Crystal Structure of the Ribonucleotide Reductase R2 Mutant that Accumulates a μ-1,2-Peroxodiiron(III) Intermediate during Oxygen Activation

Mechanistic Insights into the N-Hydroxylations Catalyzed by the Binuclear Iron Domain of SznF Enzyme: Key Piece in the Synthesis of Streptozotocin

SznF, a member of the emerging family of heme-oxygenase-like (HO-like) di-iron oxidases and oxygenases, employs two distinct domains to catalyze the conversion of Nω-methyl-L-arginine (L-NMA) into N-nitroso-containing product, which can subsequently be transformed into streptozotocin. Using unrestricted density functional theory (UDFT) with the hybrid functional B3LYP, we have mechanistically investigated the two sequential hydroxylations of L-NMA catalyzed by SznF's binuclear iron central domain. Mechanism B primarily involves the O-O bond dissociation, forming Fe(IV)=O, induced by the H+/e- introduction to the FeA side of μ-1,2-peroxo-Fe2(III/III), the substrate hydrogen abstraction by Fe(IV)=O, and the hydroxyl rebound to the substrate N radical. The stochastic addition of H+/e- to the FeB side (mechanism C) can transition to mechanism B, thereby preventing enzyme deactivation. Two other competing mechanisms, involving the direct O-O bond dissociation (mechanism A) and the addition of H2O as a co-substrate (mechanism D), have been ruled out.

Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway

The diiron cluster-containing oxygenase CmlI catalyzes the conversion of the aromatic amine precursor of chloramphenicol to the nitroaromatic moiety of the active antibiotic. The X-ray crystal structures of the fully active, N-terminally truncated CmlIΔ33 in the chemically reduced Fe(2+)/Fe(2+) state and a cis μ-1,2(η (1):η (1))-peroxo complex are presented. These structures allow comparison with the homologous arylamine oxygenase AurF as well as other types of diiron cluster-containing oxygenases. The structural model of CmlIΔ33 crystallized at pH 6.8 lacks the oxo-bridge apparent from the enzyme optical spectrum in solution at higher pH. In its place, residue E236 forms a μ-1,3(η (1):η (2)) bridge between the irons in both models. This orientation of E236 stabilizes a helical region near the cluster which closes the active site to substrate binding in contrast to the open site found for AurF. A very similar closed structure was observed for the inactive dimanganese form of AurF. The observation of this same structure in different arylamine oxygenases may indicate that there are two structural states that are involved in regulation of the catalytic cycle. Both the structural studies and single crystal optical spectra indicate that the observed cis μ-1,2(η (1):η (1))-peroxo complex differs from the μ-η (1):η (2)-peroxo proposed from spectroscopic studies of a reactive intermediate formed in solution by addition of O2 to diferrous CmlI. It is proposed that the structural changes required to open the active site also drive conversion of the µ-1,2-peroxo species to the reactive form.

An unusual peroxo intermediate of the arylamine oxygenase of the chloramphenicol biosynthetic pathway

Streptomyces venezuelae CmlI catalyzes the six-electron oxygenation of the arylamine precursor of chloramphenicol in a nonribosomal peptide synthetase (NRPS)-based pathway to yield the nitroaryl group of the antibiotic. Optical, EPR, and Mössbauer studies show that the enzyme contains a nonheme dinuclear iron cluster. Addition of O(2) to the diferrous state of the cluster results in an exceptionally long-lived intermediate (t(1/2) = 3 h at 4 °C) that is assigned as a peroxodiferric species (CmlI-peroxo) based upon the observation of an (18)O(2)-sensitive resonance Raman (rR) vibration. CmlI-peroxo is spectroscopically distinct from the well characterized and commonly observed cis-μ-1,2-peroxo (μ-η(1):η(1)) intermediates of nonheme diiron enzymes. Specifically, it exhibits a blue-shifted broad absorption band around 500 nm and a rR spectrum with a ν(O-O) that is at least 60 cm(-1) lower in energy. Mössbauer studies of the peroxo state reveal a diferric cluster having iron sites with small quadrupole splittings and distinct isomer shifts (0.54 and 0.62 mm/s). Taken together, the spectroscopic comparisons clearly indicate that CmlI-peroxo does not have a μ-η(1):η(1)-peroxo ligand; we propose that a μ-η(1):η(2)-peroxo ligand accounts for its distinct spectroscopic properties. CmlI-peroxo reacts with a range of arylamine substrates by an apparent second-order process, indicating that CmlI-peroxo is the reactive species of the catalytic cycle. Efficient production of chloramphenicol from the free arylamine precursor suggests that CmlI catalyzes the ultimate step in the biosynthetic pathway and that the precursor is not bound to the NRPS during this step.

Novel metal–organic framework with tunable fluorescence property: supramolecular signaling platform for polynitrophenolics

With the aid of a rotational C₃-symmetric tricarboxytriphenylamine based ligand, a new Cd-MOF was synthesized and characterized by various spectroscopic techniques as well as by single-crystal X-ray diffraction analysis.

Hexa-μ-acetato-1:2κ(4) O,O';1:2κ(2) O:O;2:3κ(4) O,O';2:3κ(2) O:O-bis-(4,4'-dimethyl-2,2'-bi-pyridine)-1κ(2) N,N';3κ(2) N,N'-2-calcium-1,3-dizinc

In the centrosymmetric trinuclear Zn^II⋯Ca^II⋯Zn^II title complex, [CaZn₂(CH₃COO)₆(C₁₂H₁₂N₂)₂], the Ca^II ion lies on an inversion centre and is octa­hedrally coordinated by six acetate O atoms. The Zn^II ion is coordinated by two N atoms from a bidentate di­methyl­bipyridine ligand and three O atoms from acetate ligands bridging to the Ca^II ion, leading to a distorted square-pyramidal coordination sphere. The Zn⋯Ca distance is 3.4668 (5) Å.

Structure of a dinuclear iron cluster-containing β-hydroxylase active in antibiotic biosynthesis

A family of dinuclear iron cluster-containing oxygenases that catalyze β-hydroxylation tailoring reactions in natural product biosynthesis by nonribosomal peptide synthetase (NRPS) systems was recently described [Makris, T. M., Chakrabarti, M., Münck, E., and Lipscomb, J. D. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 15391-15396]. Here, the 2.17 Å X-ray crystal structure of the archetypal enzyme from the family, CmlA, is reported. CmlA catalyzes β-hydroxylation of l-p-aminophenylalanine during chloramphenicol biosynthesis. The fold of the N-terminal domain of CmlA is unlike any previously reported, but the C-terminal domain has the αββα fold of the metallo-β-lactamase (MBL) superfamily. The diiron cluster bound in the C-terminal domain is coordinated by an acetate, three His residues, two Asp residues, one Glu residue, and a bridging oxo moiety. One of the Asp ligands forms an unusual monodentate bridge. No other oxygen-activating diiron enzyme utilizes this ligation or the MBL protein fold. The N-terminal domain facilitates dimerization, but using computational docking and a sequence-based structural comparison to homologues, we hypothesize that it likely serves additional roles in NRPS recognition and the regulation of O2 activation.

Insights into the nitric oxide reductase mechanism of flavodiiron proteins from a flavin-free enzyme

Flavodiiron proteins (FDPs) catalyze reductive scavenging of dioxygen and nitric oxide in air-sensitive microorganisms. FDPs contain a distinctive non-heme diiron/flavin mononucleotide (FMN) active site. Alternative mechanisms for the nitric oxide reductase (NOR) activity consisting of either protonation of a diiron-bridging hyponitrite or "super-reduction" of a diferrous-dinitrosyl by the proximal FMNH(2) in the rate-determining step have been proposed. To test these alternative mechanisms, we examined a deflavinated FDP (deflavo-FDP) from Thermotoga maritima. The deflavo-FDP retains an intact diiron site but does not exhibit multiturnover NOR or O(2) reductase (O(2)R) activity. Reactions of the reduced (diferrous) deflavo-FDP with nitric oxide were examined by UV-vis absorption, EPR, resonance Raman, and FTIR spectroscopies. Anaerobic addition of nitric oxide up to one NO per diferrous deflavo-FDP results in formation of a diiron-mononitrosyl complex characterized by a broad S = (1)/(2 )EPR signal arising from antiferromagnetic coupling of an S = (3)/(2) {FeNO}(7) with an S = 2 Fe(II). Further addition of NO results in two reaction pathways, one of which produces N(2)O and the diferric site and the other of which produces a stable diiron-dinitrosyl complex. Both NO-treated and as-isolated deflavo-FDPs regain full NOR and O(2)R activities upon simple addition of FMN. The production of N(2)O upon addition of NO to the mononitrosyl deflavo-FDP supports the hyponitrite mechanism, but the concomitant formation of a stable diiron-dinitrosyl complex in the deflavo-FDP is consistent with a super-reduction pathway in the flavinated enzyme. We conclude that a diiron-mononitrosyl complex is an intermediate in the NOR catalytic cycle of FDPs.

Circular dichroism and magnetic circular dichroism studies of the active site of p53R2 from human and mouse: iron binding and nature of the biferrous site relative to other ribonucleotide reductases

Ribonucleotide reductases (RNR) catalyze the rate-limiting step in the synthesis of deoxyribonucleotides from the corresponding ribonucleotides in the synthesis of DNA. Class I RNR has two subunits: R1 with the substrate binding and active site and R2 with a stable tyrosyl radical and diiron cluster. Biferrous R2 reacts with oxygen to form the tyrosyl radical needed for enzymatic activity. A novel R2 form, p53R2, is a 351-amino acid protein induced by the "tumor suppressor gene" p53. p53R2 has been studied using a combination of circular dichroism, magnetic circular dichroism, variable-temperature variable-field MCD, and EPR spectroscopies. The active site of biferrous p53R2 in both the human (hp53R2) and mouse (mp53R2) forms is found to have one five-coordinate and one four-coordinate iron, which are weakly antiferromagnetically coupled through mu-1,3-carboxylate bridges. These spectroscopic data are very similar to those of Escherichia coli R2, and mouse R2, with a stronger resemblance to data of the former. Titrations of apo-hp53R2 and apo-mp53R2 with Fe(II) were pursued for the purpose of comparing their metal binding affinities to those of other R2s. Both p53R2s were found to have a high affinity for Fe(II), which is different from that of mouse R2 and may reflect differences in the regulation of enzymatic activity, as p53R2 is mainly triggered during DNA repair. The difference in ferrous affinity between mammalian R2 and p53R2 suggests the possibility of specific inhibition of DNA precursor synthesis during cell division.

Artificial diiron proteins: from structure to function

De novo protein design provides an attractive approach for the construction of models to probe the features required for the function of complex metalloproteins. These minimal models contain the essential elements believed necessary for activity of the protein. In this article, we summarize the design, structure determination, and functional properties of a family of artificial diiron proteins.

Structure and interactions of amino acid radicals in class I ribonucleotide reductase studied by ENDOR and high-field EPR spectroscopy

This short review compiles high-field electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies on different intermediate amino acid radicals, which emerge in wild-type and mutant class I ribonucleotide reductase (RNR) both in the reaction of protein subunit R2 with molecular oxygen, which generates the essential tyrosyl radical, and in the catalytic reaction, which involves a radical transfer between subunits R2 and R1. Recent examples are presented, how different amino acid radicals (tyrosyl, tryptophan, and different cysteine-based radicals) were identified, assigned to a specific residue, and their interactions, in particular hydrogen bonding, were investigated using high-field EPR and ENDOR spectroscopy. Thereby, unexpected diiron-radical centers, which emerge in mutants of R2 with changed iron coordination, and an important catalytic cysteine-based intermediate in the substrate turnover reaction in R1 were identified and characterized. Experiments on the essential tyrosyl radical in R2 single crystals revealed the so far unknown conformational changes induced by formation of the radical. Interesting structural differences between the tyrosyl radicals of class Ia and Ib enzymes were revealed. Recently accurate distances between the tyrosyl radicals in the protein dimer R2 could be determined using pulsed electron-electron double resonance (PELDOR), providing a new tool for docking studies of protein subunits. These studies show that high-field EPR and ENDOR are important tools for the identification and investigation of radical intermediates, which contributed significantly to the current understanding of the reaction mechanism of class I RNR.

Remarkable aliphatic hydroxylation by the diiron enzyme toluene 4-monooxygenase in reactions with radical or cation diagnostic probes norcarane, 1,1-dimethylcyclopropane, and 1,1-diethylcyclopropane

Toluene 4-monooxygenase (T4MO) catalyzes the hydroxylation of toluene to yield 96% p-cresol. This diiron enzyme complex was used to oxidize norcarane (bicyclo[4.1.0]heptane), 1,1-dimethylcyclopropane, and 1,1-diethylcyclopropane, substrate analogues that can undergo diagnostic reactions upon the production of transient radical or cationic intermediates. Norcarane closely matches the shape and volume of the natural substrate toluene. Reaction of isoforms of the hydroxylase component of T4MO (T4moH) with different regiospecificities for toluene hydroxylation (k(cat) approximately 1.9-2.3 s(-)(1) and coupling efficiency approximately 81-96%) revealed similar catalytic parameters for norcarane oxidation (k(cat) approximately 0.3-0.5 s(-)(1) and coupling efficiency approximately 72%). The products included variable amounts of the un-rearranged isomeric norcaranols and cyclohex-2-enyl methanol, a product attributed to rearrangement of a radical oxidation intermediate. A ring-expansion product derived from the norcaranyl C-2 cation, cyclohept-3-enol, was not produced by either the natural enzyme or any of the T4moH isoforms tested. Comparative studies of 1,1-dimethylcyclopropane and 1,1-diethylcyclopropane, diagnostic substrates with differences in size and with approximately 50-fold slower k(cat) values, gave products consistent with both radical rearrangement and cation ring expansion. Examination of the isotopic enrichment of the incorporated O-atoms for all products revealed high-fidelity incorporation of an O-atom from O(2) in the un-rearranged and radical-rearranged products, while the O-atom found in the cation ring-expansion products was predominantly obtained by reaction with H(2)O. The results show a divergence of radical and cation pathways for T4moH-mediated hydroxylation that can be dissected by diagnostic substrate probe rearrangements and by changes in the source of oxygen used for substrate oxygenation.

X-ray Crystallography and Biological Metal Centers: Is Seeing Believing?

Metalloenzyme crystal structures have a major impact on our understanding of biological metal centers. They are often the starting point for mechanistic and computational studies and inspire synthetic modeling chemistry. The strengths and limitations of X-ray crystallography in determining properties of biological metal centers and their corresponding ligand spheres are explored through examples, including ribonucleotide reductase R2 and particulate methane monooxygenase. Protein crystal structures locate metal ions within a protein fold and reveal the identities and coordination geometries of amino acid ligands. Data collection strategies that exploit the anomalous scattering effect of metal ions can establish metal ion identity. The quality of crystallographic data, particularly the resolution, determines the level of detail that can be extracted from a protein crystal structure. Complementary spectroscopic techniques can provide crucial information regarding the redox state of the metal center as well as the presence, type, and protonation state of exogenous ligands. The final result of the crystallographic characterization of a metalloenzyme is a model based on crystallographic data, supported by information from biophysical and modeling studies, influenced by sample handling, and interpreted carefully by the crystallographer.

Dioxygen Binding to Complexes with FeII2(μ-OH)2 Cores: Steric Control of Activation Barriers and O2-Adduct Formation

A series of complexes with [Fe(II)(2)(mu-OH)(2)] cores has been synthesized with N3 and N4 ligands and structurally characterized to serve as models for nonheme diiron(II) sites in enzymes that bind and activate O(2). These complexes react with O(2) in solution via bimolecular rate-limiting steps that differ in rate by 10(3)-fold, depending on ligand denticity and steric hindrance near the diiron center. Low-temperature trapping of a (mu-oxo)(mu-1,2-peroxo)diiron(III) intermediate after O(2) binding requires sufficient steric hindrance around the diiron center and the loss of a proton (presumably that of a hydroxo bridge or a yet unobserved hydroperoxo intermediate). The relative stability of these and other (mu-1,2-peroxo)diiron(III) intermediates suggests that these species may not be on the direct pathway for dioxygen 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.

The oxo/peroxo debate: a nonheme iron perspective

The oxygen activation mechanisms proposed for nonheme iron systems generally follow the heme paradigm in invoking the involvement of iron-peroxo and iron-oxo species in their catalytic cycles. However, the nonheme ligand environments allow for end-on and side-on dioxygen coordination and impart greater flexibility in the modes of dioxygen activation. The currently available evidence for nonheme iron-peroxo and iron-oxo intermediates is summarized and discussed in light of the ongoing discussion on the nature of the oxidant(s) in heme enzymes.

Electronic and spectroscopic studies of the non-heme reduced binuclear iron sites of two ribonucleotide reductase variants: comparison to reduced methane monooxygenase and contributions to O2 reactivity

Circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD have been used to probe the biferrous active site of two variants of ribonucleotide reductase. The aspartate to glutamate substitution (R2-D84E) at the binuclear iron site modifies the endogenous ligand set of ribonucleotide reductase to match that of the binuclear center in the hydroxylase component of methane monooxygenase (MMOH). The crystal structure of chemically reduced R2-D84E suggests that the active-site structure parallels that of MMOH. However, CD, MCD, and VTVH MCD data combined with spin-Hamiltonian analysis of reduced R2-D84E indicate a different coordination environment relative to reduced MMOH, with no mu-(1,1)(eta(1),eta(2)) carboxylate bridge. To further understand the variations in geometry of the active site, which lead to differences in reactivity, density functional theory (DFT) calculations have been carried out to identify active-site structures for R2-wt and R2-D84E consistent with these spectroscopic data. The effects of varying the ligand set, positions of bound and free waters, and additional protein constraints on the geometry and energy of the binuclear site of both R2-wt and variant R2s are also explored to identify the contributions to their structural differences and their relation to reduced MMOH.

Reactions of the diiron enzyme stearoyl-acyl carrier protein desaturase

Stearoyl-acyl carrier protein Delta(9) desaturase (Delta9D) produces oleic acid, a nutritionally valuable fatty acid containing a cis double bond between C-9 and C-10. This multiprotein diiron enzyme complex reacts with stearoyl-acyl carrier protein, reduced [2Fe-2S] ferredoxin, and O(2) to complete the highly regiospecific and stereoselective desaturation reaction. Interactions with the acyl chain provide stability to the enzyme-substrate complex, give an energetic contribution to catalytic selectivity, and help to order the electron transfer, O(2) binding, and C-H bond cleavage steps of catalysis. Reactions with natural acyl chains indicate the involvement of a highly reactive diiron intermediate capable of oxidizing secondary C-H bonds (bond dissociation energy approximately 95 kcal/mol), but also capable of diagnostic O-atom transfer reactions with the appropriate substrate analogues. For soluble Delta9D, the natural reaction may initiate at the C-10 position, in contrast to the well-established initial reactivity of the membrane enzyme homologue stearoyl-coenzyme A (CoA) Delta(9) desaturase at the C-9 position.

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.

Structural characterization of the peroxodiiron(III) intermediate generated during oxygen activation by the W48A/D84E variant of ribonucleotide reductase protein R2 from Escherichia coli

The diiron(II) cluster in the R2 subunit of Escherichia coli ribonucleotide reductase (RNR) activates oxygen to generate a mu-oxodiiron(III) cluster and the stable tyrosyl radical that is critical for the conversion of ribonucleotides to deoxyribonucleotides. Like those in other diiron carboxylate proteins, such as methane monooxygenase (MMO), the R2 diiron cluster is proposed to activate oxygen by formation of a peroxodiiron(III) intermediate followed by an oxidizing high-valent cluster. Substitution of key active site residues results in perturbations of the normal oxygen activation pathway. Variants in which the active site ligand, aspartate (D) 84, is changed to glutamate (E) are capable of accumulating a mu-peroxodiiron(III) complex in the reaction pathway. Using rapid freeze-quench techniques, this intermediate in a double variant, R2-W48A/D84E, was trapped for characterization by Mössbauer and X-ray absorption spectroscopy. These samples contained 70% peroxodiiron(III) intermediate and 30% diferrous R2. An Fe-Fe distance of 2.5 A was found to be associated with the peroxo intermediate. As has been proposed for the structures of the higher valent intermediates in both R2 and MMO, carboxylate shifts to a mu-(eta(1),eta(2)) or a mu-1,1 conformation would most likely be required to accommodate the short 2.5 A Fe-Fe distance. In addition, the diferrous form of the enzyme present in the reacted sample has a longer Fe-Fe distance (3.5 A) than does a sample of anaerobically prepared diferrous R2 (3.4 A). Possible explanations for this difference in detected Fe-Fe distance include an O(2)-induced conformational change prior to covalent chemistry or differing O(2) reactivity among multiple diiron(II) forms of the cluster.

Synthesis and structural characterization of di- and tetranuclear zinc complexes with phenolate and carboxylate bridges. Correlations between 13C NMR chemical shifts and carboxylate binding modes

Two di- and a tetranuclear zinc-carboxylate complexes with different coordination modes, [Zn(2)L(mu(1,3)-OAc)(2)](ClO(4)) (1), [Zn(2)L(mu(1,3)-Pro)(2)](ClO(4)) (2), and [Zn(2)L(mu(1,1)-HCO(2))(mu(1,3)-HCO(2))](2)(ClO(4))(2) (3) (where L = 2,6-bis(N-2-(2'-pyridylethyl)formimidoyl)-4-methylphenol, OAc = acetate, and Pro = propionate) have been synthesized. Their compositions and structures have been identified by elemental analyses, IR, NMR, and X-ray single-crystal diffraction. The cations in both 1 and 2 reveal that the two zinc ions are assembled by a phenolate and a pair of syn-syn mu(1,3)-carboxylate bridges with metal-metal distances of 3.281 and 3.331 A, respectively, and each polyhedron around the zinc ion is a slightly distorted trigonal bipyramid. Compound 3 is a tetranuclear complex consisting of two identical dinuclear subunits that connect to each other by the two formate groups. In each subunit, the pair of metal ions separated at 3.130(1) A is assembled by a phenolate oxygen from L, and a monodentate and a syn-syn bidentate formate bridges. The formate group displays a novel tridentate mode, namely, monodentate and syn-anti bidentate bridges. On the other hand, the solid-state (13)C NMR technique was employed to distinguish the different binding modes of acetate group in five-coordinate zinc complexes. The chemical shifts are as follows: chelating mode (ca. 184 ppm) > bidentate bridge (ca. 180 ppm) > monodentate bridge (ca. 176 ppm).

Cobalt substitution of mouse R2 ribonucleotide reductase as a model for the reactive diferrous state: spectroscopic and structural evidence for a ferromagnetically coupled dinuclear cobalt cluster

The R2 dimer of mouse ribonucleotide reductase contains a dinuclear iron-oxygen cluster and tyrosyl radical/subunit. The dinuclear diferrous form reacts with dioxygen to generate the tyrosyl radical essential for the catalytic reaction that occurs at the R1 dimer. It is important to understand how the reactivity toward oxygen is related to the crystal structure of the dinuclear cluster. For the mouse R2 protein, no structure has been available with a fully occupied dinuclear metal ion site. A cobalt substitution of mouse R2 was performed to produce a good model for the very air-sensitive diferrous form of the enzyme. X-band EPR and light absorption studies (epsilon(550 nm) = 100 mm(-1) cm(-1)/Co(II)) revealed a strong cooperative binding of cobalt to the dinuclear site. In perpendicular mode EPR, the axial signal from mouse R2 incubated with Co(II) showed a typical S = 3/2 Co(II) signal, and its low intensity indicated that the majority of the Co(II) bound to R2 is magnetically coupled. In parallel mode EPR, a typical integer spin signal (M(s) = +/-3) with g approximately 12 is observed at 3.6 K and 10 K, showing that the two Co(II) ions (S = 3/2) in the dinuclear site are ferromagnetically coupled. We have solved the 2.4 A crystal structure of the Co(II)-substituted R2 with a fully occupied dinuclear cluster. The bridging Co(II) carboxylate ligand Glu-267 adopts an altered orientation compared with its counterpart Glu-238 in Escherichia coli R2. This might be important for proper O(2) activation of the more exposed native diferrous site in mouse R2 compared with E. coli R2.

Computational de novo design, and characterization of an A(2)B(2) diiron protein

Diiron proteins are found throughout nature and have a diverse range of functions; proteins in this class include methane monooxygenase, ribonucleotide reductase, Delta(9)-acyl carrier protein desaturase, rubrerythrin, hemerythrin, and the ferritins. Although each of these proteins has a very different overall fold, in every case the diiron active site is situated within a four-helix bundle. Additionally, nearly all of these proteins have a conserved Glu-Xxx-Xxx-His motif on two of the four helices with the Glu and His residues ligating the iron atoms. Intriguingly, subtle differences in the active site can result in a wide variety of functions. To probe the structural basis for this diversity, we designed an A(2)B(2) heterotetrameric four-helix bundle with an active site similar to those found in the naturally occurring diiron proteins. A novel computational approach was developed for the design, which considers the energy of not only the desired fold but also alternatively folded structures. Circular dichroism spectroscopy, analytical ultracentrifugation, and thermal unfolding studies indicate that the A and B peptides specifically associate to form an A(2)B(2) heterotetramer. Further, the protein binds Zn(II) and Co(II) in the expected manner and shows ferroxidase activity under single turnover conditions.

Variable-temperature nuclear magnetic resonance spectroscopy allows direct observation of carboxylate shift in zinc carboxylate complexes

Tetranuclear complexes [Zn(4)(bdmap)(2)(OOCR)(6)] 1 (R = Me) and 2 (R = Et), where Hbdmap = 1,3-bis(dimethylamino)-2-propanol, were prepared from zinc carboxylates and Hbdmap in tetrahydrofuran (THF). The solid-state structures of isomers 1a and 2a consist of two pairs of zinc atoms, each bridged by two mu-1,2 and one mu-1,1 carboxylate ligands. Two pairs are connected by two tridentate bdmap ligands with oxygen acting as a bridging donating atom. The complexes retain the tetranuclear structure in solution and two dynamic processes are observed from variable-temperature (1)H and (13)C NMR spectra. A low-temperature process (LT dynamics) observed already below 200 K is a coalescence of the mu-1,2 and the mu-1,1 resonances to a single resonance. An additional dynamic process (HT dynamics) is observed above 247 K (1) and 263 K (2), leading to a coalescence of two dimethylamino resonances. Both dynamic processes are rationalized by a mechanism involving changes in the carboxylate coordination mode termed as carboxylate shift. The LT dynamics is ascribed to interconversions of a single mu-1,2 and a single mu-1,1 carboxylate ligation by rotations of 60 degrees. The interconversions involve all carboxylate ligands in 1 and 2. The HT dynamics is ascribed to the exchange of the coordinating geometries of two carboxylate-bridged zinc atoms. We propose a mechanism that starts with a cleavage of the Zn-N coordination bond. The resulting coordinatively unsaturated zinc atom acquires an additional oxygen donor atom by carboxylate shift of mu-1,2 carboxylate to mu-1,1 mode. The activation parameters (DeltaH values in kilocalories per mole, DeltaS values in calories per mole per kelvin) were determined by line-shape analysis of VT NMR spectra: for 1 in THF-d(8), DeltaH(LT) = 8.1(3), DeltaS(LT) = -12(2), DeltaH(HT) = 17.9(2), DeltaS(HT) = 14(1); for 1 in CDCl(3), DeltaH(HT) = 13.6(5), DeltaS(HT) = 3(3); for 1 in CD(2)Cl(2), DeltaH(HT) = 9.9(3), DeltaS(HT) = -8(2); for 2 in THF-d(8), DeltaH(LT) = 11(1), DeltaS(LT) = -5(3), DeltaH(HT) = 19.6(5), DeltaS(HT) = 18(3). Polymeric [Zn(4)(bdmap)(2)(OOCMe)(6)](n) 1-catena crystallizes from a dichloromethane solution of 1. In 1-catena, the zinc atoms are linked into a chain through mu-1,2 and mu-1,1 acetate alternated by mu-1,2 acetate and bdmap.

Combined participation of hydroxylase active site residues and effector protein binding in a para to ortho modulation of toluene 4-monooxygenase regiospecificity

Toluene 4-monooxygenase (T4MO) is a diiron hydroxylase that exhibits high regiospecificity for para hydroxylation. This fidelity provides the basis for an assessment of the interplay between active site residues and protein complex formation in producing an essential biological outcome. The function of the T4MO catalytic complex (hydroxylase, T4moH, and effector protein T4moD) is evaluated with respect to effector protein concentration, the presence of T4MO electron-transfer components (Rieske ferredoxin, T4moC, and NADH oxidoreductase), and use of mutated T4moH isoforms with different hydroxylation regiospecificities. Steady-state kinetic analyses indicate that T4moC and T4moD form complexes of similar affinity with T4moH. At low T4moD concentrations, the steady-state hydroxylation rate is linearly dependent on T4moD-T4moH complex formation, whereas regiospecificity and the coupling efficiency between NADH consumption and hydroxylation are associated with intrinsic properties of the T4moD-T4moH complex. The optimized complex gives both efficient coupling and high regiospecificity with p-cresol representing >96% of total products from toluene. Similar coupling and regiospecificity for para hydroxylation are obtained with T3buV (an effector protein from a toluene 3-monooxygenase), demonstrating that effector protein binding does not uniquely determine or alter the regiospecificity of toluene hydroxylation. The omission of T4moD causes an approximately 20-fold decrease in hydroxylation rate, nearly complete uncoupling, and a decrease in regiospecificity so that p-cresol represents approximately 60% of total products. Similar shifts in regiospecificity are observed in oxidations of alternative substrates in the absence or upon the partial removal of either T4moD or T3buV from toluene oxidations. The mutated T4moH isoforms studied have apparent V(max)/K(M) specificities differing by approximately 2-4-fold and coupling efficiencies ranging from 88% to 95%, indicating comparable catalytic function, but also exhibit unique regiospecificity patterns for all substrates tested, suggesting unique substrate binding preferences within the active site. The G103L isoform has enhanced selectivity for ortho hydroxylation with all substrates tested except nitrobenzene, which gives only m-nitrophenol. The regiospecificity of the G103L isoform is comparable to that observed from naturally occurring variants of the toluene/benzene/o-xylene monooxygenase subfamily. Evolutionary and mechanistic implications of these findings are considered.

Computational studies of reaction mechanisms of methane monooxygenase and ribonucleotide reductase

An overview of the computational efforts made by our group during the last few years in the field of nonheme diiron proteins is presented. Through application of ab initio methodology to a reasonable set of molecular models, significant progress is made in understanding how the soluble Methane Monooxygenase system achieves the hydroxylation of methane and how the catalytic cycle of Ribonucleotide Reductase is initiated. In particular, the current studies reveal in more detail (1) the nature of key intermediates in the reaction cycles of these two metalloenzymes, (2) details of how the iron centers regulate the systems, and (3) important aspects of how the carboxylate ligands in the active sites may tailor the enzymatic needs of the metalloprotein. This knowledge also leads to novel connections between the two enzymes. The coordinative unsaturation and carboxylate shifts investigated herein are two properties that are likely to be of more general impact in nonheme proteins. The control of the redox chemistry of the enzyme by the binuclear metal center, also analyzed here, should find common ground among other bimetallic systems as well.

Density functional studies of oxidized and reduced methane monooxygenase. Optimized geometries and exchange coupling of active site clusters

The conflicting protein crystallography data for the oxidized form (MMOH(ox)) of methane monooxygenase present a dilemma regarding the identity of the solvent-derived bridging ligands within the active site: do they comprise a diiron unit bridged by 1H2O and 1OH(-) as postulated for Methylococcus capsulatus or 2OH(-) ligands as suggested for Methylosinus trichosporium? Using models derived explicitly from the M. capsulatus and M. trichosporium protein data, spin-unrestricted density functional methods have been used to study two structurally characterized forms of the hydroxylase component of methane monooxygenase. The active site geometries of the oxidized (MMOH(ox)) and two-electron-reduced (MMOH(red)) states have been geometry optimized using several quantum cluster models which take into account the antiferromagnetic (AF) and ferromagnetic (F) coupling of electron spins. Trends in cluster geometries, energetics, and Heisenberg J values have been evaluated. For the majority of models, calculated geometries are in good agreement with the X-ray analyses and appear relatively insensitive to the F or AF alignment of electron spins on adjacent Fe sites. Discrepancies between calculation and experiment appear in the orientation of the coordinated His and Glu amino acid side chains for both MMOH(ox) and MMOH(red) and also in unexpected intramolecular proton transfer in the MMOH(ox) cluster models. There is additional dispersion between (and among) calculated and experimental Fe(3+)-OH(-) distances with relevance to the correct protonation state of the solvent-derived ligands. In an accompanying paper (Lovell, T.; Li, J.; Noodleman, L. Inorg. Chem. 2001, 40, 5267), a comparison of the related energetics of the active site models examined herein is further evaluated in the full protein and solvent environment.

Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer

The R2 subunits of class I ribonucleotide reductases (RNRs) house a diferric-tyrosyl radical (Y*) cofactor essential for DNA synthesis. In yeast, there are two R2 proteins, Y2 and Y4. Although both Y2 and Y4 are homologous to R2s from other organisms, Y4 lacks three conserved iron-binding residues, and its exact function is unclear. Y4 is required for assembly of the diferric-Y* cofactor in Y2, and the two proteins can form both homodimeric and heterodimeric complexes. The Y2Y4 heterodimer was crystallized from a mixture of the two proteins, and its structure was determined to 2.8 A resolution. Both Y2 and Y4 are completely alpha helical and resemble the mouse and Escherichia coli R2s in overall fold. Three alpha helices not observed in the mouse R2 structure are present at the Y2 N terminus, and one extra N-terminal helix is observed in Y4. In addition, one of the eight principal helices in both Y2 and Y4, alphaD, is shifted significantly from its position in mouse R2. The heterodimer interface is similar to the mouse R2 homodimer interface in size and interacting residues, but loop regions at the interface edges differ. A single metal ion, assigned as Zn(II), occupies the Fe2 position in the Y2 active site. Treatment of the crystals with Fe(II) results in difference electron density consistent with formation of a diiron center. No metal-binding site is observed in Y4. Instead, the residues in the active site region form a hydrogen-bonding network involving an arginine, two glutamic acids, and a water molecule.

Rational reprogramming of the R2 subunit of Escherichia coli ribonucleotide reductase into a self-hydroxylating monooxygenase

The outcome of O2 activation at the diiron(II) cluster in the R2 subunit of Escherichia coli (class I) ribonucleotide reductase has been rationally altered from the normal tyrosyl radical (Y122*) production to self-hydroxylation of a phenylalanine side-chain by two amino acid substitutions that leave intact the (histidine)2-(carboxylate)4 ligand set characteristic of the diiron-carboxylate family. Iron ligand Asp (D) 84 was replaced with Glu (E), the amino acid found in the cognate position of the structurally similar diiron-carboxylate protein, methane monooxygenase hydroxylase (MMOH). We previously showed that this substitution allows accumulation of a mu-1,2-peroxodiiron(III) intermediate, which does not accumulate in the wild-type (wt) protein and is probably a structural homologue of intermediate P (H(peroxo)) in O2 activation by MMOH. In addition, the near-surface residue Trp (W) 48 was replaced with Phe (F), blocking transfer of the "extra" electron that occurs in wt R2 during formation of the formally Fe(III)Fe(IV) cluster X. Decay of the mu-1,2-peroxodiiron(III) complex in R2-W48F/D84E gives an initial brown product, which contains very little Y122* and which converts very slowly (t1/2 approximately 7 h) upon incubation at 0 degrees C to an intensely purple final product. X-ray crystallographic analysis of the purple product indicates that F208 has undergone epsilon-hydroxylation and the resulting phenol has shifted significantly to become a ligand to Fe2 of the diiron cluster. Resonance Raman (RR) spectra of the purple product generated with 16O2 or 18O2 show appropriate isotopic sensitivity in bands assigned to O-phenyl and Fe-O-phenyl vibrational modes, confirming that the oxygen of the Fe(III)-phenolate species is derived from O2. Chemical analysis, experiments involving interception of the hydroxylating intermediate with exogenous reductant, and Mössbauer and EXAFS characterization of the brown and purple species establish that F208 hydroxylation occurs during decay of the peroxo complex and formation of the initial brown product. The slow transition to the purple Fe(III)-phenolate species is ascribed to a ligand rearrangement in which mu-O2- is lost and the F208-derived phenolate coordinates. The reprogramming to F208 monooxygenase requires both amino acid substitutions, as very little epsilon-hydroxyphenylalanine is formed and pathways leading to Y122* formation predominate in both R2-D84E and R2-W48F.

A mechanistic study of the reaction between a diiron(II) complex [FeII(2)(mu-OH)2(6-Me3-TPA)2](2+) and O2 to form a diiron(III) peroxo complex

A kinetic study of the reaction between a diiron(II) complex [Fe(II)(2)(mu-OH)(2)(6-Me(3)-TPA)(2)](2+) 1, where 6-Me(3)-TPA = tris(6-methyl-2-pyridylmethyl)amine, and dioxygen is presented. A diiron(III) peroxo complex [Fe(III)(2)(mu-O)(mu-O(2))(6-Me(3)-TPA)(2)](2+) 2 forms quantitatively in dichloromethane at temperatures from -80 to -40 degrees C. The reaction is first order in [Fe(II)(2)] and [O(2)], with the activation parameters DeltaH(double dagger) = 17 +/- 2 kJ mol(-1) and DeltaS(double dagger) = -175 +/- 20 J mol(-1) K(-1). The reaction rate is not significantly influenced by the addition of H(2)O or D(2)O. The reaction proceeds faster in more polar solvents (acetone and acetonitrile), but the yield of 2 is not quantitative in these solvents. Complex 1 reacts with NO at a rate about 10(3) faster than with O(2). The mechanistic analysis suggests an associative rate-limiting step for the oxygenation of 1, similar to that for stearoyl-ACP Delta(9)-desaturase, but distinct from the probable dissociative pathway of methane monoxygenase. An eta(1)-superoxo Fe(II)Fe(III) species is a likely steady-state intermediate during the oxygenation of complex 1.

Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site

The oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (MMOH). Previous structural studies of MMOH, and the related R2 subunit of ribonucleotide reductase, have demonstrated the occurrence of carboxylate shifts involving glutamate residues that ligate the catalytic iron atoms. These shifts are thought to have important mechanistic implications. Recent kinetic and theoretical studies have also emphasized the importance of hydrogen bonding and pH effects at the active site. We report here crystal structures of MMOH from Methylococcus capsulatus (Bath) in the diiron(II), diiron(III), and mixed-valent Fe(II)Fe(III) oxidation states, and at pH values of 6.2, 7.0, and 8.5. These structures were investigated in an effort to delineate the range of possible motions at the MMOH active site and to identify hydrogen-bonding interactions that may be important in understanding catalysis by the enzyme. Our results present the first view of the diiron center in the mixed-valent state, and they indicate an increased lability for ferrous ions in the enzyme. Alternate conformations of Asn214 near the active site according to redox state and a distortion in one of the alpha-helices adjacent to the metal center in the diiron(II) state have also been identified. These changes alter the surface of the protein in the vicinity of the catalytic core and may have implications for small-molecule accessibility to the active site and for protein component interactions in the methane monooxygenase system. Collectively, these results help to explain previous spectroscopic observations and provide new insight into catalysis by the enzyme.