Structure–function correlations in oxygen activating non-heme iron enzymes

Experimental and Theoretical Investigation of the Mechanism of the Reduction of O2 from Air to O22- by VIVO2+-N,N,N-Amidate Compounds and Their Potential Use in Fuel Cells

The two-electron reductive activation of O2 to O22- is of particular interest to the scientific community mainly due to the use of peroxides as green oxidants and in powerful fuel cells. Despite of the great importance of vanadium(IV) species to activate the two-electron reductive activation of O2, the mechanism is still unclear. Reaction of VIVO2+ species with the tridentate-planar N,N,N-carboxamide (ΗL) ligands in solution (CH3OH:H2O) under atmospheric O2, at room temperature, resulted in the quick formation of [VV(═O)(η2-O2)(κ3-L)(H2O)] and cis-[VV(═O)2(κ3-L)] compounds. Oxidation of the VIVO2+ complexes with the sterically hindered tridentate-planar N,N,N-carboxamide ligands by atmospheric O2 gave only cis-[VV(═O)2(κ3-L)] compounds. The mechanism of formation of [VV(═O)(η2-O2)(κ3-L)(H2O)] (I) and cis-[VV(═O)2(κ3-L)] (II) complexes vs time, from the interaction of [VIV(═O)(κ3-L)(Η2Ο)2]+ with atmospheric O2, was investigated with 51V, 1H NMR, UV-vis, cw-X-band EPR, and 18O2 labeling IR and resonance Raman spectroscopies revealing the formation of a stable intermediate (Id). EPR, MS, and theoretical calculations of the mechanism of the formation of I and II revealed a pathway, through a binuclear [VIV(═O)(κ3-L)(H2O)(η1,η1-O2)VIV(═O)(κ3-L)(H2O)]2+ intermediate. The results from cw-EPR, 1H NMR spectroscopies, cyclic voltammetry, and the reactivity of the complexes [VIV(═O)(κ3-L)(Η2Ο)2]+ toward O2 reduction fit better to an intermediate with a binuclear nature. Dynamic experiments in combination with computational calculations were undertaken to fully elucidate the mechanism of the O2 reduction to O22- by [VIV(═O)(κ3-L)(Η2Ο)2]+. The galvanic cell {Zn|VIII,VII||Id, [VIVO(κ3-L)(H2O)2]+|O2|C(s)} was manufactured, demonstrating the important applicability of this new chemistry to Zn|H2O2 fuel cells technology generating H2O2 in situ from the atmospheric O2.

Spectroscopic and Theoretical Investigation of High-Spin Square-Planar and Trigonal Fe(II) Complexes Supported by Fluorinated Alkoxides

The electronic structures and spectroscopic behavior of three high-spin FeII complexes of fluorinated alkoxides were studied: square-planar {K(DME)2}2[Fe(pinF)2] (S) and quasi square-planar {K(C222)}2[Fe(pinF)2] (S') and trigonal-planar {K(18C6)}[Fe(OC4F9)3] (T) where pinF = perfluoropinacolate and OC4F9 = tris-perfluoro-t-butoxide. The zero-field splitting (ZFS) and hyperfine structure parameters of the S = 2 ground states were determined using field-dependent 57Fe Mössbauer and high-field and -frequency electron paramagnetic resonance (HFEPR) spectroscopies. The spin Hamiltonian parameters were analyzed with crystal field theory and corroborated by density functional theory (DFT) and ab initio complete active space self-consistent field (CASSCF) calculations. Whereas the ZFS tensor of S has a small rhombicity, E/D = 0.082, and a positive D = 15.17 cm-1, T exhibits a negative D = -9.16 cm-1 and a large rhombicity, E/D = 0.246. Computational investigation of the structural factors suggests that the ground-state electronic configuration and geometry of T's Fe site are determined by the interaction of [Fe(OC4F9)3]- with {K(18C6)}+. In contrast, two distinct countercations of S/S' have a negligible influence on their [Fe(pinF)2]2- moieties. Instead, the distortions in S' are likely induced by the chelate ring conformation change from δλ, observed for S, to the δδ conformation, determined for S'.

Characterization and genomic analysis of a novel halovirus infecting Chromohalobacter beijerinckii

Bacteriophages function as a regulator of host communities and metabolism. Many phages have been isolated and sequenced in environments such as the ocean, but very little is known about hypersaline environments. Phages infecting members of the genus Chromohalobacter remain poorly understood, and no Chromohalobacter phage genome has been reported. In this study, a halovirus infecting Chromohalobacter sp. F3, YPCBV-1, was isolated from Yipinglang salt mine. YPCBV-1 could only infect host strain F3 with burst size of 6.3 PFU/cell. It could produce progeny in 5%-20% (w/v) NaCl with an optimal concentration of 10% (w/v), but the optimal adsorption NaCl concentration was 5%-8% (w/v). YPCBV-1 is sensitive to pure water and depends on NaCl or KCl solutions to survive. YPCBV-1 stability increased with increasing salinity but decreased in NaCl saturated solutions, and it has a broader salinity adaptation than the host. YPCBV-1 has a double-stranded DNA of 36,002 bp with a G + C content of 67.09% and contains a total of 55 predicted ORFs and no tRNA genes. Phylogenetic analysis and genomic network analysis suggested that YPCBV-1 is a novel Mu-like phage under the class Caudoviricetes. Auxiliary metabolic gene, SUMF1/EgtB/PvdO family non-heme iron enzyme, with possible roles in antioxidant was found in YPCBV-1. Moreover, DGR-associated genes were predicted in YPCBV-1 genome, which potentially produce hypervariable phage tail fiber. These findings shed light on the halovirus-host interaction in hypersaline environments.

Thermodynamics of iron, tetrahydrobiopterin, and phenylalanine binding to phenylalanine hydroxylase from Chromobacterium violaceum

Phenylalanine hydroxylase (PheH) is a pterin-dependent, mononuclear nonheme iron(II) oxygenase that uses the oxidative power of O2 to hydroxylate phenylalanine to form tyrosine. PheH is a member of a superfamily of O2-activating enzymes that utilizes a common metal binding motif: the 2-His-1-carboxylate facial triad. Like most members of this superfamily, binding of substrates to PheH results in a reorganization of its active site to allow O2 activation. Exploring the energetics of each step before O2 activation can provide mechanistic insight into the initial steps that support the highly specific O2 activation pathway carried out by this metalloenzyme. Here the thermal stability of PheH and its substrate complexes were investigated under an anaerobic environment by using differential scanning calorimetry. In context with known binding constants for PheH, a thermodynamic cycle associated with iron(II), tetrahydrobiopterin (BH4), and phenylalanine binding to the active site was generated, showing a distinctive cooperativity between the binding of BH4 and Phe. The addition of phenylalanine and BH4 to PheH·Fe increased the stability of this enzyme (ΔTm of 8.5 (±0.7) °C with an associated δΔH of 43.0 (±2.9) kcal/mol). The thermodynamic data presented here gives insight into the complicated interactions between metal center, cofactor, and substrate, and how this interplay sets the stage for highly specific, oxidative C-H activation in this enzyme.

Substrate-Specific Coupling of O2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases

Rieske dioxygenases catalyze the initial steps in the hydroxylation of aromatic compounds and are critical for the metabolism of xenobiotic substances. Because substrates do not bind to the mononuclear non-heme Fe^II center, elementary steps leading to O₂ activation and substrate hydroxylation are difficult to delineate, thus making it challenging to rationalize divergent observations on enzyme mechanisms, reactivity, and substrate specificity. Here, we show for nitrobenzene dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes to nitrite and substituted catechols, that unproductive O₂ activation with the release of the unreacted substrate and reactive oxygen species represents an important path in the catalytic cycle. Through correlation of O₂ uncoupling for a series of substituted nitroaromatic compounds with ¹⁸O and ¹³C kinetic isotope effects of dissolved O₂ and aromatic substrates, respectively, we show that O₂ uncoupling occurs after the rate-limiting formation of Fe^III-(hydro)peroxo species from which substrates are hydroxylated. Substituent effects on the extent of O₂ uncoupling suggest that the positioning of the substrate in the active site rather than the susceptibility of the substrate for attack by electrophilic oxygen species is responsible for unproductive O₂ uncoupling. The proposed catalytic cycle provides a mechanistic basis for assessing the very different efficiencies of substrate hydroxylation vs unproductive O₂ activation and generation of reactive oxygen species in reactions catalyzed by Rieske dioxygenases.

Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1

The 2-oxoglutarate (2OG)-dependent non-heme enzyme FtmOx1 catalyzes the endoperoxide biosynthesis of verruculogen. Although several mechanistic studies have been carried out, the catalytic mechanism of FtmOx1 is not well determined owing to the lack of a reliable complex structure of FtmOx1 with fumitremorgin B. Herein we provide the X-ray crystal structure of the ternary complex FtmOx1⋅2OG⋅fumitremorgin B at a resolution of 1.22 Å. Our structures show that the binding of fumitremorgin B induces significant compression of the active pocket and that Y68 is in close proximity to C26 of the substrate. Further MD simulation and QM/MM calculations support a CarC-like mechanism, in which Y68 acts as the H atom donor for quenching the C26-centered substrate radical. Our results are consistent with all available experimental data and highlight the importance of accurate complex structures in the mechanistic study of enzymatic catalysis.

Preparation of carotenoid cleavage dioxygenases for X-ray crystallography

Carotenoid cleavage dioxygenases (CCDs) constitute a superfamily of enzymes that are found in all domains of life where they play key roles in the metabolism of carotenoids and apocarotenoids as well as certain phenylpropanoids such as resveratrol. Interest in these enzymes stems not only from their biological importance but also from their remarkable catalytic properties including their regioselectivity, their ability to accommodate diverse substrates, and the additional activities (e.g., isomerase) that some of these enzyme possess. X-ray crystallography is a key experimental approach that has allowed detailed investigation into the structural basis behind the interesting biochemical features of these enzymes. Here, we describe approaches used by our lab that have proven successful in generating single crystals of these enzymes in resting or ligand-bound states for high-resolution X-ray diffraction analysis.

Functional role of residues involved in substrate binding of human 4-hydroxyphenylpyruvate dioxygenase

4-Hydroxylphenylpyruvate dioxygenase (HPPD) catalyzes the conversion of 4-hydroxylphenylpyruvate (HPP) to homogentisate, the important step for tyrosine catabolism. Comparison of the structure of human HPPD with the substrate-bound structure of A. thaliana HPPD revealed notably different orientations of the C-terminal helix. This helix performed as a closed conformation in human enzyme. Simulation revealed a different substrate-binding mode in which the carboxyl group of HPP interacted by a H-bond network formed by Gln334, Glu349 (the metal-binding ligand), and Asn363 (in the C-terminal helix). The 4-hydroxyl group of HPP interacted with Gln251 and Gln265. The relative activity and substrate-binding affinity were preserved for the Q334A mutant, implying the alternative role of Asn363 for HPP binding and catalysis. The reduction in kcat/Km of the Asn363 mutants confirmed the critical role in catalysis. Compared to the N363A mutant, the dramatic reduction in the Kd and thermal stability of the N363D mutant implies the side-chain effect in the hinge region rotation of the C-terminal helix. The activity and binding affinity were not recovered by double mutation; however, the 4-hydroxyphenylacetate intermediate formation by the uncoupled reaction of Q334N/N363Q and Q334A/N363D mutants indicated the importance of the H-bond network in the electrophilic reaction. These results highlight the functional role of the H-bond network in a closed conformation of the C-terminal helix to stabilize the bound substrate. The extremely low activity and reduction in Q251E's Kd suggest that interaction coupled with the H-bond network is crucial to locate the substrate for nucleophilic reaction.

Engineering the Oxidative Potency of Non-Heme Iron(IV) Oxo Complexes in Water for C-H Oxidation by a cis Donor and Variation of the Second Coordination Sphere

A series of iron(IV) oxo complexes, which differ in the donor (CH₂py or CH₂COO^-) cis to the oxo group, three with hemilabile pendant donor/second coordination sphere base/acid arms (pyH/py or ROH), have been prepared in water at pH 2 and 7. The ν_Fe═O values of 832 ± 2 cm^-1 indicate similar Fe^IV═O bond strengths; however, different reactivities toward C-H substrates in water are observed. HAT occurs at rates that differ by 1 order of magnitude with nonclassical KIEs (k_H/k_D = 30-66) consistent with hydrogen atom tunneling. Higher KIEs correlate with faster reaction rates as well as a greater thermodynamic stability of the iron(III) resting states. A doubling in rate from pH 7 to pH 2 for substrate C-H oxidation by the most potent complex, that with a cis-carboxylate donor, [Fe^IVO(Htpena)]²⁺, is observed. Supramolecular assistance by the first and second coordination spheres in activating the substrate is proposed. The lifetime of this complex in the absence of a C-H substrate is the shortest (at pH 2, 3 h vs up to 1.3 days for the most stable complex), implying that slow water oxidation is a competing background reaction. The iron(IV)═O complex bearing an alcohol moiety in the second coordination sphere displays significantly shorter lifetimes due to a competing selective intramolecular oxidation of the ligand.

Dioxygen Binding to all 3d, 4d, and 5d Transition Metals from Coupled-Cluster Theory

Understanding how transition metals bind and activate dioxygen (O₂ ) is limited by experimental and theoretical uncertainties, making accurate quantum mechanical descriptors of interest. Here we report coupled-cluster CCSD(T) energies with large basis sets and vibrational and relativistic corrections for 160 3d, 4d, and 5d metal-O₂ systems. We define four reaction energies (120 in total for the 30 metals) that quantify O-O activation and reveal linear relationships between metal-oxygen and O-O binding energies. The CCSD(T) data can be combined with thermochemical cycles to estimate chemisorption and physisorption energies for each metal from metal oxide embedding energies, in good correlation with atomization enthalpies (R² =0.75). Spin-geometry variations can break the linearities, of interest to circumventing the Sabatier principle. Pt, Pd, Co, and Fe form a distinct group with the weakest O₂ binding. R² up to 0.84 between surface adsorption energies and our energies for MO₂ systems indicate relevance also to real catalytic systems.

Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation

PHF8 (KDM7B) is a human non-heme 2-oxoglutarate (2OG) JmjC domain oxygenase that catalyzes the demethylation of the di/mono-Nε-methylated K9 residue of histone H3. Altered PHF8 activity is linked to genetic diseases and cancer; thus, it is an interesting target for epigenetic modulation. We describe the use of combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of PHF8, including dioxygen activation, 2OG binding modes, and substrate demethylation steps. A PHF8 crystal structure manifests the 2OG C-1 carboxylate bound to iron in a nonproductive orientation, i.e., trans to His247. A ferryl-oxo intermediate formed by activating dioxygen bound to the vacant site in this complex would be nonproductive, i.e., "off-line" with respect to reaction with Nε-methylated K9. We show rearrangement of the "off-line" ferryl-oxo intermediate to a productive "in-line" geometry via a solvent exchange reaction (called "ferryl-flip") is energetically unfavorable. The calculations imply that movement of the 2OG C-1 carboxylate prior to dioxygen binding at a five-coordination stage in catalysis proceeds with a low barrier, suggesting that two possible 2OG C-1 carboxylate geometries can coexist at room temperature. We explored alternative mechanisms for hydrogen atom transfer and show that second sphere interactions orient the Nε-methylated lysine in a conformation where hydrogen abstraction from a methyl C-H bond is energetically more favorable than hydrogen abstraction from the N-H bond of the protonated Nε-methyl group. Using multiple HAT reaction path calculations, we demonstrate the crucial role of conformational flexibility in effective hydrogen transfer. Subsequent hydroxylation occurs through a rebound mechanism, which is energetically preferred compared to desaturation, due to second sphere interactions. The overall mechanistic insights reveal the crucial role of iron-center rearrangement, second sphere interactions, and conformational flexibility in PHF8 catalysis and provide knowledge useful for the design of mechanism-based PHF8 inhibitors.

Evidence for distinct rate-limiting steps in the cleavage of alkenes by carotenoid cleavage dioxygenases

Carotenoid cleavage dioxygenases (CCDs) use a nonheme Fe(II) cofactor to split alkene bonds of carotenoid and stilbenoid substrates. The iron centers of CCDs are typically five-coordinate in their resting states, with solvent occupying an exchangeable site. The involvement of this iron-bound solvent in CCD catalysis has not been experimentally addressed, but computational studies suggest two possible roles. 1) Solvent dissociation provides a coordination site for O₂, or 2) solvent remains bound to iron but changes its equilibrium position to allow O₂ binding and potentially acts as a proton source. To test these predictions, we investigated isotope effects (H₂O versus D₂O) on two stilbenoid-cleaving CCDs, Novosphingobium aromaticivorans oxygenase 2 (NOV2) and Neurospora crassa carotenoid oxygenase 1 (CAO1), using piceatannol as a substrate. NOV2 exhibited an inverse isotope effect (k _H/k _D ∼ 0.6) in an air-saturated buffer, suggesting that solvent dissociates from iron during the catalytic cycle. By contrast, CAO1 displayed a normal isotope effect (k _H/k _D ∼ 1.7), suggesting proton transfer in the rate-limiting step. X-ray absorption spectroscopy on NOV2 and CAO1 indicated that the protonation states of the iron ligands are unchanged within pH 6.5-8.5 and that the Fe(II)-aquo bond is minimally altered by substrate binding. We pinpointed the origin of the differential kinetic behaviors of NOV2 and CAO1 to a single amino acid difference near the solvent-binding site of iron, and X-ray crystallography revealed that the substitution alters binding of diffusible ligands to the iron center. We conclude that solvent-iron dissociation and proton transfer are both associated with the CCD catalytic mechanism.

Conformational Dynamics Underlies Different Functions of Human KDM7 Histone Demethylases

The human KDM7 subfamily histone H3 Nϵ-methyl lysine demethylases PHF8 (KDM7B) and KIAA1718 (KDM7A) have different substrate selectivities and are linked to genetic diseases and cancer. We describe experimentally based computational studies revealing that flexibility of the region linking the PHD finger and JmjC domains in PHF8 and KIAA1718 regulates interdomain interactions, the nature of correlated motions, and ultimately H3 binding and demethylation site selectivity. F279S an X-linked mental retardation mutation in PHF8 is involved in correlated motions with the iron ligands and second sphere residues. The calculations reveal key roles of a flexible protein environment in productive formation of enzyme-substrate complexes and suggest targeting the flexible KDM7 linker region is of interest from a medicinal chemistry perspective.

Magnetic circular dichroism spectra of transition metal complexes calculated from restricted active space wavefunctions

Multiconfigurational restricted active space (RAS) self-consistent field (SCF) or configuration interaction (CI) approaches, augmented with a treatment of spin–orbit coupling by state interaction, were used to calculate the magnetic circular dichroism , , and/or for closed- and open-shell transition metal complexes.

Deciphering the mechanism of O2 reduction with electronically tunable non-heme iron enzyme model complexes

A homologous series of electronically tuned 2,2',2''-nitrilotris(N-arylacetamide) pre-ligands (H3LR ) were prepared (R = NO2, CN, CF3, F, Cl, Br, Et, Me, H, OMe, NMe2) and some of their corresponding Fe and Zn species synthesized. The iron complexes react rapidly with O2, the final products of which are diferric mu-oxo bridged species. The crystal structure of the oxidized product obtained from DMA solutions contain a structural motif found in some diiron proteins. The mechanism of iron mediated O2 reduction was explored to the extent that allowed us to construct an empirically consistent rate law. A Hammett plot was constructed that enabled insightful information into the rate-determining step and hence allows for a differentiation between two kinetically equivalent O2 reduction mechanisms.

Iron(II) Complexes of a Hemilabile SNS Amido Ligand: Synthesis, Characterization, and Reactivity

We report an easily prepared bis(thioether) amine ligand, S^MeN^HS^Me, along with the synthesis, characterization, and reactivity of the paramagnetic iron(II) bis(amido) complex, [Fe(κ³-S^MeNS^Me)₂] (1). Binding of the two different thioethers to Fe generates both five- and six-membered rings with Fe-S bonds in the five-membered rings (av 2.54 Å) being significantly shorter than those in the six-membered rings (av 2.71 Å), suggesting hemilability of the latter thioethers. Consistent with this hypothesis, magnetic circular dichroism (MCD) and computational (TD-DFT) studies indicate that 1 in solution contains a five-coordinate component [Fe(κ³-S^MeNS^Me)(κ²-S^MeNS^Me)] (2). This ligand hemilability was demonstrated further by reactivity studies of 1 with 2,2'-bipyridine, 1,2-bis(dimethylphosphino)ethane, and 2,6-dimethylphenyl isonitrile to afford iron(II) complexes [L₂Fe(κ²-S^MeNS^Me)₂] (3-5). Addition of a Brønsted acid, HNTf₂, to 1 produces the paramagnetic, iron(II) amine-amido cation, [Fe(κ³-S^MeNS^Me)(κ³-S^MeN^HS^Me)](NTf₂) (6; Tf = SO₂CF₃). Cation 6 readily undergoes amine ligand substitution by triphos, affording the 16e^- complex [Fe(κ²-S^MeNS^Me)(κ³-triphos)](NTf₂) (7; triphos = bis(2-diphenylphosphinoethyl)phenylphosphine). These complexes are characterized by elemental analysis; ¹H NMR, Mössbauer, IR, and UV-vis spectroscopy; and single-crystal X-ray diffraction. Preliminary results of amine-borane dehydrogenation catalysis show complex 7 to be a selective and particularly robust precatalyst.

Investigations on the role of a solvent tunnel in the α-ketoglutarate dependent oxygenase factor inhibiting HIF (FIH)

Non-heme Fe(II)/α-ketoglutarate (αKG)-dependent oxygenases catalyze a wide array of reactions through coupling oxidative decarboxylation of αKG to substrate oxygenation. This class of enzymes follows a sequential mechanism in which O₂ reacts only after binding primary substrate, raising questions over how protein structure tailors molecular access to the Fe(II) cofactor. The enzyme "factor inhibiting hypoxia inducible factor" (FIH) senses pO₂ in human cells by hydroxylating the C-terminal transactivation domain (CTAD), suggesting that structural elements limiting molecular access to the active site may limit the pO₂ response. In this study, we tested the impact of a solvent-accessible tunnel in FIH on molecular access to the active site in FIH. The size of the tunnel was increased through alanine point mutagenesis (Y93A, E105A, and Q147A), followed by a suite of mechanistic and spectroscopic probes. Steady-state kinetics varying O₂ or CTAD indicated that O₂ passage through the tunnel was not affected by Ala substitutions, allowing us to conclude that this narrow tunnel did not impact pO₂ sensing by FIH. Steady-state kinetics with varied αKG concentrations revealed increased substrate inhibition for the Ala variants, suggesting that a second αKG molecule may bind near the active site of FIH. If this solvent-accessible tunnel is the O₂ entry tunnel, it may be narrow in order to permit O₂ access while preventing metabolic intermediates, such as αKG, from inhibiting FIH under physiological conditions.

Magnetic circular dichroism studies of iron(ii) binding to human calprotectin

Calprotectin (CP) is an abundant metal-chelating protein involved in host defense, and the ability of human CP to bind Fe(ii) in a calcium-dependent manner was recently discovered. In the present study, near-infrared magnetic circular dichroism spectroscopy is employed to investigate the nature of Fe(ii) coordination at the two transition-metal-binding sites of CP that are a His3Asp motif (site 1) and a His6 motif (site 2). Upon the addition of sub-stoichiometric Fe(ii), a six-coordinate (6C) Fe(ii) center associated with site 2 is preferentially formed in the presence of excess Ca(ii). This site exhibits an exceptionally large ligand field (10Dq = 11 045 cm-1) for a non-heme Fe(ii) protein. Analysis of CP variants lacking residues of the His6 motif supports that CP coordinates Fe(ii) at site 2 by employing six His ligands. In the presence of greater than one equiv. of Fe(ii) or upon mutation of the His6 motif, the metal ion also binds at site 1 of CP to form a five-coordinate (5C) Fe(ii)-His3Asp motif that was previously unidentified in this system. Notably, the introduction of His-to-Ala mutations at the His6 motif results in a mixture of 6C (site 2) and 5C (site 1) signals in the presence of sub-stoichiometric Fe(ii). These results are consistent with a reduced Fe(ii)-binding affinity of site 2 as more weakly coordinating water-derived ligands complete the 6C site. In the absence of Ca(ii), both sites 1 and 2 are occupied upon addition of sub-stoichiometric Fe(ii), and a stronger ligand field is observed for the 5C site. These spectroscopic studies provide further evaluation of a unique non-heme Fe(ii)-His6 site for metalloproteins and support the notion that Ca(ii) ions influence the Fe(ii)-binding properties of CP.

Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants

The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O₂ and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions. Activated dioxygen-derived species involved in the enzyme mechanisms include iron(III)-superoxo, iron(III)-peroxo, and high-valent iron(IV)-oxo intermediates. In this article, we highlight the major crystallographic, spectroscopic, and mechanistic advances of the past 20 years that have significantly enhanced our understanding of the mechanisms of O₂ activation and the key roles played by iron-based oxidants.

Magnetic circular dichroism of UCl6− in the ligand-to-metal charge-transfer spectral region

We present a combined ab initio theoretical and experimental study of the magnetic circular dichroism (MCD) spectrum of the octahedral UCl₆⁻ complex ion in the UV-Vis spectral region.

Structure/function correlations over binuclear non-heme iron active sites

Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed.

Utilization of Dioxygen by Carotenoid Cleavage Oxygenases

Carotenoid cleavage oxygenases (CCOs) are non-heme, Fe(II)-dependent enzymes that participate in biologically important metabolic pathways involving carotenoids and apocarotenoids, including retinoids, stilbenes, and related compounds. CCOs typically catalyze the cleavage of non-aromatic double bonds by dioxygen (O2) to form aldehyde or ketone products. Expressed only in vertebrates, the RPE65 sub-group of CCOs catalyzes a non-canonical reaction consisting of concerted ester cleavage and trans-cis isomerization of all-trans-retinyl esters. It remains unclear whether the former group of CCOs functions as mono- or di-oxygenases. Additionally, a potential role for O2 in catalysis by the RPE65 group of CCOs has not been evaluated to date. Here, we investigated the pattern of oxygen incorporation into apocarotenoid products of Synechocystis apocarotenoid oxygenase. Reactions performed in the presence of (18)O-labeled water and (18)O2 revealed an unambiguous dioxygenase pattern of O2 incorporation into the reaction products. Substitution of Ala for Thr at position 136 of apocarotenoid oxygenase, a site predicted to govern the mono- versus dioxygenase tendency of CCOs, greatly reduced enzymatic activity without altering the dioxygenase labeling pattern. Reevaluation of the oxygen-labeling pattern of the resveratrol-cleaving CCO, NOV2, previously reported to be a monooxygenase, using a purified enzyme sample revealed that it too is a dioxygenase. We also demonstrated that bovine RPE65 is not dependent on O2 for its cleavage/isomerase activity. In conjunction with prior research, the results of this study resolve key issues regarding the utilization of O2 by CCOs and indicate that dioxygenase activity is a feature common among double bond-cleaving CCOs.

3-Ketosteroid 9α-hydroxylase enzymes: Rieske non-heme monooxygenases essential for bacterial steroid degradation

Various micro-organisms are able to use sterols/steroids as carbon- and energy sources for growth. 3-Ketosteroid 9α-hydroxylase (KSH), a two component Rieske non-heme monooxygenase comprised of the oxygenase KshA and the reductase KshB, is a key-enzyme in bacterial steroid degradation. It initiates opening of the steroid polycyclic ring structure. The enzyme has industrial relevance in the synthesis of pharmaceutical steroids. Deletion of KSH activity in sterol degrading bacteria results in blockage of steroid ring opening and is used to produce valuable C19-steroids such as 4-androstene-3,17-dione and 1,4-androstadiene-3,17-dione. Interestingly, KSH activity is essential for the pathogenicity of Mycobacterium tuberculosis. Detailed information about KSH thus is of medical relevance, and KSH inhibitory compounds may find application in combatting tuberculosis. In recent years, the 3D structure of the KshA protein of M. tuberculosis H37Rv has been elucidated and various studies report biochemical characteristics and possible physiological roles of KSH. The current knowledge is reviewed here and forms a solid basis for further studies on this highly interesting enzyme. Future work may result in the construction of KSH mutants capable of production of specific bioactive steroids. Furthermore, KSH provides an promising target for drugs against the pathogenic agent M. tuberculosis.

Oxygen sensing strategies in mammals and bacteria

The ability to sense and adapt to changes in pO2 is crucial for basic metabolism in most organisms, leading to elaborate pathways for sensing hypoxia (low pO2). This review focuses on the mechanisms utilized by mammals and bacteria to sense hypoxia. While responses to acute hypoxia in mammalian tissues lead to altered vascular tension, the molecular mechanism of signal transduction is not well understood. In contrast, chronic hypoxia evokes cellular responses that lead to transcriptional changes mediated by the hypoxia inducible factor (HIF), which is directly controlled by post-translational hydroxylation of HIF by the non-heme Fe(II)/αKG-dependent enzymes FIH and PHD2. Research on PHD2 and FIH is focused on developing inhibitors and understanding the links between HIF binding and the O2 reaction in these enzymes. Sulfur speciation is a putative mechanism for acute O2-sensing, with special focus on the role of H2S. This sulfur-centered model is discussed, as are some of the directions for further refinement of this model. In contrast to mammals, bacterial O2-sensing relies on protein cofactors that either bind O2 or oxidatively decompose. The sensing modality for bacterial O2-sensors is either via altered DNA binding affinity of the sensory protein, or else due to the actions of a two-component signaling cascade. Emerging data suggests that proteins containing a hemerythrin-domain, such as FBXL5, may serve to connect iron sensing to O2-sensing in both bacteria and humans. As specific molecular machinery becomes identified, these hypoxia sensing pathways present therapeutic targets for diseases including ischemia, cancer, or bacterial infection.

A Mononuclear Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Metal Ions

Redox-inactive metal ions that function as Lewis acids play pivotal roles in modulating reactivities of oxygen-containing metal complexes in a variety of biological and biomimetic reactions, including dioxygen activation/formation and functionalization of organic substrates. Mononuclear nonheme iron(III)-peroxo species are invoked as active oxygen intermediates in the catalytic cycles of dioxygen activation by nonheme iron enzymes and their biomimetic compounds. Here, we report mononuclear nonheme iron(III)-peroxo complexes binding redox-inactive metal ions, [(TMC)FeIII(O2)]+-M3+ (M3+ = Sc3+ and Y3+; TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), which are characterized spectroscopically as a 'side-on' iron(III)-peroxo complex binding a redox-inactive metal ion, (TMC)FeIII-(μ,η2:η2-O2)-M3+ (2-M). While an iron(III)-peroxo complex, [(TMC)FeIII(O2)]+, does not react with electron donors (e.g., ferrocene), one-electron reduction of the iron(III)-peroxo complexes binding redox-inactive metal ions occurs readily upon addition of electron donors, resulting in the generation of an iron(IV)-oxo complex, [(TMC)FeIV(O)]2+ (4), via heterolytic O-O bond cleavage of the peroxide ligand. The rates of the conversion of 2-M to 4 are found to depend on the Lewis acidity of the redox-inactive metal ions and the oxidation potential of the electron donors. We have also determined the fundamental electron-transfer properties of 2-M, such as the reduction potential and the reorganization energy in electron-transfer reaction. Based on the results presented herein, we have proposed a mechanism for the reactions of 2-M and electron donors; the reduction of 2-M to the reduced species, (TMC)FeII-(O2)-M3+ (2'-M), is the rate-determining step, followed by heterolytic O-O bond cleavage of the reduced species to form 4. The present results provide a biomimetic example demonstrating that redox-inactive metal ions bound to an iron(III)-peroxo intermediate play a significant role in activating the peroxide O-O bond to form a high-valent iron(IV)-oxo species.

Sulfide Oxidation by O2: Synthesis, Structure and Reactivity of Novel Sulfide-Incorporated Fe(II) Bis(imino)pyridine Complexes

The unsymmetrical iron(II) bis(imino)pyridine complexes [FeII(LN3SMe)(H2O)3](OTf)2 (1), and [FeII(LN3SMe)Cl2] (2) were synthesized and their reactivity with O2 was examined. Complexes 1 and 2 were characterized by single crystal X-ray crystallography, LDI-MS, 1H-NMR and elemental analysis. The LN3SMe ligand was designed to incorporate a single sulfide donor and relies on the bis(imino)pyridine scaffold. This scaffold was selected for its ease of synthesis and its well-precedented ability to stabilize Fe(II) ions. Complexes 1 and 2 ware prepared via a metal-assisted template reaction from the unsymmetrical pyridyl ketone precursor 2-(O=CMe)-6-(2,6-(iPr2-C6H3N=CMe)-C5H3N. Reaction of 1 with O2 was shown to afford the S-oxygenated sulfoxide complex [Fe(LN3S(O)Me)(OTf)]2+(3), whereas compound 2, under the same reaction conditions, afforded the corresponding sulfone complex [Fe(LN3S(O2)Me)Cl]2+ (4).

Spectroscopic studies of the mononuclear non-heme Fe(II) enzyme FIH: second-sphere contributions to reactivity

Factor inhibiting hypoxia-inducible factor (FIH) is an α-ketoglutarate (αKG)-dependent enzyme which catalyzes hydroxylation of residue Asn803 in the C-terminal transactivation domain (CAD) of hypoxia-inducible factor 1α (HIF-1α) and plays an important role in cellular oxygen sensing and hypoxic response. Circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies are used to determine the geometric and electronic structures of FIH in its (Fe(II)), (Fe(II)/αKG), and (Fe(II)/αKG/CAD) forms. (Fe(II))FIH and (Fe(II)/αKG)FIH are found to be six-coordinate (6C), whereas (Fe(II)/αKG/CAD)FIH is found to be a 5C/6C mixture. Thus, FIH follows the general mechanistic strategy of non-heme Fe(II) enzymes. Modeling shows that, when Arg238 of FIH is removed, the facial triad carboxylate binds to Fe(II) in a bidentate mode with concomitant lengthening of the Fe(II)/αKG carbonyl bond, which would inhibit the O2 reaction. Correlations over α-keto acid-dependent enzymes and with the extradiol dioxygenases show that members of these families (where both the electron source and O2 bind to Fe(II)) have a second-sphere residue H-bonding to the terminal oxygen of the carboxylate, which stays monodentate. Alternatively, structures of the pterin-dependent and Rieske dioxygenases, which do not have substrate binding to Fe(II), lack H-bonds to the carboxylate and thus allow its bidentate coordination which would direct O2 reactivity. Finally, vis-UV MCD spectra show an unusually high-energy Fe(II) → αKG π* metal-to-ligand charge transfer transition in (Fe(II)/αKG)FIH which is red-shifted upon CAD binding. This red shift indicates formation of H-bonds to the αKG that lower the energy of its carbonyl LUMO, activating it for nucleophilic attack by the Fe-O2 intermediate formed along the reaction coordinate.

Comparison of high-spin and low-spin nonheme Fe(III)-OOH complexes in O-O bond homolysis and H-atom abstraction reactivities

The geometric and electronic structures and reactivity of an S = 5/2 (HS) mononuclear nonheme (TMC)Fe(III)-OOH complex are studied by spectroscopies, calculations, and kinetics and compared with the results of previous studies of S = 1/2 (LS) Fe(III)-OOH complexes to understand parallels and differences in mechanisms of O-O bond homolysis and electrophilic H-atom abstraction reactions. The homolysis reaction of the HS [(TMC)Fe(III)-OOH](2+) complex is found to involve axial ligand coordination and a crossing to the LS surface for O-O bond homolysis. Both HS and LS Fe(III)-OOH complexes are found to perform direct H-atom abstraction reactions but with very different reaction coordinates. For the LS Fe(III)-OOH, the transition state is late in O-O and early in C-H coordinates. However, for the HS Fe(III)-OOH, the transition state is early in O-O and further along in the C-H coordinate. In addition, there is a significant amount of electron transfer from the substrate to the HS Fe(III)-OOH at transition state, but that does not occur in the LS transition state. Thus, in contrast to the behavior of LS Fe(III)-OOH, the H-atom abstraction reactivity of HS Fe(III)-OOH is found to be highly dependent on both the ionization potential and the C-H bond strength of the substrate. LS Fe(III)-OOH is found to be more effective in H-atom abstraction for strong C-H bonds, while the higher reduction potential of HS Fe(III)-OOH allows it to be active in electrophilic reactions without the requirement of O-O bond cleavage. This is relevant to the Rieske dioxygenases, which are proposed to use a HS Fe(III)-OOH to catalyze cis-dihydroxylation of a wide range of aromatic compounds.

Structure and function of atypically coordinated enzymatic mononuclear non-heme-Fe(II) centers

Mononuclear, non-heme-Fe(II) centers are key structures in O₂ metabolism and catalyze an impressive variety of enzymatic reactions. While most are bound via two histidines and a carboxylate, some show a different organization. A short overview of atypically coordinated O₂ dependent mononuclear-non-heme-Fe(II) centers is presented here Enzymes with 2-His, 3-His, 3-His-carboxylate and 4-His bound Fe(II) centers are discussed with a focus on their reactivity, metal ion promiscuity and recent progress in the elucidation of their enzymatic mechanisms. Observations concerning these and classically coordinated Fe(II) centers are used to understand the impact of the metal binding motif on catalysis.

Structural and computational enzymology: bringing experiments and computations together

In this introductory chapter, we present how the experimental and computational strategies in enzyme research are developed and how they complement each other to provide better insights for understanding enzyme structures and mechanisms.

Activation of α-keto acid-dependent dioxygenases: application of an {FeNO}7/{FeO2}8 methodology for characterizing the initial steps of O2 activation

The α-keto acid-dependent dioxygenases are a major subgroup within the O(2)-activating mononuclear nonheme iron enzymes. For these enzymes, the resting ferrous, the substrate plus cofactor-bound ferrous, and the Fe(IV)═O states of the reaction have been well studied. The initial O(2)-binding and activation steps are experimentally inaccessible and thus are not well understood. In this study, NO is used as an O(2) analogue to probe the effects of α-keto acid binding in 4-hydroxyphenylpyruvate dioxygenase (HPPD). A combination of EPR, UV-vis absorption, magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies in conjunction with computational models is used to explore the HPPD-NO and HPPD-HPP-NO complexes. New spectroscopic features are present in the α-keto acid bound {FeNO}(7) site that reflect the strong donor interaction of the α-keto acid with the Fe. This promotes the transfer of charge from the Fe to NO. The calculations are extended to the O(2) reaction coordinate where the strong donation associated with the bound α-keto acid promotes formation of a new, S = 1 bridged Fe(IV)-peroxy species. These studies provide insight into the effects of a strong donor ligand on O(2) binding and activation by Fe(II) in the α-keto acid-dependent dioxygenases and are likely relevant to other subgroups of the O(2) activating nonheme ferrous enzymes.

Spectroscopic and computational studies of α-keto acid binding to Dke1: understanding the role of the facial triad and the reactivity of β-diketones

The O(2) activating mononuclear nonheme iron enzymes generally have a common facial triad (two histidine and one carboxylate (Asp or Glu) residue) ligating Fe(II) at the active site. Exceptions to this motif have recently been identified in nonheme enzymes, including a 3His triad in the diketone cleaving dioxygenase Dke1. This enzyme is used to explore the role of the facial triad in directing reactivity. A combination of spectroscopic studies (UV-vis absorption, MCD, and resonance Raman) and DFT calculations is used to define the nature of the binding of the α-keto acid, 4-hydroxyphenlpyruvate (HPP), to the active site in Dke1 and the origin of the atypical cleavage (C2-C3 instead of C1-C2) pattern exhibited by this enzyme in the reaction of α-keto acids with dioxygen. The reduced charge of the 3His triad induces α-keto acid binding as the enolate dianion, rather than the keto monoanion, found for α-keto acid binding to the 2His/1 carboxylate facial triad enzymes. The mechanistic insight from the reactivity of Dke1 with the α-keto acid substrate is then extended to understand the reaction mechanism of this enzyme with its native substrate, acac. This study defines a key role for the 2His/1 carboxylate facial triad in α-keto acid-dependent mononuclear nonheme iron enzymes in stabilizing the bound α-keto acid as a monoanion for its decarboxylation to provide the two additional electrons required for O(2) activation.