performed on this model of NO-FeSOD reveal that the NO ligand is formally reduced by the ferrous center to yield NO(-) and an Fe(3+) center that are strongly antiferromagnetically coupled. DFT calculations reveal that NO binding to Fe(2+)SOD also lowers the pK of the coordinated water ligand by at least 3.3 pH units, suggesting that this process is associated with increased acidity and probable ionization of the axial solvent ligand. To explore the origin of the two [Fe-NO]7 systems observed by EPR spectroscopy, additional calculations have been performed on slightly perturbed NO-FeSOD models. Significantly, semiempirical INDO/S-CI computations reveal that the rhombicity of NO-FeSOD is altered by changes in the Fe-N-O angle or rotation about the Fe-N(O) bond, suggesting that the two species observed by EPR spectroscopy merely differ slightly with respect to the orientation of the NO ligand. Indeed, our EPR data obtained on NO-FeSOD variants indicate that the relative population of the S = 3/2 signals can be altered by perturbations in the second sphere of the protein active site. These results provide compelling evidence that the second coordination sphere is able to modulate the geometric and electronic structures of NO-FeSOD.

The first direct characterization of a high-valent iron intermediate in the reaction of an alpha-ketoglutarate-dependent dioxygenase: a high-spin FeIV complex in taurine/alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli

The Fe(II)- and alpha-ketoglutarate(alphaKG)-dependent dioxygenases have roles in synthesis of collagen and sensing of oxygen in mammals, in acquisition of nutrients and synthesis of antibiotics in microbes, and in repair of alkylated DNA in both. A consensus mechanism for these enzymes, involving (i) addition of O(2) to a five-coordinate, (His)(2)(Asp)-facially coordinated Fe(II) center to which alphaKG is also bound via its C-1 carboxylate and ketone oxygen; (ii) attack of the uncoordinated oxygen of the bound O(2) on the ketone carbonyl of alphaKG to form a bicyclic Fe(IV)-peroxyhemiketal complex; (iii) decarboxylation of this complex concomitantly with formation of an oxo-ferryl (Fe(IV)=O(2)(-)) intermediate; and (iv) hydroxylation of the substrate by the Fe(IV)=O(2)(-) complex via a substrate radical intermediate, has repeatedly been proposed, but none of the postulated intermediates occurring after addition of O(2) has ever been detected. In this work, an oxidized Fe intermediate in the reaction of one of these enzymes, taurine/alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli, has been directly demonstrated by rapid kinetic and spectroscopic methods. Characterization of the intermediate and its one-electron-reduced form (obtained by low-temperature gamma-radiolysis of the trapped intermediate) by Mössbauer and electron paramagnetic resonance spectroscopies establishes that it is a high-spin, formally Fe(IV) complex. Its Mössbauer isomer shift is, however, significantly greater than those of other known Fe(IV) complexes, suggesting that the iron ligands in the TauD intermediate confer significant Fe(III) character to the high-valent site by strong electron donation. The properties of the complex and previous results on related alphaKG-dependent dioxygenases and other non-heme-Fe(II)-dependent, O(2)-activating enzymes suggest that the TauD intermediate is most probably either the Fe(IV)-peroxyhemiketal complex or the taurine-hydroxylating Fe(IV)=O(2)(-) species. The detection of this intermediate sets the stage for a more detailed dissection of the TauD reaction mechanism than has previously been reported for any other member of this important enzyme family.

Examples of high-frequency EPR studies in bioinorganic chemistry

Low-temperature EPR spectroscopy with frequencies between 95 and 345 GHz and magnetic fields up to 12 T has been used to study metal sites in proteins or inorganic complexes and free radicals. The high-field EPR method was used to resolve g-value anisotropy by separating it from overlapping hyperfine couplings. The presence of hydrogen bonding interactions to the tyrosyl radical oxygens in ribonucleotide reductases were detected. At 285 GHz the g-value anisotropy from the rhombic type 2 Cu(II) signal in the enzyme laccase has its g-value anisotropy clearly resolved from slightly different overlapping axial species. Simple metal site systems with S>1/2 undergo a zero-field splitting, which can be described by the spin Hamiltonian. From high-frequency EPR, the D values that are small compared to the frequency (high-field limit) can be determined directly by measuring the distance of the outermost signal to the center of the spectrum, which corresponds to (2 S-1)* mid R: Dmid R: For example, D values of 0.8 and 0.3 cm(-1) are observed for S=5/2 Fe(III)-EDTA and transferrin, respectively. When D values are larger compared to the frequency and in the case of half-integer spin systems, they can be obtained from the frequency dependence of the shifts of g(eff), as observed for myoglobin in the presence ( D=5 cm(-1)) or absence ( D=9.5 cm(-1)) of fluoride. The 285 and 345 GHz spectra of the Fe(II)-NO-EDTA complex show that it is best described as a S=3/2 system with D=11.5 cm(-1), E=0.1 cm(-1), and g(x)= g(y)= g(z)=2.0. Finally, the effects of HF-EPR on X-band EPR silent states and weak magnetic interactions are demonstrated.

Spectroscopic studies of the effect of ligand donor strength on the Fe-NO bond intradiol dioxygenases

The geometric and electronic structure of NO bound to reduced protocatechuate 3,4-dioxygenase and its substrate (3,4-dihydroxybenzoate, PCA) complex have been examined by X-ray absorption (XAS), UV-vis absorption (Abs), magnetic circular dichroism (MCD), and variable temperature variable field (VTVH) MCD spectroscopies. The results are compared to those previously published on model complexes described as [FeNO]7 systems in which an S = 5/2 ferric center is antiferromagnetically coupled to an S = 1 NO-. XAS pre-edge analysis indicates that the Fe-NO units in FeIIIPCD[NO-] and FeIIIPCD[PCA,NO-] lack the greatly increased pre-edge intensity representative of most [FeNO]7 model sites. Furthermore, from extended X-ray absorption fine structure (EXAFS) analysis, the FeIIIPCD[NO-] and FeIIIPCD[PCA,NO-] active sites are shown to have an Fe-NO distance of at least 1.91 A, approximately 0.2 A greater than those found in the model complexes. The weakened Fe-NO bond is consistent with the overall lengthening of the bond lengths and the fact that VTVH MCD data show that NO(-)-->FeIII CT transitions are no longer polarized along the z-axis of the zero-field splitting tensor. The weaker Fe-NO bond derives from the strong donor interaction of the endogenous phenolate and substrate catecholate ligands, which is observed from the increased intensity in the CT region relative to that of [FeNO]7 model complexes, and from the shift in XAS edge position to lower energy. As NO is an analogue of O2, the effect of endogenous ligand donor strength on the Fe-NO bond has important implications with respect to O2 activation by non-heme iron enzymes.

Benzoate 1,2-dioxygenase from Pseudomonas putida: single turnover kinetics and regulation of a two-component Rieske dioxygenase

The benzoate 1,2-dioxygenase system (BZDOS) from Pseudomonas putida mt-2 catalyzes the NADH-dependent oxidation of benzoate to 1-carboxy-1,2-cis-dihydroxycyclohexa-3,5-diene. Both the oxygenase (BZDO) and reductase (BZDR) components of BZDOS have been purified and characterized kinetically and by optical, EPR, and Mössbauer spectroscopies. BZDO has an (alpha beta)(3) subunit structure in which each alpha subunit contains a Rieske [2Fe-2S] cluster and a mononuclear iron site. Two different purification protocols were developed for BZDO allowing the mononuclear iron to be stabilized in either the Fe(III) or the Fe(II) state for spectroscopic characterization. Using single turnover reactions, it is shown that fully reduced BZDO alone is capable of yielding the cis-diol product in high yield at rates that exceed the BZDOS turnover number. At the conclusion of turnover, quantification of each oxidation state of the metal sites by EPR and Mössbauer spectroscopies shows that the Rieske cluster and mononuclear iron are each oxidized in amounts equal to the product yield, suggesting that the two electrons required for catalysis derive from the two metal centers. These results are in agreement with our previous study of naphthalene 1,2-dioxygenase [Wolfe, M. D., Parales, J. V., Gibson, D. T., and Lipscomb, J. D. (2001) J. Biol. Chem. 276, 1945-1953], which belongs to a different Rieske dioxygenase subclass, suggesting that it is a universal characteristic of Rieske dioxygenases that oxygen activation and substrate oxidation are catalyzed by the oxygenase component alone. The EPR spectrum of the Fe(III) center after a single turnover is distinct from either of those of substrate-free or substrate-bound enzyme. The complex with this spectrum is not formed by addition of cis-diol product to the resting Fe(III) form of the enzyme but is observed when the Fe(II) form is oxidized in the presence of product. Together, these results suggest that product exchange occurs only when the mononuclear iron is reduced. Stopped-flow and rapid scan analyses monitoring the oxidation of the Rieske cluster during the single turnover reaction show that it occurs in three phases that are kinetically competent for catalysis. The rate of each phase was found to be dependent on the type of substrate present, suggesting that the substrate influences the rate of electron transfer between the metal clusters. The participation of substrate in the oxygen activation reaction suggests a new aspect of the mechanism of this process by the Rieske dioxygenase class.

Tuning the electronic structure of octahedral iron complexes [FeL(X)] (L = 1-alkyl-4,7-bis(4-tert-butyl-2-mercaptobenzyl)-1,4,7-triazacyclononane, X = Cl, CH(3)O, CN, NO). The S = 1/2 <==>3/2 Spin equilibrium of [FeL(Pr)(NO)]

Two new pentadentate, pendent arm macrocyclic ligands of the type 1-alkyl-4,7-bis(4-tert-butyl-2-mercaptobenzyl)-1,4,7-triazacyclononane where alkyl represents an isopropyl, (L(Pr))(2-), or an ethyl group, (L(Et))(2-), have been synthesized. It is shown that they bind strongly to ferric ions generating six-coordinate species of the type [Fe(L(alk))X]. The ground state of these complexes is governed by the nature of the sixth ligand, X: [Fe(III)(L(Et))Cl] (2) possesses an S = 5/2 ground state as do [Fe(III)(L(Et))(OCH(3))] (3) and [Fe(III)(L(Pr))(OCH(3))] (4). In contrast, the cyano complexes [Fe(III)(L(Et))(CN)] (5) and [Fe(III)(L(Pr))(CN)] (6) are low spin ferric species (S = 1/2). The octahedral [FeNO](7) nitrosyl complex [Fe(L(Pr))(NO)] (7) displays spin equilibrium behavior S = 1/2<==>S = (3)/(2) in the solid state. Complexes [Zn(L(Pr))] (1), 4.CH(3)OH, 5.0.5toluene.CH(2)Cl(2), and 7.2.5CH(2)Cl(2) have been structurally characterized by low-temperature (100 K) X-ray crystallography. All iron complexes have been carefully studied by zero- and applied-field Mössbauer spectroscopy. In addition, Sellmann's complexes [Fe(pyS(4))(NO)](0/1+) and [Fe(pyS(4))X] (X = PR(3), CO, SR(2)) have been studied by EPR and Mössbauer spectroscopies and DFT calculations (pyS(4) = 2,6-bis(2-mercaptophenylthiomethyl)pyridine(2-)). It is concluded that the electronic structure of 7 with an S = 1/2 ground state is low spin ferrous (S(Fe) = 0) with a coordinated neutral NO radical (Fe(II)-NO) whereas the S = 3/2 state corresponds to a high spin ferric (S(Fe) = 5/2) antiferromagnetically coupled to an NO(-) anion (S = 1). The S = 1/2<==>S = 3/2 equilibrium is then that of valence tautomers rather than that of a simple high spin<==>low spin crossover.

Mechanistic information on the reversible binding of NO to selected iron(II) chelates from activation parameters

Mechanistic insight on the reversible binding of NO to Fe(II) chelate complexes as potential catalysts for the removal of NO from effluent gas streams has been obtained from the temperature and pressure parameters for the "on" and "off" reactions determined using a combination of flash photolysis and stopped-flow techniques. These parameters are correlated with those for water exchange reactions on the corresponding Fe(II) and Fe(III) chelate complexes, from which mechanistic conclusions are drawn. Small and positive Delta V(++) values are found for NO binding to and release from all the selected complexes, consistent with a dissociative interchange (I(d)) mechanism. The only exception in the series of studied complexes is the binding of NO to [Fe(II)(nta)(H(2)O)(2)](-). The negative volume of activation observed for this reaction supports the operation of an I(a) ligand substitution mechanism. The apparent mechanistic differences can be accounted for in terms of the electronic and structural features of the studied complexes. The results indicate that the aminocarboxylate chelates affect the rate and overall equilibrium constants, as well as the nature of the substitution mechanism by which NO coordinates to the selected complexes. There is, however, no simple correlation between the rate and activation parameters and the selected donor groups or overall charge on the iron(II) complexes.

The use of high field/frequency EPR in studies of radical and metal sites in proteins and small inorganic models

Low temperature electron paramagnetic resonance (EPR) spectroscopy with frequencies between 95 and 345 GHz and magnetic fields up to 12 T have been used to study radicals and metal sites in proteins and small inorganic model complexes. We have studied radicals, Fe, Cu and Mn containing proteins. For S = 1/2 systems, the high frequency method can resolve the g-value anisotropy. It was used in mouse ribonucleotide reductase (RNR) to show the presence of a hydrogen bond to the tyrosyl radical oxygen. At 285 GHz the type 2 Cu(II) signal in the complex enzyme laccase is clearly resolved from the Hg(II) containing laccase peroxide adduct. For simple metal sites, the systems over S = 1/2 can be described by the spin Hamiltonian: H(S) = BgS + D[Sz2 - S(S + 1)/3 + E/D (Sx2 - Sy2)]. From the high frequency EPR the D-value can be determined directly by, (I) shifts of g(eff) for half-integer spin systems with large D-values as observed at 345 GHz on an Fe(II)-NO-EDTA complex, which is best described as S = 3/2 system with D = 11.5 cm(-1), E = 0.1 cm(-1) and gx = gy = gz = 2.0; (II) measuring the outermost signal, for systems with small D values, distant of (2S - 1) x absolute value(D) from the center of the spectrum as observed in S= 5/2 Fe(III)-EDTA. In Mn(II) substituted mouse RNR R2 protein the weakly interacting Mn(II) at X-band could be observed as decoupled Mn(II) at 285 GHz.

The mechanism-based inactivation of 2,3-dihydroxybiphenyl 1,2-dioxygenase by catecholic substrates

2,3-Dihydroxybiphenyl 1,2-dioxygenase (EC ), the extradiol dioxygenase of the biphenyl biodegradation pathway, is subject to inactivation during the steady-state cleavage of catechols. Detailed analysis revealed that this inactivation was similar to the O(2)-dependent inactivation of the enzyme in the absence of catecholic substrate, resulting in oxidation of the active site Fe(II) to Fe(III). Interestingly, the catecholic substrate not only increased the reactivity of the enzyme with O(2) to promote ring cleavage but also increased the rate of O(2)-dependent inactivation. Thus, in air-saturated buffer, the apparent rate constant of inactivation of the free enzyme was (0.7 +/- 0.1) x 10(-3) s(-1) versus (3.7 +/- 0.4) x 10(-3) s(-1) for 2,3-dihydroxybiphenyl, the preferred catecholic substrate of the enzyme, and (501 +/- 19) x 10(-3) s(-1) for 3-chlorocatechol, a potent inactivator of 2,3-dihydroxybiphenyl 1,2-dioxygenase (partition coefficient = 8 +/- 2, K(m)(app) = 4.8 +/- 0.7 microm). The 2,3-dihydroxybiphenyl 1,2-dioxygenase-catalyzed cleavage of 3-chlorocatechol yielded predominantly 2-pyrone-6-carboxylic acid and 2-hydroxymuconic acid, consistent with the transient formation of an acyl chloride. However, the enzyme was not covalently modified by this acyl chloride in vitro or in vivo. The study suggests a general mechanism for the inactivation of extradiol dioxygenases during catalytic turnover involving the dissociation of superoxide from the enzyme-catecholic-dioxygen ternary complex and is consistent with the catalytic mechanism.

Kinetics, mechanism, and spectroscopy of the reversible binding of nitric oxide to aquated iron(II). An undergraduate text book reaction revisited

A detailed kinetic and mechanistic analysis of the classical "brown-ring" reaction of [Fe(H(2)O)(6)](2+) with NO was performed using stopped-flow and laser flash photolysis techniques at ambient and high pressure. The kinetic parameters for the "on" and "off" reactions at 25 degrees C were found to be k(on) = 1.42 x 10(6) M(-1) s(-1), DeltaH(++)(on) = 37.1 +/- 0.5 kJ mol(-1), DeltaS(++)(on) = -3 +/- 2 J K(-1) mol(-1), DeltaV(++)(on) = +6.1 +/- 0.4 cm(3) mol(-1), and k(off) = 3240 +/- 750 s(-1), DeltaH(++)(off) = 48.4 +/- 1.4 kJ mol(-1), DeltaS(++)(off) = -15 +/- 5 J K(-1) mol(-1), DeltaV(++)(off) = +1.3 +/- 0.2 cm(3) mol(-1). These parameters suggest that both reactions follow an interchange dissociative (I(d)) ligand substitution mechanism, which correlates well with the suggested mechanism for the water exchange reaction on [Fe(H(2)O)(6)](2+). In addition, Mössbauer spectroscopy and EPR measurements were performed on the reaction product [Fe(H(2)O)(5)(NO)](2+). The Mössbauer and EPR parameters closely resemble those of the [FeNO](7) units in any of the other well-characterized nitrosyl complexes. It is concluded that its electronic structure is best described by the presence of high-spin Fe(III) antiferromagnetically coupled to NO(-) (S = 1) yielding the observed spin quartet ground state (S = (3)/(2)), i.e., [Fe(III)(H(2)O)(5)(NO(-))](2+), and not [Fe(I)(H(2)O)(5)(NO(+))](2+) as usually quoted in undergraduate text books.

Models for extradiol cleaving catechol dioxygenases: syntheses, structures, and reactivities of iron(II)-monoanionic catecholate complexes

Crystallographic and spectroscopic studies of extradiol cleaving catechol dioxygenases indicate that the enzyme-substrate complexes have both an iron(II) center and a monoanionic catecholate. Herein we report a series of iron(II)-monoanionic catecholate complexes, [(L)Fe(II)(catH)](X) (1a, L = 6-Me(3)-TPA (tris(6-methyl-2-pyridylmethyl)amine), catH = CatH (1,2-catecholate monoanion); 1b, L = 6-Me(3)-TPA, catH = DBCH (3,5-di-tert-butyl-1,2-catecholate monoanion); 1c, L = 6-Me(2)-bpmcn (N,N'-dimethyl-N,N'-bis(6-methyl-2-pyridylmethyl)-trans-1,2-diaminocyclohexane), catH = CatH; 1d, L = 6-Me(2)-bpmcn, catH = DBCH), that model such enzyme complexes. The crystal structure of [(6-Me(2)-bpmcn)Fe(II)(DBCH)](+) (1d) shows that the DBCH ligand binds to the iron asymmetrically as previously reported for 1b, with two distinct Fe-O bonds of 1.943(1) and 2.344(1) A. Complexes 1 react with O(2) or NO to afford blue-purple iron(III)-catecholate dianion complexes, [(L)Fe(III)(cat)](+) (2). Interestingly, crystallographically characterized 2d, isolated from either reaction, has the N-methyl groups in a syn configuration, in contrast to the anti configuration of the precursor complex, so epimerization of the bound ligand must occur in the course of isolating 2d. This notion is supported by the fact that the UV-vis and EPR properties of in situ generated 2d(anti) differ from those of isolated 2d(syn). While the conversion of 1 to 2 in the presence of O(2) occurs without an obvious intermediate, that in the presence of NO proceeds via a metastable S = (3)/(2) [(L)Fe(catH)(NO)](+) adduct 3, which can only be observed spectroscopically but not isolated. Intermediates 3a and 3b subsequently disproportionate to afford two distinct complexes, [(6-Me(3)-TPA)Fe(III)(cat)](+) (2a and 2b) and [(6-Me(3)-TPA)Fe(NO)(2)](+) (4) in comparable yield, while 3d converts to 2d in 90% yield. Complexes 2b and anti-2d react further with O(2) over a 24 h period and afford a high yield of cleavage products. Product analysis shows that the products mainly derive from intradiol cleavage but with a small extent of extradiol cleavage (89:3% for 2b and 78:12% for anti-2d). The small amounts of the extradiol cleavage products observed may be due to the dissociation of an alpha-methyl substituted pyridyl arm, generating a complex with a tridentate ligand. Surprisingly, syn-2d does not react with O(2) over the course of 4 days. These results suggest that there are a number of factors that influence the mode and rate of cleavage of catechols coordinated to iron centers.

Single turnover chemistry and regulation of O2 activation by the oxygenase component of naphthalene 1,2-dioxygenase

Naphthalene 1,2-dioxygenase (NDOS) is a three-component enzyme that catalyzes cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene formation from naphthalene, O2, and NADH. We have determined the conditions for a single turnover of NDOS for the first time and studied the regulation of catalysis. As isolated, the alpha3beta3 oxygenase component (NDO) has up to three catalytic pairs of metal centers (one mononuclear Fe2+ and one diferric Rieske iron-sulfur cluster). This form of NDO is unreactive with O2. However, upon reduction of the Rieske cluster and exposure to naphthalene and O2, approximately 0.85 cis-diol product per occupied mononuclear iron site rapidly forms. Substrate binding is required for oxygen reactivity. Stopped-flow and chemical quench analyses indicate that the rate constant of the single turnover product-forming reaction significantly exceeds the NDOS turnover number. UV-visible and electron paramagnetic resonance spectroscopies show that during catalysis, one mononuclear iron and one Rieske cluster are oxidized per product formed, satisfying the two-electron reaction stoichiometry. The addition of oxidized or reduced NDOS ferredoxin component (NDF) increases both the product yield and rate of oxidation of formerly unreactive Rieske clusters. The results show that NDO alone catalyzes dioxygenase chemistry, whereas NDF appears to serve only an electron transport role, in this case redistributing electrons to competent active sites.

Hydrogen peroxide sensitivity of catechol-2,3-dioxygenase: a cautionary note on use of xylE reporter fusions under aerobic conditions

Catechol-2,3-dioxygenase (C23O) of Pseudomonas putida, encoded by the xylE gene, was found to be sensitive to hydrogen peroxide (H(2)O(2)) when used as a reporter in gene fusion constructs. Exposure of Pseudomonas aeruginosa katA or katA katB mutants harboring katA- or katB-lacZ (encoding beta-galactosidase) or -xylE fusion plasmids to H(2)O(2) stimulated beta-galactosidase activity, while there was little or no detectable C23O activity in these strains. More than 95% of C23O activity was lost after a 5-min exposure to equimolar H(2)O(2), while a 10,000-fold excess was required for similar inhibition of beta-galactosidase. Electron paramagnetic resonance spectra of the nitrosyl complexes of C23O showed that H(2)O(2) nearly stoichiometrically oxidized the essential active-site ferrous ion, thus accounting for the loss of activity. Our results suggest using caution in interpreting data derived from xylE reporter fusions under aerobic conditions, especially where oxidative stress is present or when catalase-deficient strains are used.

Detection and imaging of endogenously produced nitric oxide with electron paramagnetic resonance spectroscopy

Nitric oxide (NO) represents a new paradigm for second messengers in regulation. Despite the numerous physiological and pathophysiological functions of NO, its importance as an endogenous second messenger and a cytostatic and/or cytotoxic agent was unknown until 1987. Recent developments in detection methods for endogenous NO produced directly or indirectly from NO synthases (NOSs) have enabled major advances in our understanding of the role of NO in biological systems. The spin-trapping technique combined with electron paramagnetic resonance (EPR) spectroscopy is a method for analyzing NO production directly both in vivo and in vitro. Iron complexes with dithiocarbamate derivatives are noteworthy among the spin-trapping reagents for NO because NO has a high affinity for iron complexes. The resultant stable nitrosyl iron complexes exhibit an intense three-line signal at room temperature and an axial signal at low temperature. Besides the facility and wide applicability of this method, its outstanding feature is that noninvasive in vivo measurements are available by using a low-frequency EPR spectrometer. In this article, we review on previous and recent developments of in vitro, in vivo, and ex vivo EPR detection and imaging of endogenously produced NO.

Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions

BACKGROUND

Sphingomonas paucimobilis SYK-6 utilizes an extradiol-type catecholic dioxygenase, the LigAB enzyme (a protocatechuate 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic acid, PCA). The enzyme belongs to the family of class III extradiol-type catecholic dioxygenases catalyzing the ring-opening reaction of protocatechuate and related compounds. The primary structure of LigAB suggests that the enzyme has no evolutionary relationship with the family of class II extradiol-type catecholic dioxygenases. Both the class II and class III enzymes utilize a non-heme ferrous center for adding dioxygen to the substrate. By elucidating the structure of LigAB, we aimed to provide a structural basis for discussing the function of class III enzymes.

RESULTS

The crystal structure of substrate-free LigAB was solved at 2.2 A resolution. The molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit. Because of the apparent oxidation of the Fe ion into the nonphysiological Fe(III) state, we could also solve the structure of LigAB complexed with a substrate, PCA. The iron coordination sphere in this complex is a distorted tetragonal bipyramid with one ligand missing, which is presumed to be the O2-binding site.

CONCLUSIONS

The structure of LigAB is completely different from those of the class II extradiol-type dioxygenases exemplified by the BphC enzyme, a 2,3-dihydroxybiphenyl 1,2-dioxygenase from a Pseudomonas species. Thus, as already implicated by the primary structures, no evolutionary relationship exists between the class II and III enzymes. However, the two classes of enzymes share many geometrical characteristics with respect to the nature of the iron coordination sphere and the position of a putative catalytic base, strongly suggesting a common catalytic mechanism.

Reactions of nitric oxide with the reduced non-heme diiron center of the soluble methane monooxygenase hydroxylase

The soluble methane monooxygenase system from Methylococcus capsulatus (Bath) catalyzes the oxidation of methane to methanol and water utilizing dioxygen at a non-heme, carboxylate-bridged diiron center housed in the hydroxylase (H) component. To probe the nature of the reductive activation of dioxygen in this system, reactions of an analogous molecule, nitric oxide, with the diiron(II) form of the enzyme (Hred) were investigated by both continuous and discontinuous kinetics methodologies using optical, EPR, and Mössbauer spectroscopy. Reaction of NO with Hred affords a dinitrosyl species, designated Hdinitrosyl, with optical spectra (lambdamax = 450 and 620 nm) and Mössbauer parameters (delta = 0.72 mm/s, DeltaEQ = 1.55 mm/s) similar to those of synthetic dinitrosyl analogues and of the dinitrosyl adduct of the reduced ribonucleotide reductase R2 (RNR-R2) protein. The Hdinitrosyl species models features of the Hperoxo intermediate formed in the analogous dioxygen reaction. In the presence of protein B, Hdinitrosyl builds up with approximately the same rate constant as Hperoxo ( approximately 26 s-1) at 4 degrees C. In the absence of protein B, the kinetics of Hdinitrosyl formation were best fit with a biphasic A --> B --> C model, indicating the presence of an intermediate species between Hred and Hdinitrosyl. This result contrasts with the reaction of Hred with dioxygen, in which the Hperoxo intermediate forms in measurable quantities only in the presence of protein B. These findings suggest that protein B may alter the positioning but not the availability of coordination sites on iron for exogenous ligand binding and reactivity.

Biochemical and genetic characterization of a gentisate 1, 2-dioxygenase from Sphingomonas sp. strain RW5

A 4,103-bp long DNA fragment containing the structural gene of a gentisate 1,2-dioxygenase (EC 1.13.11.4), gtdA, from Sphingomonas sp. strain RW5 was cloned and sequenced. The gtdA gene encodes a 350-amino-acid polypeptide with a predicted size of 38.85 kDa. Comparison of the gtdA gene product with protein sequences in databases, including those of intradiol or extradiol ring-cleaving dioxygenases, revealed no significant homology except for a low similarity (27%) to the 1-hydroxy-2-naphthoate dioxygenase (phdI) of the phenanthrene degradation in Nocardioides sp. strain KP7 (T. Iwabuchi and S. Harayama, J. Bacteriol. 179:6488-6494, 1997). This gentisate 1,2-dioxygenase is thus a member of a new class of ring-cleaving dioxygenases. The gene was subcloned and hyperexpressed in E. coli. The resulting product was purified to homogeneity and partially characterized. Under denaturing conditions, the polypeptide exhibited an approximate size of 38.5 kDa and migrated on gel filtration as a species with a molecular mass of 177 kDa. The enzyme thus appears to be a homotetrameric protein. The purified enzyme stoichiometrically converted gentisate to maleylpyruvate, which was identified by gas chromatography-mass spectrometry analysis as its methyl ester. Values of affinity constants (Km) and specificity constants (Kcat/Km) of the enzyme were determined to be 15 microM and 511 s-1 M-1 x 10(4) for gentisate and 754 microM and 20 s-1 M-1 x 10(4) for 3, 6-dichlorogentisate. Three further open reading frames (ORFs) were found downstream of gtdA. The deduced amino acid sequence of ORF 2 showed homology to several isomerases and carboxylases, and those of ORFs 3 and 4 exhibited significant homology to enzymes of the glutathione isomerase superfamily and glutathione reductase superfamily, respectively.

Cyanide and nitric oxide binding to reduced protocatechuate 3,4-dioxygenase: insight into the basis for order-dependent ligand binding by intradiol catecholic dioxygenases

EPR-silent, chemically reduced protocatechuate 3,4-dioxygenase (Er) binds NO at the active site Fe2+ to yield an EPR-active, S = 3/2 species that blocks subsequent binding of all other exogenous ligands. In contrast, addition of NO to a preformed Er.CN- complex yields an EPR-active, S = 1/2 species [Er.(CN)x.NO] that exhibits resolved superhyperfine splitting from 13CN-, 15/14NO, and a protein-derived 14N. Simulations of the EPR spectra observed for the Er.(CN)x.NO complex formed with 12CN- and 13CN- (1:1) show that CN- binds in two iron ligand sites (x >/= 2). The two cyanides exhibit similar, but distinguishable, hyperfine coupling constants. This demonstrates unambiguously that at least three exogenous ligands (two cyanides and NO) can bind to the Fe2+ simultaneously and strongly suggests that at least one histidine ligand is retained in the complex. The Er.(CN)>/=2.NO complex readily exchanges both of the bound cyanides for the substrate analog, 2-hydroxyisonicotinic acid N-oxide (INO), to form a Er.INO.NO complex exhibiting the same S = 3/2 type EPR spectrum that is observed for this complex in the absence of CN-. Because the dead-end Er.NO complex does not accumulate during the exchange, the results suggest that Er.(CN)>/=2. NO and Er.INO.NO are in conformational states that allow facile exchange of INO and CN- but not NO. The results are interpreted in the context of the known X-ray crystal structures for the ferric form of the resting enzyme (Eox) and numerous Eox.substrate, inhibitor, and CN- complexes, all of which have a charge neutral iron center. It is proposed that the binding of one CN- causes dissociation of an anionic endogenous ligand which begins a series of conformational changes analogous to those initiated by anionic substrate binding to Eox. This results in a new unique coordination site for NO, and a new second site for CN-; both cyanide sites are utilized when the enzyme subsequently binds substrates or INO.

Mössbauer study of 4-hydroxybutyryl-CoA dehydratase--probing the role of an iron-sulfur cluster in an overall non-redox reaction

4-Hydroxybutyryl-CoA dehydratase from Clostridium aminobutyricum catalyzes the dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA. Although dehydration is an overall non-redox reaction, the enzyme contains FAD and Fe-S clusters. Previous work has shown that the Fe-S clusters are difficult to reduce and therefore unlikely to be redox-active in catalysis. Here, Mössbauer spectroscopy has been used to characterise the Fe-S clusters in active as well as in air-inactivated enzyme. In zero magnetic field at 80 K and 4.2 K, the spectra of active dehydratase consisted mainly of one species (95%) with quadrupole splitting, deltaE(Q) = 1.00 mm s(-1) and isomer shift, delta = 0.43 mm s(-1). Magnetically perturbed Mössbauer spectra indicated a spin of zero. In the presence of 6 mM crotonyl-CoA, the spectra remained unchanged. Taken together, the data show that there are [4Fe-4S]2+ in the enzyme, most probably two clusters/homotetramer, that the four iron atoms in each cluster are coordinated in an identical fashion, and that there is no direct interaction with substrates. We therefore infer that the Fe-S clusters serve a structural rather than a catalytic role in 4-hydroxybutyryl-CoA dehydratase. In air-inactivated enzyme (10% residual activity), a new doublet appeared (58%) with deltaE(Q) = 0.72 mm s(-1), delta = 0.32 mm s(-1) and S = 0. The assignment of this subspectrum to [3Fe-4S]+ clusters, based on the typical Mössbauer parameters, is contradicted by the finding of spin zero for the species. One possible explanation could be spin-coupling of two [3Fe-4S]+ clusters in close proximity.

Novel genes encoding 2-aminophenol 1,6-dioxygenase from Pseudomonas species AP-3 growing on 2-aminophenol and catalytic properties of the purified enzyme

2-Aminophenol 1,6-dioxygenase was purified from the cell extracts of Pseudomonas sp. AP-3 grown on 2-aminophenol. The product from 2-aminophenol by catalysis of the purified enzyme was identified as 2-aminomuconic 6-semialdehyde by gas chromatographic and mass spectrometric analyses. The molecular mass of the native enzyme was 140 kDa based on gel filtration. It was dissociated into molecular mass subunits of 32 (alpha-subunit) and 40 kDa (beta-subunit) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating that the dioxygenase was a heterotetramer of alpha2beta2. The genes coding for the alpha- and beta-subunits of the enzyme were cloned and sequenced. Open reading frames of the genes (amnA and amnB) were 816 and 918 base pairs in length, respectively. The amino acid sequences predicted from the open reading frames of amnA and amnB corresponded to the NH2-terminal amino acid sequences of the alpha-subunit (AmnA) and beta-subunit (AmnB), respectively. The deduced amino acid sequences of AmnB showed identities to some extent with HpaD (25.4%) and HpcB (24.4%) that are homoprotocatechuate 2,3-dioxygenases from Escherichia coli W and C, respectively, belonging to class III in the extradiol dioxygenases. On the other hand, AmnA had identity (23.3%) with only AmnB among the enzymes examined.

Cloning, overexpression, and mutagenesis of the gene for homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum

Homoprotocatechuate (hpca, 3,4-dihydroxyphenylacetate) is a central intermediate for the bacterial degradation of aromatic compounds. Homoprotocatechuate 2,3-dioxygenase (HPCD) catalyzes the key ring cleavage step in the metabolism of hpca by the Gram (+) bacterium Brevibacterium fuscum to yield alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. A genomic DNA library of B. fuscum was constructed in Escherichia coli using a cosmid vector and screened by spraying the cells with hpca. One clone was found to contain the gene for HPCD based on its ability to convert hpca into the yellow-colored product. This cosmid clone was further subcloned and the gene for HPCD was localized and sequenced. The open reading frame codes for a protein with 365 amino acids and M(r) = 41,699, in accord with the characteristics of the previously purified wild-type enzyme. The gene for HPCD was overexpressed in E. coli to approximately 30% of the total soluble protein, and purification of the recombinant enzyme to apparent homogeneity was achieved by a two-step procedure. Iron was the only abundant metal found in the purified recombinant enzyme, and the specific activity per iron was comparable to that observed for the wild-type enzyme. The deduced amino acid sequence of HPCD has a very high level of homology (78.6% identity in the 337-aa overlap) to the manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) from Arthrobacter globiformis CM-2. The basis for the difference in metal selection by HPCD and MndD was investigated by mutagenesis of a 50-base-pair region of the HPCD gene containing three frame shifts relative to the MndD gene. The purified triple mutant of HPCD did not exhibit a significant change in the metal content; therefore, other factors must contribute to the selection of the active site metal.

Evidence for an iron center in the ammonia monooxygenase from Nitrosomonas europaea

Binding of the ligand, nitric oxide, in the presence of reductant was used to identify a ferrous S = 3/2 signal, characteristic of a ferrous nitrosyl complex, and a g= 2.03 copper or iron signal in membranes of the ammonia-oxidizing bacterium, Nitrosomonas europaea. The same ferrous S = 3/2 signal is thought to be a component of the membrane-associated methane monooxygenase (pMMO) of Methylococcus capsulatus Bath, since it is seen in the membrane fraction of cells expressing pMMO and in the purified enzyme, but not in the membrane fraction of cells expressing the soluble MMO [Zahn, J.A. and DiSpirito, A.A. (1996) J. Bacteriol. 178, 1018-1029]. Treatment of resting membranes or cells of N. europaea with nitrapyrin, 2-chloro,6-trichloromethylpyridine, resulted in the increase in magnitude of a g = 6, high-spin ferric iron signal. In the presence of NO and reductant, nitrapyrin prevented the formation of the S = 3/2 nitrosyl-iron complex while increasing the intensity of the g = 6 signal. Nitrapyrin is a specific inhibitor of, and is reduced by, the ammonia monoxygenase (AMO) [Bédard, C. and Knowles, R. (1989) Microbiol. Rev. 53, 68-83]. Taken together the data suggest that iron capable of forming the S = 3/2 complex is a catalytic component of AMO of N. europaea, possibly a part of the oxygen-activating center. Inactivation of the membrane-associated AMO with acetylene did not diminish the S = 3/2 nitrosyl-iron signal, the g = 6 signal, or the g = 6 signal.

A Carboxylate-Bridged Non-Heme Diiron Dinitrosyl Complex

The reaction of nitric oxide with the carboxylate-bridged diiron(II) complex [Fe(2)(Et-HPTB)(O(2)CPh)](BF(4))(2) (1a) afforded the dinitrosyl adduct, [Fe(2)(NO)(2)(Et-HPTB)(O(2)CPh)](BF(4))(2) (1b), where Et-HPTB = N,N,N',N'-tetrakis(N-ethyl-2-benzimidazolylmethyl)-2-hydroxy-1,3-diaminopropane, in 69% yield. Compound 1b further reacts with dioxygen to form the bis(nitrato) complex, [Fe(2)(Et-HPTB)(NO(3))(2)(OH)](BF(4))(2) (1c). The structure of 1b was determined by X-ray crystallography (triclinic, P&onemacr;, a = 13.5765(8) Å, b = 15.4088(10) Å, c = 16.2145(10) Å, alpha = 73.656(1) degrees, beta = 73.546(1) degrees, gamma = 73.499(1) degrees, V = 3043.8(7) Å(3), T = -80 degrees C, Z = 2, and R = 0.085 and R(w) = 0.095 for 5644 independent reflections with I > 3sigma(I)). The two nitrosyl units are equivalent with an average Fe-N-O angle of 167.4 +/- 0.8 degrees. Spectroscopic characterization of solid 1b revealed an NO stretch at 1785 cm(-)(1) in the infrared and Mössbauer parameters of delta = 0.67 mm s(-)(1) and DeltaE(Q) = 1.44 mm s(-)(1) at 4.2 K. These data are comparable to those for other {FeNO}(7) systems. An S = (3)/(2) spin state was assigned from magnetic susceptibility studies to the two individual {FeNO} centers, each of which has a nitrosyl ligand antiferromagnetically coupled to iron. A least-squares fit of the chi vs temperature plots to a theoretical model yielded an exchange coupling constant J of -23 cm(-)(1), where H = -2JS(1).S(2), indicating that the two S = (3)/(2) centers are antiferromagnetically coupled to one another. An extended Hückel calculation on a model complex, [Fe(2)(NO)(2)(NH(3))(6)(O(2)CH)(OH)](2+), revealed that the magnitudes of Fe-N-O angles are dictated by pi-bonding interactions between the Fe d(xz)() and NO pi orbitals.

Spectroscopic and kinetic properties of unphosphorylated rat hepatic phenylalanine hydroxylase expressed in Escherichia coli. Comparison of resting and activated states

The non-heme iron-dependent metalloenzyme, rat hepatic phenylalanine hydroxylase (EC 1.14.16.1; phenylalanine 4-monooxygenase (PAH) was overexpressed in Escherichia coli and purified to homogeneity, allowing a detailed comparison of the kinetic, hydrodynamic, and spectroscopic properties of its allosteric states. The homotetrameric recombinant enzyme, which is highly active and contains 0.7-0.8 iron atoms per subunit, is identical to the native enzyme in several properties: Km, 6-methyltetrahydropterin = 61 microM and L-Phe = 170 microM; Vmax = 9 s-1 (compared to 45 microM, 180 microM, and 13 s-1 for the rat hepatic enzyme). L-Phe and lysolecithin treatment induce the rPAHT-->rPAHR (where r is recombinant) allosteric transformation necessary for rPAH activity. Characteristic changes in the fluorescence spectra, increased hydrophobicity, a large activation energy barrier, and a 10% volume increase of the tetrameric structure are consistent with a significant reorganization of the protein following allosteric activation. However, optical and EPR spectroscopic data suggest that only minor changes occur in the primary coordination sphere (carboxylate/histidine/water) of the catalytic iron center. Detailed steady state kinetic investigations, using 6-methyltetrahydropterin as cofactor and lysolecithin as activator, indicate rPAH follows a sequential mechanism. A catalytic Arrhenius Eact of 14.6 +/- 0.3 kcal/mol subunit was determined from temperature-dependent stopped-flow kinetics data. rPAH inactivates during L-Phe hydroxylation with a half-life of 4.3 min at 25 degrees C, corresponding to an Arrhenius Eact of 10 +/- 1 kcal/mol subunit for the inactivation process. Catechol binding (2.4 x 10(6) M-1) is shown to occur only at catalytically competent iron sites. Ferrous rPAH binds NO, giving rise to an ST = 3/2 spin system.