myo-Inositol oxygenase: a radical new pathway for O(2) and C-H activation at a nonheme diiron cluster

Crystallographic analysis of active site contributions to regiospecificity in the diiron enzyme toluene 4-monooxygenase

Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric μ-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201. In contrast, complexes with inhibitors p-NH(2)-benzoate and p-Br-benzoate showed a μ-1,1 coordination of carboxylate oxygen between the iron atoms and only a partial shift in the position of E231. Among active site residues, F176 trapped the aromatic ring of products against a surface of the active site cavity formed by G103, E104 and A107, while F196 positioned the aromatic ring against this surface via a π-stacking interaction. The proximity of G103 and F176 to the para substituent of the substrate aromatic ring and the structure of G103L T4moHD suggest how changes in regiospecificity arise from mutations at G103. Although effector protein binding produced significant shifts in the positions of residues along the outer portion of the active site (T201, N202, and Q228) and in some iron ligands (E231 and E197), surprisingly minor shifts (<1 Å) were produced in F176, F196, and other interior residues of the active site. Likewise, products bound to the diiron center in either the presence or absence of effector protein did not significantly shift the position of the interior residues, suggesting that positioning of the cognate substrates will not be strongly influenced by effector protein binding. Thus, changes in product distributions in the absence of the effector protein are proposed to arise from differences in rates of chemical steps of the reaction relative to motion of substrates within the active site channel of the uncomplexed, less efficient enzyme, while structural changes in diiron ligand geometry associated with cycling between diferrous and diferric states are discussed for their potential contribution to product release.

Comparative reactivity of ferric-superoxo and ferryl-oxo species in heme and non-heme complexes

Ferryl-oxo species have been recognized as a key oxidant in many heme and non-heme enzymes. Recently, less-characterized ferric-superoxo species have been found or suggested to be another electrophilic oxidant. Reactivity of several vital ferryl-oxo and ferric-superoxo model complexes was examined by DFT calculations. Reactivity is found to correlate well with thermodynamic driving force and can increase with higher electrophilicity of the oxidant. Reactivity of the ferric-superoxo oxidants generally is not "superior" to the ferryl-oxo ones. Compared to the high-spin non-heme ferric-superoxo, the lower reactivity of low-spin heme ferric-superoxo, seldom utilized in nature, can be attributed to lower electrophilicity and more pronounced quenching of anti-ferromagnetic coupling between the ferric and superoxo parts. The present comparison should shed some light on mechanistic strategies in heme and non-heme enzymes and provide clues to rational design of ferric-superoxo oxidants.

Cyanobacterial alkane biosynthesis further expands the catalytic repertoire of the ferritin-like 'di-iron-carboxylate' proteins

Enzymes that activate dioxygen at carboxylate-bridged non-heme diiron clusters residing within ferritin-like, four-helix-bundle protein architectures have crucial roles in, among other processes, the global carbon cycle (e.g. soluble methane monooxygenase), fatty acid biosynthesis [plant fatty acyl-acyl carrier protein (ACP) desaturases], DNA biosynthesis [the R2 or β2 subunits of class Ia ribonucleotide reductases (RNRs)], and cellular iron trafficking (ferritins). Classic studies on class Ia RNRs showed long ago how this obligatorily oxidative di-iron/O2 chemistry can be used to activate an enzyme for even a reduction reaction, and more recent investigations of class Ib and Ic RNRs, coupled with earlier studies on dimanganese catalases, have shown that members of this protein family can also incorporate either one or two Mn ions and use them in place of iron for redox catalysis. These two strategies--oxidative activation for non-oxidative reactions and use of alternative metal ions--expand the catalytic repertoire of the family, probably to include activities that remain to be discovered. Indeed, a recent study has suggested that fatty aldehyde decarbonylases (ADs) from cyanobacteria, purported to catalyze a redox-neutral cleavage of a Cn aldehyde to the Cn-1 alkane (or alkene) and CO, also belong to this enzyme family and are most similar in structure to two other members with heterodinuclear (Mn-Fe) cofactors. Here, we first briefly review both the chemical principles underlying the O2-dependent oxidative chemistry of the 'classical' di-iron-carboxylate proteins and the two aforementioned strategies that have expanded their functional range, and then consider what metal ion(s) and what chemical mechanism(s) might be employed by the newly discovered cyanobacterial ADs.

Valence-to-core X-ray emission spectroscopy: a sensitive probe of the nature of a bound ligand

The sensitivity of iron Kβ X-ray emission spectroscopy (XES) to the nature of the bound ligands (σ-donating, π-donating, and π-accepting) has been explored. A combination of experiment and theory has been employed, with a DFT approach being utilized to elucidate ligand effects on the spectra and to assign the spectral intensity mechanisms. Knowledge of the various contributions to the spectra allows for a deeper understanding of spectral features and demonstrates the sensitivity of this method to the identity of the interacting ligands. The potential of XES for identifying intermediate species in nonheme iron enzymes is highlighted.

Substrate activation by iron superoxo intermediates

A growing number of non-heme-iron oxygenases and oxidases catalyze reactions for which the well-established mechanistic paradigm involving a single C-H-bond-cleaving intermediate of the Fe(IV)-oxo (ferryl) type [1(•)] is insufficient to explain the chemistry. It is becoming clear that, in several of these cases, Fe(III)-superoxide complexes formed by simple addition of O(2) to the reduced [Fe(II)] cofactor initiate substrate oxidation by abstracting hydrogen [2,3(•)]. This substrate-oxidizing entry route into high-valent-iron intermediates makes possible an array of complex and elegant oxidation reactions without the consumption of valuable reducing equivalents. Examples of this novel mechanistic strategy are discussed with the goal of bringing forth unifying principles.

Oxygen activation at mononuclear nonheme iron centers: a superoxo perspective

Dioxygen (O(2)) activation by iron enzymes is responsible for many metabolically important transformations in biology. Often a high-valent iron oxo oxidant is proposed to form upon O(2) activation at a mononuclear nonheme iron center, presumably via intervening iron superoxo and iron peroxo species. While iron(IV) oxo intermediates have been trapped and characterized in enzymes and models, less is known of the putative iron(III) superoxo species. Utilizing a synthetic model for the 2-oxoglutarate-dependent monoiron enzymes, [(Tp(iPr2))Fe(II)(O(2)CC(O)CH(3))], we have obtained indirect evidence for the formation of the putative iron(III) superoxo species, which can undergo one-electron reduction, hydrogen-atom transfer, or conversion to an iron(IV) oxo species, depending on the reaction conditions. These results demonstrate the various roles that the iron(III) superoxo species can play in the course of O(2) activation at a nonheme iron center.

Current challenges of modeling diiron enzyme active sites for dioxygen activation by biomimetic synthetic complexes

This tutorial review describes recent progress in modeling the active sites of carboxylate-rich non-heme diiron enzymes that activate dioxygen to carry out several key reactions in Nature. The chemistry of soluble methane monooxygenase, which catalyzes the selective oxidation of methane to methanol, is of particular interest for (bio)technological applications. Novel synthetic diiron complexes that mimic structural, and, to a lesser extent, functional features of these diiron enzymes are discussed. The chemistry of the enzymes is also briefly summarized. A particular focus of this review is on models that mimic characteristics of the diiron systems that were previously not emphasized, including systems that contain (i) aqua ligands, (ii) different substrates tethered to the ligand framework, (iii) dendrimers attached to carboxylates to mimic the protein environment, (iv) two N-donors in a syn-orientation with respect to the iron-iron vector, and (v) a N-rich ligand environment capable of accessing oxygenated high-valent diiron intermediates.

Insights into the (superoxo)Fe(III)Fe(III) intermediate and reaction mechanism of myo-inositol oxygenase: DFT and ONIOM(DFT:MM) study

The (superoxo)Fe(III)Fe(III) reactive species and the catalytic reaction mechanism of a diiron enzyme, myo-inositol oxygenase (MIOX), were theoretically investigated by means of density functional theory (DFT) and ONIOM quantum mechanical/molecular mechanical (QM/MM) approaches. The ground state of the (superoxo)Fe(III)Fe(III) intermediate was shown to have a side-on coordination geometry and an S = 1/2 spin state, wherein the two iron sites are antiferromagnetically coupled while the superoxide site and the nearest iron are ferromagnetically coupled. A full reaction pathway leading to a D-glucuronate product from myo-inositol was proposed based on ONIOM computational results. Two major roles of the enzyme surrounding during the catalytic reaction were identified. One is to facilitate the initial H-abstraction step, and the other is to restrict the movement of the substrate via H-bonding interactions in order to avoid unwanted side reactions. In our proposed mechanism, O-O bond cleavage has the highest barrier, thus constituting the rate-limiting step of the reaction. The unique role of the bridging hydroxide ligand as a catalytic base was also identified.

Hydroperoxylation by hydroxyethylphosphonate dioxygenase

Hydroxyethylphosphonate dioxygenase (HEPD) catalyzes the O(2)-dependent cleavage of the carbon-carbon bond of 2-hydroxyethylphosphonate (2-HEP) to afford hydroxymethylphosphonate (HMP) and formate without input of electrons or use of any organic cofactors. Two mechanisms have been proposed to account for this reaction. One involves initial hydroxylation of substrate to an acetal intermediate and its subsequent attack onto an Fe(IV)-oxo species. The second mechanism features initial hydroperoxylation of substrate followed by a Criegee rearrangement. To distinguish between the two mechanisms, substrate analogues were synthesized and presented to the enzyme. Hydroxymethylphosphonate was converted into phosphate and formate, and 1-hydroxyethylphosphonate was converted to acetylphosphate, which is an inhibitor of the enzyme. These results provide strong support for a Criegee rearrangement with a phosphorus-based migrating group and require that the O-O bond of molecular oxygen is not cleaved prior to substrate activation. (2R)-Hydroxypropylphosphonate partitioned between conversion to 2-oxopropylphosphonate and hydroxymethylphosphonate, with the latter in turn converted to phosphate and formate. Collectively, these results support a mechanism that proceeds by hydroperoxylation followed by a Criegee rearrangement.

Characterization of two distinct adducts in the reaction of a nonheme diiron(II) complex with O2

Two [Fe(II)(2)(N-EtHPTB)(mu-O(2)X)](2+) complexes, where N-EtHPTB is the anion of N,N,N'N'-tetrakis(2-benzimidazolylmethyl)-2-hydroxy-1,3-diaminopropane and O(2)X is O(2)PPh(2) (1 x O(2)PPh(2)) or O(2)AsMe(2) (1 x O(2)AsMe(2)), have been synthesized. Their crystal structures both show interiron distances of 3.54 A that arise from a (mu-alkoxo)diiron(II) core supported by an O(2)X bridge. These diiron(II) complexes react with O(2) at low temperatures in MeCN (-40 degrees C) and CH(2)Cl(2) (-60 degrees C) to form long-lived O(2) adducts that are best described as (mu-eta(1):eta(1)-peroxo)diiron(III) species (2 x O(2)X) with nu(O-O) approximately 850 cm(-1). Upon warming to -30 degrees C, 2 x O(2)PPh(2) converts irreversibly to a second (mu-eta(1):eta(1)-peroxo)diiron(III) intermediate (3 x O(2)PPh(2)) with nu(O-O) approximately 900 cm(-1), a value which matches that reported for [Fe(2)(N-EtHPTB)(O(2))(O(2)CPh)](2+) (3 x O(2)CPh) (Dong et al. J. Am. Chem. Soc. 1993, 115, 1851-1859). Mossbauer spectra of 2 x O(2)PPh(2) and 3 x O(2)PPh(2) indicate that the iron centers within each species are antiferromagnetically coupled with J approximately 60 cm(-1), while extended X-ray absorption fine structure analysis reveals interiron distances of 3.25 and 3.47 A for 2 x O(2)PPh(2) and 3 x O(2)PPh(2), respectively. A similarly short interiron distance (3.27 A) is found for 2 x O(2)AsMe(2). The shorter interiron distance associated with 2 x O(2)PPh(2) and 2 x O(2)AsMe(2) is proposed to derive from a triply bridged diiron(III) species with alkoxo (from N-EtHPTB), 1,2-peroxo, and 1,3-O(2)X bridges, while the longer distance associated with 3 x O(2)PPh(2) results from the shift of the O(2)PPh(2) bridge to a terminal position on one iron. The differences in nu(O-O) are also consistent with the different interiron distances. It is suggested that the O...O bite distance of the O(2)X moiety affects the thermal stability of 2 x O(2)X, with the O(2)X having the largest bite distance (O(2)AsMe(2)) favoring the 2 x O(2)X adduct and the O(2)X having the smallest bite distance (O(2)CPh) favoring the 3 x O(2)X adduct. Interestingly, neither 3 x O(2)AsMe(2) nor the benzoate analog of 2 x O(2)X (2 x O(2)Bz) are observed.

Anaerobic functionalization of unactivated C-H bonds

The functionalization of alkanes was once thought to lie strictly within the domain of enzymes that activate dioxygen in order to generate an oxidant with suitable potency to cleave inert C-H bonds. The emergence of the radical SAM superfamily of enzymes-those which use S-adenosyl-l-methionine as a precursor to a 5'-deoxyadenosyl 5'-radical-has kindled a renaissance in the study of radical-dependent enzymatic reactions, and is ushering in a wealth of new and intriguing chemistry that remains to be elucidated. This review will focus on a special subclass of radical SAM enzymes that functionalize inert C-H bonds, highlighting the functional groups and the chemistry that leads to their insertion. Within this class are first, enzymes that catalyze sulfur insertion, the prototype of which is biotin synthase; second, enzymes that catalyze P-methylation or C-methylation, such as P-methylase or Fom3; third, enzymes that catalyze oxygen insertion, such as the anaerobic magnesium protoporphyrin-IX oxidative cyclase (BchE); and fourth, enzymes that functionalize n-hexane or other alkanes as the first step in the metabolism of these inert compounds by certain bacteria. In addition to surveying reactions that have been studied at various levels of detail, this review will speculate on the mechanisms of other types of reactions that this chemistry lends itself to.