Mechanistic implications for the formation of the diiron cluster in ribonucleotide reductase provided by quantitative EPR spectroscopy

Can iron chelators ameliorate viral infections?

The redox reactivity of iron is a double-edged sword for cell functions, being either essential or harmful depending on metal concentration and location. Deregulation of iron homeostasis is associated with several clinical conditions, including viral infections. Clinical studies as well as in silico, in vitro and in vivo models show direct effects of several viruses on iron levels. There is support for the strategy of iron chelation as an alternative therapy to inhibit infection and/or viral replication, on the rationale that iron is required for the synthesis of some viral proteins and genes. In addition, abnormal iron levels can affect signaling immune response. However, other studies report different effects of viral infections on iron homeostasis, depending on the class and genotype of the virus, therefore making it difficult to predict whether iron chelation would have any benefit. This review brings general aspects of the relationship between iron homeostasis and the nonspecific immune response to viral infections, along with its relevance to the progress or inhibition of the inflammatory process, in order to elucidate situations in which the use of iron chelators could be efficient as antivirals.

X-Band Parallel-Mode and Multifrequency Electron Paramagnetic Resonance Spectroscopy of S = 1/2 Bismuth Centers

The recent successes in the isolation and characterization of several bismuth radicals inspire the development of new spectroscopic approaches for the in-depth analysis of their electronic structure. Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for the characterization of main group radicals. However, the large electron-nuclear hyperfine interactions of Bi (²⁰⁹Bi, I = 9/2) have presented difficult challenges to fully interpret the spectral properties for some of these radicals. Parallel-mode EPR (B₁∥B₀) is almost exclusively employed for the study of S > 1/2 systems but becomes feasible for S = 1/2 systems with large hyperfine couplings, offering a distinct EPR spectroscopic approach. Herein, we demonstrate the application of conventional X-band parallel-mode EPR for S = 1/2, I = 9/2 spin systems: Bi-doped crystalline silicon (Si:Bi) and the molecular Bi radicals [L(X)Ga]₂Bi^• (X = Cl or I) and [L(Cl)GaBi(^MecAAC)]^•+ (L = HC[MeCN(2,6-iPr₂C₆H₃)]₂). In combination with multifrequency perpendicular-mode EPR (X-, Q-, and W-band frequencies), we were able to fully refine both the anisotropic g- and A-tensors of these molecular radicals. The parallel-mode EPR experiments demonstrated and discussed here have the potential to enable the characterization of other S = 1/2 systems with large hyperfine couplings, which is often challenging by conventional perpendicular-mode EPR techniques. Considerations pertaining to the choice of microwave frequency are discussed for relevant spin-systems.

The periodic table of ribonucleotide reductases

In most organisms, transition metal ions are necessary cofactors of ribonucleotide reductase (RNR), the enzyme responsible for biosynthesis of the 2'-deoxynucleotide building blocks of DNA. The metal ion generates an oxidant for an active site cysteine (Cys), yielding a thiyl radical that is necessary for initiation of catalysis in all RNRs. Class I enzymes, widespread in eukaryotes and aerobic microbes, share a common requirement for dioxygen in assembly of the active Cys oxidant and a unique quaternary structure, in which the metallo- or radical-cofactor is found in a separate subunit, β, from the catalytic α subunit. The first class I RNRs, the class Ia enzymes, discovered and characterized more than 30 years ago, were found to use a diiron(III)-tyrosyl-radical Cys oxidant. Although class Ia RNRs have historically served as the model for understanding enzyme mechanism and function, more recently, remarkably diverse bioinorganic and radical cofactors have been discovered in class I RNRs from pathogenic microbes. These enzymes use alternative transition metal ions, such as manganese, or posttranslationally installed tyrosyl radicals for initiation of ribonucleotide reduction. Here we summarize the recent progress in discovery and characterization of novel class I RNR radical-initiating cofactors, their mechanisms of assembly, and how they might function in the context of the active class I holoenzyme complex.

Probing the Structure and Binding Mode of EDTA on the Surface of Mn3O4 Nanoparticles for Water Oxidation by Advanced Electron Paramagnetic Resonance Spectroscopy

Identification of the surface structure of nanoparticles is important for understanding the catalytic mechanism and improving the properties of the particles. Here, we provide a detailed description of the coordination modes of ethylenediaminetetraacetate (EDTA) on Mn₃O₄ nanoparticles at the atomic level, as obtained by advanced electron paramagnetic resonance (EPR) spectroscopy. Binding of EDTA to Mn₃O₄ leads to dramatic changes in the EPR spectrum, with a 5-fold increase in the axial zero-field splitting parameter of Mn(II). This indicates significant changes in the coordination environment of the Mn(II) site; hence, the binding of EDTA causes a profound change in the electronic structure of the manganese site. Furthermore, the electron spin echo envelope modulation results reveal that two ¹⁴N atoms of EDTA are directly coordinated to the Mn site and a water molecule is coordinated to the surface of the nanoparticles. An Fourier transform infrared spectroscopy study shows that the Ca(II) ion is coordinated to the carboxylic ligands via the pseudobridging mode. The EPR spectroscopic results provide an atomic picture of surface-modified Mn₃O₄ nanoparticles for the first time. These results can enhance our understanding of the rational design of catalysts, for example, for the water oxidation reaction.

X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase

Inorganic pyrophosphatase (PPase) catalyses the hydrolysis reaction of inorganic pyrophosphate to phosphates. Our previous studies showed that manganese (Mn) activated PPase from the psychrophilic bacterium Shewanella sp. AS-11 (Mn-Sh-PPase) has a characteristic temperature dependence of the activity with an optimum at 5 °C. Here we report the X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy structural analyses of Sh-PPase in the absence and presence of substrate analogues. We successfully determined the crystal structure of Mn-Sh-PPase without substrate and Mg-activated Sh-PPase (Mg-Sh-PPase) complexed with substrate analogue (imidodiphosphate; PNP). Crystallographic studies revealed a bridged water placed at a distance from the di-Mn centre in Mn-Sh-PPase without substrate. The water came closer to the metal centre when PNP bound. EPR analysis of Mn-Sh-PPase without substrate revealed considerably weak exchange coupling, whose magnitude was increased by binding of substrate analogues. The data indicate that the bridged molecule has weak bonds with the di-Mn centre, which suggests a 'loose' structure, whereas it comes closer to di-Mn centre by substrate binding, which suggests a 'well-tuned' structure for catalysis. Thus, we propose that Sh-PPase can rearrange the active site and that the 'loose' structure plays an important role in the cold adaptation mechanism.

Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor

A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its β subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O₂^-) for activation, but it does not require the O₂^--supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj β has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj β directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) βs. This tendency makes Fj β unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O₂^- to the Mn₂^II/II cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj β is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-β.

Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Coordinated Two-Stage Mn(II)/(III) and Mn(III)/(IV) Mechanism

The bacterial manganese oxidase MnxG of the Mnx protein complex is unique among multicopper oxidases (MCOs) in carrying out a two-electron metal oxidation, converting Mn(II) to MnO₂ nanoparticles. The reaction occurs in two stages: Mn(II) → Mn(III) and Mn(III) → MnO₂. In a companion study , we show that the electron transfer from Mn(II) to the low-potential type 1 Cu of MnxG requires an activation step, likely forming a hydroxide bridge at a dinuclear Mn(II) site. Here we study the second oxidation step, using pyrophosphate (PP) as a Mn(III) trap. PP chelates Mn(III) produced by the enzyme and subsequently allows it to become a substrate for the second stage of the reaction. EPR spectroscopy confirms the presence of Mn(III) bound to the enzyme. The Mn(III) oxidation step does not involve direct electron transfer to the enzyme from Mn(III), which is shown by kinetic measurements to be excluded from the Mn(II) binding site. Instead, Mn(III) is proposed to disproportionate at an adjacent polynuclear site, thereby allowing indirect oxidation to Mn(IV) and recycling of Mn(II). PP plays a multifaceted role, slowing the reaction by complexing both Mn(II) and Mn(III) in solution, and also inhibiting catalysis, likely through binding at or near the active site. An overall mechanism for Mnx-catalyzed MnO₂ production from Mn(II) is presented.

Characterization of monomeric Mn(II/III/IV)-hydroxo complexes from X- and Q-band dual mode electron paramagnetic resonance (EPR) spectroscopy

Manganese-hydroxo species have been implicated in C-H bond activation performed by metalloenzymes, but the electronic properties of many of these intermediates are not well characterized. The present work presents a detailed characterization of three Mn(n)-OH complexes (where n = II, III, and IV) of the tris[(N'-tert-butylureaylato)-N-ethylene]aminato ([H3buea](3-)) ligand using X- and Q-band dual mode electron paramagnetic resonance (EPR). Quantitative simulations for the [Mn(II)H3buea(OH)](2-) complex demonstrated the ability to characterize similar Mn(II) species commonly present in the resting states of manganese-containing enzymes. The spin states of the Mn(III) and Mn(IV) complexes determined from EPR spectroscopy are S = 2 and 3/2, respectively, as expected for the C3 symmetry imposed by the [H3buea](3-) ligand. Simulations of the spectra indicated the constant presence of two Mn(IV) species in solutions of [Mn(IV)H3buea(OH)] complex. The simulations of perpendicular- and parallel-mode EPR spectra allow determination of zero-field splitting and hyperfine parameters for all complexes. For the Mn(III) and Mn(IV) complexes, density functional theory calculations are used to determine the isotropic Mn hyperfine values, to compare the excited electronic state energies, and to give theoretical estimates of the zero-field energy.

Peroxide-shunt substrate-specificity for the Salmonella typhimurium O2-dependent tRNA modifying monooxygenase (MiaE)

Post-transcriptional modifications of tRNA are made to structurally diversify tRNA. These modifications alter noncovalent interactions within the ribosomal machinery, resulting in phenotypic changes related to cell metabolism, growth, and virulence. MiaE is a carboxylate bridged, nonheme diiron monooxygenase, which catalyzes the O2-dependent hydroxylation of a hypermodified-tRNA nucleoside at position 37 (2-methylthio-N(6)-isopentenyl-adenosine(37)-tRNA) [designated ms(2)i(6)A37]. In this work, recombinant MiaE was cloned from Salmonella typhimurium , purified to homogeneity, and characterized by UV-visible and dual-mode X-band EPR spectroscopy for comparison to other nonheme diiron enzymes. Additionally, three nucleoside substrate-surrogates (i(6)A, Cl(2)i(6)A, and ms(2)i(6)A) and their corresponding hydroxylated products (io(6)A, Cl(2)io(6)A, and ms(2)io(6)A) were synthesized to investigate the chemo- and stereospecificity of this enzyme. In the absence of the native electron transport chain, the peroxide-shunt was utilized to monitor the rate of substrate hydroxylation. Remarkably, regardless of the substrate (i(6)A, Cl(2)i(6)A, and ms(2)i(6)A) used in peroxide-shunt assays, hydroxylation of the terminal isopentenyl-C4-position was observed with >97% E-stereoselectivity. No other nonspecific hydroxylation products were observed in enzymatic assays. Steady-state kinetic experiments also demonstrate that the initial rate of MiaE hydroxylation is highly influenced by the substituent at the C2-position of the nucleoside base (v0/[E] for ms(2)i(6)A > i(6)A > Cl(2)i(6)A). Indeed, the >3-fold rate enhancement exhibited by MiaE for the hydroxylation of the free ms(2)i(6)A nucleoside relative to i(6)A is consistent with previous whole cell assays reporting the ms(2)io(6)A and io(6)A product distribution within native tRNA-substrates. This observation suggests that the nucleoside C2-substituent is a key point of interaction regulating MiaE substrate specificity.

Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study

How cells ensure correct metallation of a given protein and whether a degree of promiscuity in metal binding has evolved are largely unanswered questions. In a classic case, iron- and manganese-dependent superoxide dismutases (SODs) catalyze the disproportionation of superoxide using highly similar protein scaffolds and nearly identical active sites. However, most of these enzymes are active with only one metal, although both metals can bind in vitro and in vivo. Iron(ii) and manganese(ii) bind weakly to most proteins and possess similar coordination preferences. Their distinct redox properties suggest that they are unlikely to be interchangeable in biological systems except when they function in Lewis acid catalytic roles, yet recent work suggests this is not always the case. This review summarizes the diversity of ways in which iron and manganese are substituted in similar or identical protein frameworks. As models, we discuss (1) enzymes, such as epimerases, thought to use Fe(II) as a Lewis acid under normal growth conditions but which switch to Mn(II) under oxidative stress; (2) extradiol dioxygenases, which have been found to use both Fe(II) and Mn(II), the redox role of which in catalysis remains to be elucidated; (3) SODs, which use redox chemistry and are generally metal-specific; and (4) the class I ribonucleotide reductases (RNRs), which have evolved unique biosynthetic pathways to control metallation. The primary focus is the class Ib RNRs, which can catalyze formation of a stable radical on a tyrosine residue in their β2 subunits using either a di-iron or a recently characterized dimanganese cofactor. The physiological roles of enzymes that can switch between iron and manganese cofactors are discussed, as are insights obtained from the studies of many groups regarding iron and manganese homeostasis and the divergent and convergent strategies organisms use for control of protein metallation. We propose that, in many of the systems discussed, "discrimination" between metals is not performed by the protein itself, but it is instead determined by the environment in which the protein is expressed.

Biologically relevant heterodinuclear iron-manganese complexes

The heterodinuclear complexes [Fe(III)Mn(II)(L-Bn)(μ-OAc)(2)](ClO(4))(2) (1) and [Fe(II)Mn(II)(L-Bn)(μ-OAc)(2)](ClO(4)) (2) with the unsymmetrical dinucleating ligand HL-Bn {[2-bis[(2-pyridylmethyl)aminomethyl]]-6-[benzyl-2-(pyridylmethyl)aminomethyl]-4-methylphenol} were synthesized and characterized as biologically relevant models of the new Fe/Mn class of nonheme enzymes. Crystallographic studies have been completed on compound 1 and reveal an Fe(III)Mn(II)μ-phenoxobis(μ-carboxylato) core. A single location of the Fe(III) ion in 1 and of the Fe(II) ion in 2 was demonstrated by Mössbauer and (1)H NMR spectroscopies, respectively. An investigation of the temperature dependence of the magnetic susceptibility of 1 revealed a moderate antiferromagnetic interaction (J = 20 cm(-1)) between the high-spin Fe(III) and Mn(II) ions in 1, which was confirmed by Mössbauer and electron paramagnetic resonance (EPR) studies. The electrochemical properties of complex 1 are described. A quasireversible electron transfer at -40 mV versus Ag/AgCl corresponding to the Fe(III)Mn(II)/Fe(II)Mn(II) couple appears in the cyclic voltammogram. Thorough investigations of the Mössbauer and EPR signatures of complex 2 were performed. The analysis allowed evidencing of a weak antiferromagnetic interaction (J = 5.72 cm(-1)) within the Fe(II)Mn(II) pair consistent with that deduced from magnetic susceptibility measurements (J = 6.8 cm(-1)). Owing to the similar value of the Fe(II) zero-field splitting (D(Fe) = 3.55 cm(-1)), the usual treatment within the strong exchange limit was precluded and a full analysis of the electronic structure of the ground state of complex 2 was developed. This situation is reminiscent of that found in many diiron and iron-manganese enzyme active sites.

Spectroscopic and magnetic properties of an iodo Co(I) tripodal phosphine complex

Reaction of the tripodal phosphine ligand 1,1,1-tris((diphenylphosphino)phenyl)ethane (PhP3) with CoI(2) spontaneously generates a one-electron reduced complex, [(PhP3)Co(I)(I)] (1). The crystal structure of 1 reveals a distorted tetrahedral environment, with an apical Co-I bond distance of ~2.52 Å. Co(II/I) redox occurs at an unusually high potential (+0.38 V vs. SCE). The electronic absorption spectrum of 1 exhibits an MLCT peak at 320 nm (ε = 8790 M(-1) cm(-1)) and a d-d feature at 850 nm (ε = 840 M(-1) cm(-1)). Two more d-d bands are observed in the NIR region, 8650 (ε = 450) and 7950 cm(-1) (ε = 430 M(-1) cm(-1)). Temperature dependent magnetic measurements (SQUID) on 1 (solid state, 20-300 K) give μ(eff) = 2.99(6) μ(B), consistent with an S = 1 ground state. Magnetic susceptibilities below 20 K are consistent with a zero field splitting (zfs) |D| = 8 cm(-1). DFT calculations also support a spin-triplet ground state for 1, as optimized (6-31G*/PW91) geometries (S = 1) closely match the X-ray structure. EPR measurements performed in parallel mode (X-band; 0-15,000 G, 15 K) on polycrystalline 1 or frozen solutions of 1 (THF/toluene) exhibit a feature at g≈ 4 that arises from a (Δm = 2) transition within the M(S) = <+1,-1> manifold. Below 10 K, the EPR signal decreases significantly, consistent with a solution zfs parameter (|D|≈ 8 cm(-1)) similar to that obtained from SQUID measurements. Our work provides an EPR signature for high-spin Co(I) in trigonal ligation.

Class I ribonucleotide reductases: metallocofactor assembly and repair in vitro and in vivo

Incorporation of metallocofactors essential for the activity of many enyzmes is a major mechanism of posttranslational modification. The cellular machinery required for these processes in the case of mono- and dinuclear nonheme iron and manganese cofactors has remained largely elusive. In addition, many metallocofactors can be converted to inactive forms, and pathways for their repair have recently come to light. The class I ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides and require dinuclear metal clusters for activity: an Fe(III)Fe(III)-tyrosyl radical (Y•) cofactor (class Ia), a Mn(III)Mn(III)-Y• cofactor (class Ib), and a Mn(IV)Fe(III) cofactor (class Ic). The class Ia, Ib, and Ic RNRs are structurally homologous and contain almost identical metal coordination sites. Recent progress in our understanding of the mechanisms by which the cofactor of each of these RNRs is generated in vitro and in vivo and by which the damaged cofactors are repaired is providing insight into how nature prevents mismetallation and orchestrates active cluster formation in high yields.

Perturbations of aromatic amino acids are associated with iron cluster assembly in ribonucleotide reductase

The β2 subunit of class Ia ribonucleotide reductases (RNR) contains an antiferromagnetically coupled μ-oxo bridged diiron cluster and a tyrosyl radical (Y122•). In this study, an ultraviolet resonance Raman (UVRR) difference technique describes the structural changes induced by the assembly of the iron cluster and by the reduction of the tyrosyl radical. Spectral contributions from aromatic amino acids are observed through UV resonance enhancement at 229 nm. Vibrational bands are assigned by comparison to histidine, phenylalanine, tyrosine, tryptophan, and 3-methylindole model compound data and by isotopic labeling of histidine in the β2 subunit. Reduction of the tyrosyl radical reveals Y122• Raman bands at 1499 and 1556 cm(-1) and Y122 Raman bands at 1170, 1199, and 1608 cm(-1). There is little perturbation of other aromatic amino acids when Y122• is reduced. Assembly of the iron cluster is shown to be accompanied by deprotonation of histidine. A p(2)H titration study supports the assignment of an elevated pK for the histidine. In addition, structural perturbations of tyrosine and tryptophan are detected. For tryptophan, comparison to model compound data suggests an increase in hydrogen bonding and a change in conformation when the iron cluster is removed. pH and (2)H(2)O studies imply that the perturbed tryptophan is in a low dielectric environment that is close to the metal center and protected from solvent exchange. Tyrosine contributions are attributed to a conformational or hydrogen-bonding change. In summary, our work shows that electrostatic and conformational perturbations of aromatic amino acids are associated with metal cluster assembly in RNR. These conformational changes may contribute to the allosteric effects, which regulate metal binding.

Theoretical and experimental investigation of the semiquinone forms of protocatechuic acid. The effect of manganese

Ten oxidized, oxygenated and dimeric forms of protocatechuic acid (PCA, 3,4-dihydroxybenzoic acid, 3,4-DHBA) have been studied using DFT calculations (at the B3LYP/TZVP level of theory) and their structural and spectroscopic parameters (electronic transitions, NMR resonances) have been calculated. Combination with experimental results (under anaerobic or aerobic environment) determines the conditions for the existence of protonated, fully deprotonate and/or oxygenated semiquinones of PCA. Several energy optimized conformers containing manganese-(PCA-semiquinones) and water or/and peroxo-groups have been drawn (species 11-16) and their structural and spectroscopic properties have been calculated at the same level of theory. Experimental parallel to the theoretical results provide evidence for the existence of Mn(II)- and Mn(III)-[PCA-semiquinone] as well the conditions of dioxygen activation. Two of the blue solids (17 and 18) isolated from these solutions, have been characterized. Elemental analyzes, TGA, IR and ESR spectra support the formulation Mn(2)(PCA)(2)(O(2))(OH)(2)(AcO)(ClO(4))(2)(H(2)O)(3) (17), and Mn(2)(PCA)(2)(O(2))(2)(OH)(2)(AcO)H(2)O (18). Their ESR spectra, in solution (blue solutions), are almost identical and indicative of Mn(IV) existence. From the whole investigation, the activation of dioxygen by the PCA, its relocation on manganese and the oxidation of the metal ion have been provided.

Metalloradical complexes of manganese and chromium featuring an oxidatively rearranged ligand

Redox events involving both metal and ligand sites are receiving increased attention since a number of biological processes direct redox equivalents toward functional residues. Metalloradical synthetic analogues remain scarce and require better definition of their mode of formation and subsequent operation. The trisamido-amine ligand [(RNC6H4)3N]3-, where R is the electron-rich 4-t-Bu Ph, is employed in this study to generate redox active residues in manganese and chromium complexes. Solutions of [(L1)Mn(II)-THF]- in THF are oxidized by dioxygen to afford [(L1re-1)Mn(III)-(O)2-Mn(III)(L1 re-1)]2-as the major product. The rare dinuclear manganese (III,III) core is stabilized by a rearranged ligand that has undergone an one-electron oxidative transformation, followed by retention of the oxidation equivalent as a pi radical in ano-diiminobenzosemiquinonate moiety. Magnetic studies indicate that the ligand-centered radical is stabilized by means of extended antiferromagnetic coupling between the S ) 1/2 radical and the adjacent S ) 2 Mn(III) site, as well as between the two Mn(III) centers via the dioxo bridge. Electrochemical and EPR data suggest that this system can store higher levels of oxidation potency. Entry to the corresponding Cr(III) chemistry is achieved by employing CrCl3 to access both[(L1)Cr(III)-THF] and [(L1re-1)Cr(III)-THF(Cl)], featuring the intact and the oxidatively rearranged ligands, respectively. The latter is generated by ligand-centered oxidation of the former compound. The rearranged ligand is perceived to be the product of an one-electron oxidation of the intact ligand to afford a metal-bound aminyl radical that subsequently mediates a radical 1,4-(N-to-N) aryl migration.

High catalytic activity achieved with a mixed manganese-iron site in protein R2 ofChlamydiaribonucleotide reductase

Ribonucleotide reductase (class I) contains two components: protein R1 binds the substrate, and protein R2 normally has a diferric site and a tyrosyl free radical needed for catalysis. In Chlamydia trachomatis RNR, protein R2 functions without radical. Enzyme activity studies show that in addition to a diiron cluster, a mixed manganese-iron cluster provides the oxidation equivalent needed to initiate catalysis. An EPR signal was observed from an antiferromagnetically coupled high-spin Mn(III)-Fe(III) cluster in a catalytic reaction mixture with added inhibitor hydroxyurea. The manganese-iron cluster in protein R2 confers much higher specific activity than the diiron cluster does to the enzyme.

Multifrequency Pulsed EPR Studies of Biologically Relevant Manganese(II) Complexes

Electron paramagnetic resonance studies at multiple frequencies (MF EPR) can provide detailed electronic structure descriptions of unpaired electrons in organic radicals, inorganic complexes, and metalloenzymes. Analysis of these properties aids in the assignment of the chemical environment surrounding the paramagnet and provides mechanistic insight into the chemical reactions in which these systems take part. Herein, we present results from pulsed EPR studies performed at three different frequencies (9, 31, and 130 GHz) on [Mn(II)(H(2)O)(6)](2+), Mn(II) adducts with the nucleotides ATP and GMP, and the Mn(II)-bound form of the hammerhead ribozyme (MnHH). Through line shape analysis and interpretation of the zero-field splitting values derived from successful simulations of the corresponding continuous-wave and field-swept echo-detected spectra, these data are used to exemplify the ability of the MF EPR approach in distinguishing the nature of the first ligand sphere. A survey of recent results from pulsed EPR, as well as pulsed electron-nuclear double resonance and electron spin echo envelope modulation spectroscopic studies applied to Mn(II)-dependent systems, is also presented.

Role of the C terminus of the ribonucleotide reductase large subunit in enzyme regeneration and its inhibition by Sml1

Ribonucleotide reductase maintains cellular deoxyribonucleotide pools and is thus tightly regulated during the cell cycle to ensure high fidelity in DNA replication. The Sml1 protein inhibits ribonucleotide reductase activity by binding to the R1 subunit. At the completion of each turnover cycle, the active site of R1 becomes oxidized and subsequently regenerated by a cysteine pair (CX2C) at its C-terminal domain (R1-CTD). Here we show that R1-CTD acts in trans to reduce the active site of its neighboring monomer. Both Sml1 and R1-CTD interact with the N-terminal domain of R1 (R1-NTD), which involves a conserved two-residue sequence motif in the R1-NTD. Mutations at these two positions enhancing the Sml1-R1 interaction cause SML1-dependent lethality. These results point to a model whereby Sml1 competes with R1-CTD for association with R1-NTD to hinder the accessibility of the CX2C motif to the active site for R1 regeneration.

Metal binding studies and EPR spectroscopy of the manganese transport regulator MntR

Manganese transport regulator (MntR) is a member of the diphtheria toxin repressor (DtxR) family of transcription factors that is responsible for manganese homeostasis in Bacillus subtilis. Prior biophysical studies have focused on the metal-mediated DNA binding of MntR [Lieser, S. A., Davis, T. C., Helmann, J. D., and Cohen, S. M. (2003) Biochemistry 42, 12634-12642], as well as metal stabilization of the MntR structure [Golynskiy, M. V., Davis, T. C., Helmann, J. D., and Cohen, S. M. (2005) Biochemistry 44, 3380-3389], but only limited data on the metal-binding affinities for MntR are available. Herein, the metal-binding affinities of MntR were determined by using electron paramagnetic resonance (EPR) spectroscopy, as well as competition experiments with the fluorimetric dyes Fura-2 and Mag-fura-2. MntR was not capable of competing with Fura-2 for the binding of transition metal ions. Therefore, the metal-binding affinities and stoichiometries of Mag-fura-2 for Mn2+, Co2+, Ni2+, Zn2+, and Cd2+ were determined and utilized in MntR/Mag-fura-2 competition experiments. The measured Kd values for MntR metal binding are comparable to those reported for DtxR metal binding [Kd from 10(-)7 to 10(-4) M; D'Aquino, J. A., et al. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 18408-18413], AntR [a homologue from Bacillus anthracis; Sen, K. I. et al. (2006) Biochemistry 45, 4295-4303], and generally follow the Irving-Williams series. Direct detection of the dinuclear Mn2+ site in MntR with EPR spectroscopy is presented, and the exchange interaction was determined, J = -0.2 cm-1. This value is lower in magnitude than most known dinuclear Mn2+ sites in proteins and synthetic complexes and is consistent with a dinuclear Mn2+ site with a longer Mn...Mn distance (4.4 A) observed in some of the available crystal structures. MntR is found to have a surprisingly low binding affinity (approximately 160 microM) for its cognate metal ion Mn2+. Moreover, the results of DNA binding studies in the presence of limiting metal ion concentrations were found to be consistent with the measured metal-binding constants. The metal-binding affinities of MntR reported here help to elucidate the regulatory mechanism of this metal-dependent transcription factor.

Mononuclear metal complexes with Piroxicam: Synthesis, structure and biological activity

Piroxicam (=Hpir) is a non-steroidal anti-inflammatory and an anti-arthritic drug. VO(2+), Mn(2+), Fe(3+), MoO(2)(2+) and UO(2)(2+) complexes with deprotonated piroxicam have been prepared and characterized with the use of infrared, UV-Vis, nuclear magnetic resonance and electron paramagnetic resonance spectroscopies. The experimental data suggest that piroxicam acts as a deprotonated bidentate ligand in all complexes and is coordinated to the metal ion through the pyridine nitrogen and the amide oxygen. Molecular mechanics calculations in the gas state have been performed in order to propose a model for the Fe(3+), VO(2+) and MoO(2)(2+) complexes. Potential anticancer cytostatic and cytotoxic effects of piroxicam complexes with VO(2+), Mn(2+) and MoO(2)(2+) on human promyelocytic leukemia HL-60 cells have been investigated. Among all complexes, only VO(pir)(2)(H(2)O) clearly induces apoptosis after 24-h incubation, whereas piroxicam induces apoptosis after 57-h incubation.

Protonation of the Binuclear Metal Center within the Active Site of Phosphotriesterase

Phosphotriesterase (PTE) is a binuclear metalloenzyme that catalyzes the hydrolysis of organophosphates, including pesticides and chemical warfare agents, at rates approaching the diffusion controlled limit. The catalytic mechanism of this enzyme features a bridging solvent molecule that is proposed to initiate nucleophilic attack at the phosphorus center of the substrate. X-band EPR spectroscopy is utilized to investigate the active site of Mn/Mn-substituted PTE. Simulation of the dominant EPR spectrum from the coupled binuclear center of Mn/Mn-PTE requires slightly rhombic zero-field splitting parameters. Assuming that the signal arises from the S = 2 manifold, an exchange coupling constant of J = -2.7 +/- 0.2 cm(-)(1) (H(ex) = -2JS(1) x S(2)) is calculated. A kinetic pK(a) of 7.1 +/- 0.1 associated with loss in activity at low pH indicates that a protonation event is responsible for inhibition of catalysis. Analysis of changes in the EPR spectrum as a function of pH provides a pK(a) of 7.3 +/- 0.1 that is assigned as the protonation of the hydroxyl bridge. From the comparison of kinetic and spectral pK(a) values, it is concluded that the loss of catalytic activity at acidic pH results from the protonation of the hydroxide that bridges the binuclear metal center.

Local and global effects of metal binding within the small subunit of ribonucleotide reductase

Each beta-protomer of the small betabeta subunit of Escherichia coli ribonucleotide reductase (R2) contains a binuclear iron cluster with inequivalent binding sites: Fe(A) and Fe(B). In anaerobic Fe(II) titrations of apoprotein under standard buffer conditions, we show that the majority of the protein binds only one Fe(II) atom per betabeta subunit. Additional iron occupation can be achieved upon exposure to O2 or in high glycerol buffers. The differential binding affinity of the A- and B-sites allows us to produce heterobinuclear Mn(II)Fe(II) and novel Mn(III)Fe(III) clusters within a single beta-protomer of R2. The oxidized species are produced with H2O2 addition. We demonstrate that no significant exchange of metal occurs between the A- and B-sites, and thus the binding of the first metal is under kinetic control, as has been suggested previously. The binding of first Fe(II) atom to the active site in a beta-protomer (betaI) induces a global protein conformational change that inhibits access of metal to the active site in the other beta-protomer (betaII). The binding of the same Fe(II) atom also induces a local effect at the active site in betaI-protomer, which lowers the affinity for metal in the A-site. The mixed metal FeMn species are quantitatively characterized with electron paramagnetic resonance spectroscopy. The previously reported catalase activity of Mn2(II)R2 is shown not to be associated with Mn.

Bacterial acetone carboxylase is a manganese-dependent metalloenzyme

Bacterial acetone carboxylase catalyzes the ATP-dependent carboxylation of acetone to acetoacetate with the concomitant production of AMP and two inorganic phosphates. The importance of manganese in Rhodobacter capsulatus acetone carboxylase has been established through a combination of physiological, biochemical, and spectroscopic studies. Depletion of manganese from the R. capsulatus growth medium resulted in inhibition of acetone-dependent but not malate-dependent cell growth. Under normal growth conditions (0.5 microm Mn2+ in medium), growth with acetone as the carbon source resulted in a 4-fold increase in intracellular protein-bound manganese over malate-grown cells and the appearance of a Mn2+ EPR signal centered at g = 2 that was absent in malate-grown cells. Acetone carboxylase purified from cells grown with 50 microm Mn2+ had a 1.6-fold higher specific activity and 1.9-fold higher manganese content than cells grown with 0.5 microm Mn2+, consistently yielding a stoichiometry of 1.9 manganese/alpha2beta2gamma2 multimer, or 0.95 manganese/alphabetagamma protomer. Manganese in acetone carboxylase was tightly bound and not removed upon dialysis against various metal ion chelators. The addition of acetone to malate-grown cells grown in medium depleted of manganese resulted in the high level synthesis of acetone carboxylase (15-20% soluble protein), which, upon purification, exhibited 7% of the activity and 6% of the manganese content of the enzyme purified from acetone-grown cells. EPR analysis of purified acetone carboxylase indicates the presence of a mononuclear Mn2+ center, with possible spin coupling of two mononuclear sites. The addition of Mg.ATP or Mg.AMP resulted in EPR spectral changes, whereas the addition of acetone, CO2, inorganic phosphate, and acetoacetate did not perturb the EPR. These studies demonstrate that manganese is essential for acetone carboxylation and suggest a role for manganese in nucleotide binding and activation.

Characterization of NO adducts of the diiron center in protein R2 of Escherichia coli ribonucleotide reductase and site-directed variants; implications for the O2 activation mechanism

The R2 subunit of Escherichia coli ribonucleotide reductase contains a diiron site that reacts with O(2) to produce a tyrosine radical (Y122.). In wild-type R2 (R2-wt), the first observable reaction intermediate is a high-valent [Fe(III)-Fe(IV)] state called compound X, but in related diiron proteins such as methane monooxygenase, Delta(9)-desaturase, and ferritin, peroxodiiron(III) complexes have been characterized. Substitution of iron ligand D84 by E within the active site of R2 allows an intermediate (mu-1,2-peroxo)diiron species to accumulate. To investigate the possible involvement of a bridging peroxo species within the O(2) activation sequence of R2-wt, we have characterized the iron-nitrosyl species that form at the diiron sites in R2-wt, R2-D84E, and R2-W48F/D84E by using vibrational spectroscopy. Previous work has shown that the diiron center in R2-wt binds one NO per iron to form an antiferromagnetically coupled [(FeNO)(7)](2) center. In the wt and variant proteins, we also observe that both irons bind one NO to form a (FeNO)(7) dimer where both Fe-N-O units share a common vibrational signature. In the wt protein, nu(Fe-NO), delta(Fe-N-O), and nu(N-O) bands are observed at 445, 434 and 1742 cm(-1), respectively, while in the variant proteins the nu(Fe-NO) and delta(Fe-N-O) bands are observed approximately 10 cm(-1) higher and the nu(N-O) approximately 10 cm(-1) lower at 1735 cm(-1). These results demonstrate that all three proteins accommodate fully symmetric [(FeNO)(7)](2) species with two identical Fe-N-O units. The formation of equivalent NO adducts in the wt and variant proteins strongly favors the formation of a symmetric bridging peroxo intermediate during the O(2) activation process in R2-wt.

Controlled Redox Conversion of New X-ray-Characterized Mono- and Dinuclear Heptacoordinated Mn(II) Complexes into Di-μ-oxo-dimanganese Core Complexes

Two heptacoordinated Mn(II) complexes are isolated and X-ray characterized using the well-known tpen ligand (tpen = N,N,N',N'-tetrakis(2-pyridylmethyl)-1,2-ethanediamine): [(tpen)Mn(OH(2))](ClO(4))(2) (1(ClO(4))(2)) and [(tpen)Mn(micro-OAc)Mn(tpen)](ClO(4))(3).2H(2)O (2(ClO(4))(3).2H(2)O). Crystallographic data for 1(ClO(4))(2) at 110(2) K (respectively at 293(2) K): monoclinic, space group C2/c, a = 15.049(3) A (15.096(3) A), b = 9.932(2) A (10.105(2) A), c = 19.246(4) A (19.443(4) A), beta = 94.21(3) degrees (94.50(3) degrees ), Z = 4. Crystallographic data for 2(ClO(4))(3).0.5(C(2)H(5))(2)O at 123(2) K: triclinic, space group P, a = 12.707(3) A, b = 12.824(3) A, c = 19.052(4) A, alpha = 102.71(3) degrees, beta = 97.83(3) degrees, gamma = 98.15(3) degrees, Z = 2. Investigation of the variation upon temperature of the molar magnetic susceptibility of compound 2(ClO(4))(3).2H(2)O reveals a weak antiferromagnetic exchange interaction between the two high-spin Mn(II) ions (J = -0.65 +/- 0.05 cm(-)(1), H = -JS(1).S(2)). EPR spectra are recorded on powder samples and on frozen acetonitrile solutions, demonstrating the maintenance upon dissolution of the heptacoordination of Mn in complex 1 while complex 2 partially dissociates. Electrochemical responses of complexes 1 and 2 are investigated in acetonitrile, and bulk electrolyses are performed at oxidative potential in the presence of various amounts of 2,6-lutidine (0-2.65 equiv per Mn ion). The formation from either 1 or 2 of the mixed-valent complex [(tpen)Mn(III)(micro-O)(2)Mn(IV)(tpen)](3+) (3) is established from mass spectrometry and EPR and IR spectroscopy measurements. When reaction is started from 2, formation of [(tpen)Mn(IV)(micro-O)(2)(micro-OAc)Mn(IV)](3+) (4) is evidenced from cyclic voltammetry, EPR, and UV-vis data. The Mn vs tpen ratio in the electrogenerated complexes is accurately controlled by the quantity of additional 2,6-lutidine. The role of tpen as a base is discussed.

Variable coordination geometries at the diiron(II) active site of ribonucleotide reductase R2

The R2 subunit of Escherichia coli ribonucleotide reductase contains a dinuclear iron center that generates a catalytically essential stable tyrosyl radical by one electron oxidation of a nearby tyrosine residue. After acquisition of Fe(II) ions by the apo protein, the resulting diiron(II) center reacts with O(2) to initiate formation of the radical. Knowledge of the structure of the reactant diiron(II) form of R2 is a prerequisite for a detailed understanding of the O(2) activation mechanism. Whereas kinetic and spectroscopic studies of the reaction have generally been conducted at pH 7.6 with reactant produced by the addition of Fe(II) ions to the apo protein, the available crystal structures of diferrous R2 have been obtained by chemical or photoreduction of the oxidized diiron(III) protein at pH 5-6. To address this discrepancy, we have generated the diiron(II) states of wildtype R2 (R2-wt), R2-D84E, and R2-D84E/W48F by infusion of Fe(II) ions into crystals of the apo proteins at neutral pH. The structures of diferrous R2-wt and R2-D48E determined from these crystals reveal diiron(II) centers with active site geometries that differ significantly from those observed in either chemically or photoreduced crystals. Structures of R2-wt and R2-D48E/W48F determined at both neutral and low pH are very similar, suggesting that the differences are not due solely to pH effects. The structures of these "ferrous soaked" forms are more consistent with circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopic data and provide alternate starting points for consideration of possible O(2) activation mechanisms.

On/off regulation of catalysis by allosteric control of metal complex nuclearity

The nature of the allosteric metal ion M (Pd2+ or Pt2+) in complexes ML of a polytopic ligand controls uptake of additional Cu2+ ions; while [Cu2Pd(L-4H)]2+ is a highly active catalyst for phosphodiester cleavage, [CuPt(L-4H)] is inactive.

Quantitative analysis of dinuclear manganese(II) EPR spectra

A quantitative method for the analysis of EPR spectra from dinuclear Mn(II) complexes is presented. The complex [(Me(3)TACN)(2)Mn(II)(2)(mu-OAc)(3)]BPh(4) (1) (Me(3)TACN=N, N('),N(")-trimethyl-1,4,7-triazacyclononane; OAc=acetate(1-); BPh(4)=tetraphenylborate(1-)) was studied with EPR spectroscopy at X- and Q-band frequencies, for both perpendicular and parallel polarizations of the microwave field, and with variable temperature (2-50K). Complex 1 is an antiferromagnetically coupled dimer which shows signals from all excited spin manifolds, S=1 to 5. The spectra were simulated with diagonalization of the full spin Hamiltonian which includes the Zeeman and zero-field splittings of the individual manganese sites within the dimer, the exchange and dipolar coupling between the two manganese sites of the dimer, and the nuclear hyperfine coupling for each manganese ion. All possible transitions for all spin manifolds were simulated, with the intensities determined from the calculated probability of each transition. In addition, the non-uniform broadening of all resonances was quantitatively predicted using a lineshape model based on D- and r-strain. As the temperature is increased from 2K, an 11-line hyperfine pattern characteristic of dinuclear Mn(II) is first observed from the S=3 manifold. D- and r-strain are the dominate broadening effects that determine where the hyperfine pattern will be resolved. A single unique parameter set was found to simulate all spectra arising for all temperatures, microwave frequencies, and microwave modes. The simulations are quantitative, allowing for the first time the determination of species concentrations directly from EPR spectra. Thus, this work describes the first method for the quantitative characterization of EPR spectra of dinuclear manganese centers in model complexes and proteins. The exchange coupling parameter J for complex 1 was determined (J=-1.5+/-0.3 cm(-1); H(ex)=-2JS(1).S(2)) and found to be in agreement with a previous determination from magnetization. The phenomenon of exchange striction was found to be insignificant for 1.