Correlating structure with function in bacterial multicomponent monooxygenases and related diiron proteins

Multiple roles of component proteins in bacterial multicomponent monooxygenases: phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas sp. OX1

Phenol hydroxylase (PH) and toluene/o-xylene monooxygenase (ToMO) from Pseudomonas sp. OX1 require three or four protein components to activate dioxygen for the oxidation of aromatic substrates at a carboxylate-bridged diiron center. In this study, we investigated the influence of the hydroxylases, regulatory proteins, and electron-transfer components of these systems on substrate (phenol; NADH) consumption and product (catechol; H(2)O(2)) generation. Single-turnover experiments revealed that only complete systems containing all three or four protein components are capable of oxidizing phenol, a major substrate for both enzymes. Under ideal conditions, the hydroxylated product yield was ∼50% of the diiron centers for both systems, suggesting that these enzymes operate by half-sites reactivity mechanisms. Single-turnover studies indicated that the PH and ToMO electron-transfer components exert regulatory effects on substrate oxidation processes taking place at the hydroxylase actives sites, most likely through allostery. Steady state NADH consumption assays showed that the regulatory proteins facilitate the electron-transfer step in the hydrocarbon oxidation cycle in the absence of phenol. Under these conditions, electron consumption is coupled to H(2)O(2) formation in a hydroxylase-dependent manner. Mechanistic implications of these results are discussed.

Active site threonine facilitates proton transfer during dioxygen activation at the diiron center of toluene/o-xylene monooxygenase hydroxylase

Toluene/o-xylene monooxygenase hydroxylase (ToMOH), a diiron-containing enzyme, can activate dioxygen to oxidize aromatic substrates. To elucidate the role of a strictly conserved T201 residue during dioxygen activation of the enzyme, T201S, T201G, T201C, and T201V variants of ToMOH were prepared by site-directed mutagenesis. X-ray crystal structures of all the variants were obtained. Steady-state activity, regiospecificity, and single-turnover yields were also determined for the T201 mutants. Dioxygen activation by the reduced T201 variants was explored by stopped-flow UV-vis and Mössbauer spectroscopy. These studies demonstrate that the dioxygen activation mechanism is preserved in all T201 variants; however, both the formation and decay kinetics of a peroxodiiron(III) intermediate, T201(peroxo), were greatly altered, revealing that T201 is critically involved in dioxygen activation. A comparison of the kinetics of O(2) activation in the T201S, T201C, and T201G variants under various reaction conditions revealed that T201 plays a major role in proton transfer, which is required to generate the peroxodiiron(III) intermediate. A mechanism is postulated for dioxygen activation, and possible structures of oxygenated intermediates are discussed.

Structural and functional studies of the Escherichia coli phenylacetyl-CoA monooxygenase complex

The utilization of phenylacetic acid (PA) in Escherichia coli occurs through a hybrid pathway that shows features of both aerobic and anaerobic metabolism. Oxygenation of the aromatic ring is performed by a multisubunit phenylacetyl-coenzyme A oxygenase complex that shares remote homology of two subunits to well studied bacterial multicomponent monooxygenases and was postulated to form a new bacterial multicomponent monooxygenase subfamily. We expressed the subunits PaaA, B, C, D, and E of the PA-CoA oxygenase and showed that PaaABC, PaaAC, and PaaBC form stable subcomplexes that can be purified. In vitro reconstitution of the oxygenase subunits showed that each of the PaaA, B, C, and E subunits are necessary for catalysis, whereas PaaD is not essential. We have determined the crystal structure of the PaaAC complex in a ligand-free form and with several CoA derivatives. We conclude that PaaAC forms a catalytic core with a monooxygenase fold with PaaA being the catalytic α subunit and PaaC, the structural β subunit. PaaAC forms heterotetramers that are organized very differently from other known multisubunit monooxygenases and lacks their conservative network of hydrogen bonds between the di-iron center and protein surface, suggesting different association with the reductase and different mechanisms of electron transport. The PaaA structure shows adaptation of the common access route to the active site for binding a CoA-bound substrate. The enzyme-substrate complex shows the orientation of the aromatic ring, which is poised for oxygenation at the ortho-position, in accordance with the expected chemistry. The PA-CoA oxygenase complex serves as a paradigm for the new subfamily multicomponent monooxygenases comprising several hundred homologs.

Manganese catalysts for C-H activation: an experimental/theoretical study identifies the stereoelectronic factor that controls the switch between hydroxylation and desaturation pathways

We describe competitive C-H bond activation chemistry of two types, desaturation and hydroxylation, using synthetic manganese catalysts with several substrates. 9,10-Dihydrophenanthrene (DHP) gives the highest desaturation activity, the final products being phenanthrene (P1) and phenanthrene 9,10-oxide (P3), the latter being thought to arise from epoxidation of some of the phenanthrene. The hydroxylase pathway also occurs as suggested by the presence of the dione product, phenanthrene-9,10-dione (P2), thought to arise from further oxidation of hydroxylation intermediate 9-hydroxy-9,10-dihydrophenanthrene. The experimental work together with the density functional theory (DFT) calculations shows that the postulated Mn oxo active species, [Mn(O)(tpp)(Cl)] (tpp = tetraphenylporphyrin), can promote the oxidation of dihydrophenanthrene by either desaturation or hydroxylation pathways. The calculations show that these two competing reactions have a common initial step, radical H abstraction from one of the DHP sp(3) C-H bonds. The resulting Mn hydroxo intermediate is capable of promoting not only OH rebound (hydroxylation) but also a second H abstraction adjacent to the first (desaturation). Like the active Mn(V)=O species, this Mn(IV)-OH species also has radical character on oxygen and can thus give H abstraction. Both steps have very low and therefore very similar energy barriers, leading to a product mixture. Since the radical character of the catalyst is located on the oxygen p orbital perpendicular to the Mn(IV)-OH plane, the orientation of the organic radical with respect to this plane determines which reaction, desaturation or hydroxylation, will occur. Stereoelectronic factors such as the rotational orientation of the OH group in the enzyme active site are thus likely to constitute the switch between hydroxylase and desaturase behavior.

Structural basis for activation of class Ib ribonucleotide reductase

The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)2-tyrosyl radical (Y•) or a Fe(III)2-Y• cofactor in the NrdF subunit. Whereas Fe(III)2-Y• can self-assemble from Fe(II)2-NrdF and O2, activation of Mn(II)2-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O2. The crystal structures reported here of E. coli Mn(II)2-NrdF and Fe(II)2-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)2-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)2 active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)2-Y• cofactor assembly.

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.

X-ray structures of ferritins and related proteins

Ferritins are members of a much larger superfamily of proteins, which are characterised by a structural motif consisting of a bundle of four parallel and anti-parallel alpha helices. The ferritin superfamily itself is widely distributed across all three living kingdoms, in both aerobic and anaerobic organisms, and a considerable number of X-ray structures are available, some at extremely high resolution. We describe first of all the subunit structure of mammalian H and L chain ferritins and then discuss intersubunit interactions in the 24-subunit quaternary structure of these ferritins. Bacteria contain two types of ferritins, FTNs, which like mammalian ferritins do not contain haem, and the haem-containing BFRs. The characteristic carboxylate-bridged di-iron ferroxidase sites of H chain ferritins, FTNs and BFRs are compared, as are the potential entry sites for iron and the 'nucleation' site of L chain ferritins. Finally we discuss the three-dimensional structures of the 12-subunit bacterial Dps (DNA-binding protein from starved cells) proteins as well as their intersubunit di-iron ferroxidase site.

Revisiting the mechanism of dioxygen activation in soluble methane monooxygenase from M. capsulatus (Bath): evidence for a multi-step, proton-dependent reaction pathway

Stopped-flow kinetic investigations of soluble methane monooxygenase (sMMO) from M. capsulatus (Bath) have clarified discrepancies that exist in the literature regarding several aspects of catalysis by this enzyme. The development of thorough kinetic analytical techniques has led to the discovery of two novel oxygenated iron species that accumulate in addition to the well-established intermediates H(peroxo) and Q. The first intermediate, P*, is a precursor to H(peroxo) and was identified when the reaction of reduced MMOH and MMOB with O(2) was carried out in the presence of >or=540 microM methane to suppress the dominating absorbance signal due to Q. The optical properties of P* are similar to those of H(peroxo), with epsilon(420) = 3500 M(-1) cm(-1) and epsilon(720) = 1250 M(-1) cm(-1). These values are suggestive of a peroxo-to-iron(III) charge-transfer transition and resemble those of peroxodiiron(III) intermediates characterized in other carboxylate-bridged diiron proteins and synthetic model complexes. The second identified intermediate, Q*, forms on the pathway of Q decay when reactions are performed in the absence of hydrocarbon substrate. Q* does not react with methane, forms independently of buffer composition, and displays a unique shoulder at 455 nm in its optical spectrum. Studies conducted at different pH values reveal that rate constants corresponding to P* decay/H(peroxo) formation and H(peroxo) decay/Q formation are both significantly retarded at high pH and indicate that both events require proton transfer. The processes exhibit normal kinetic solvent isotope effects (KSIEs) of 2.0 and 1.8, respectively, when the reactions are performed in D(2)O. Mechanisms are proposed to account for the observations of these novel intermediates and the proton dependencies of P* to H(peroxo) and H(peroxo) to Q conversion.

Degradation of alkanes by bacteria

Pollution of soil and water environments by crude oil has been, and is still today, an important problem. Crude oil is a complex mixture of thousands of compounds. Among them, alkanes constitute the major fraction. Alkanes are saturated hydrocarbons of different sizes and structures. Although they are chemically very inert, most of them can be efficiently degraded by several microorganisms. This review summarizes current knowledge on how microorganisms degrade alkanes, focusing on the biochemical pathways used and on how the expression of pathway genes is regulated and integrated within cell physiology.

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.

2-Phenoxypyridyl dinucleating ligands for assembly of diiron(II) complexes: efficient reactivity with O(2) to form (mu-Oxo)diiron(III) units

A series of 2-phenoxypyridyl and 2-phenoxyimino ligands, H(2)L(R,R') [2,2'-(5,5'-(1,2-phenylenebis(ethyne-2,1-diyl))bis(pyridine-5,2-diyl))diphenol, where R = H, Me, or t-Bu, and R' = H or Ph] and H(2)BIPS(Me,Ph) [(3,3'-(1E,1'E)-(3,3'-sulfonylbis(3,1-phenylene)bis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)bis(5-methylbiphenyl-2-ol)], were synthesized as platforms for nonheme diiron(II) protein model complexes. UV-vis spectrophotometric studies and preparative-scale reactions of L(R,R') or BIPS(Me,Ph), where L(R,R') and BIPS(Me,Ph) are the deprotonated forms of H(2)L(R,R') and H(2)BIPS(Me,Ph), respectively, with iron(II) revealed that the presence of sterically protective o-phenol substituents is necessary to obtain discrete dinuclear species. The reaction of L(Me,Ph) with iron(II) in tetrahydrofuran (THF) afforded the doubly bridged compound [Fe(2)(L(Me,Ph))(2)(THF)(3)] (1), which was characterized in the solid state by X-ray crystallography. A large internal cavity in this complex facilitates its rapid reaction with dioxygen, even at -50 degrees C, to produce the thermodynamically stable [Fe(2)(mu-O)(L(Me,Ph))(2)] (2) species. Reaction of (18)O(2) instead of (16)O(2) with 1 led to a shift in the Fe-O-Fe vibrational frequency from 833 to 798 cm(-1), confirming the presence of the (mu-oxo)diiron(III) core and molecular oxygen as the source of the bridging oxo group. The L(Me,Ph) ligand is robust toward oxidative decomposition and does not display any reversible redox activity.

Modeling the syn disposition of nitrogen donors in non-heme diiron enzymes. Synthesis, characterization, and hydrogen peroxide reactivity of diiron(III) complexes with the syn N-donor ligand H2BPG2DEV

In order to model the syn disposition of histidine residues in carboxylate-bridged non-heme diiron enzymes, we prepared a new dinucleating ligand, H(2)BPG(2)DEV, that provides this geometric feature. The ligand incorporates biologically relevant carboxylate functionalities, which have not been explored as extensively as nitrogen-only analogues. Three novel oxo-bridged diiron(III) complexes, [Fe(2)(mu-O)(H(2)O)(2)(BPG(2)DEV)](ClO(4))(2) (6), [Fe(2)(mu-O)(mu-O(2)CAr(iPrO))(BPG(2)DEV)](ClO(4)) (7), and [Fe(2)(mu-O)(mu-CO(3))(BPG(2)DEV)] (8), were prepared. Single-crystal X-ray structural characterization confirms that two pyridyl groups are bound syn with respect to the Fe-Fe vector in these compounds. The carbonato-bridged complex 8 forms quantitatively from 6 in a rapid reaction with gaseous CO(2) in organic solvents. A common maroon-colored intermediate (lambda(max) = 490 nm; epsilon = 1500 M(-1) cm(-1)) forms in reactions of 6, 7, or 8 with H(2)O(2) and NEt(3) in CH(3)CN/H(2)O solutions. Mass spectrometric analyses of this species, formed using (18)O-labeled H(2)O(2), indicate the presence of a peroxide ligand bound to the oxo-bridged diiron(III) center. The Mossbauer spectrum at 90 K of the EPR-silent intermediate exhibits a quadrupole doublet with delta = 0.58 mm/s and DeltaE(Q) = 0.58 mm/s. The isomer shift is typical for a peroxodiiron(III) species, but the quadrupole splitting parameter is unusually small compared to those of related complexes. These Mossbauer parameters are comparable to those observed for a peroxo intermediate formed in the reaction of reduced toluene/o-xylene monooxygenase hydroxylase with dioxygen. Resonance Raman studies reveal an unusually low-energy O-O stretching mode in the peroxo intermediate that is consistent with a short diiron distance. Although peroxodiiron(III) intermediates generated from 6, 7, and 8 are poor O-atom-transfer catalysts, they display highly efficient catalase activity, with turnover numbers up to 10,000. In contrast to hydrogen peroxide reactions of diiron(III) complexes that lack a dinucleating ligand, the intermediates generated here could be re-formed in significant quantities after a second addition of H(2)O(2), as observed spectroscopically and by mass spectrometry.

Synthesis, Characterization, and Oxygenation Studies of Carboxylate-Bridged Diiron(II) Complexes with Aromatic Substrates Tethered to Pyridine Ligands and the Formation of a Unique Trinuclear Complex

In this study, diiron(II) complexes were synthesized as small molecule mimics of the reduced active sites in the hydroxylase components of bacterial multicomponent monooxygenases (BMMs). Tethered aromatic substrates were introduced in the form of 2-phenoxypyridines, incorporating hydroxy and methoxy functionalities into windmill-type diiron(II) compounds [Fe(2)(μ-O(2)CAr(R))(2)-(O(2)CAr(R))(2)(L)(2)] (1-4), where (-)O(2)CAr(R) is a sterically encumbering carboxylate, 2,6-di(4-fluorophenyl)- or 2,6-di(p-tolyl)benzoate (R = 4-FPh or Tol, respectively). The inability of 1-4 to hydroxylate the aromatic substrates was ascertained. Upon reaction with dioxygen, compounds 2 and 3 (L = 2-(m-MeOPhO)Py, 2-(p-MeOPhO)Py, respectively) decompose by a known bimolecular pathway to form mixed-valent diiron(II,III) species at low temperature. Use of 2-(pyridin-2-yloxy)phenol as the ligand L resulted in a doubly-bridged diiron complex (4) and an unprecedented phenoxide-bridged triiron(II) complex (5) under slightly modified reaction conditions.

Desaturases: emerging models for understanding functional diversification of diiron-containing enzymes

Desaturases and related enzymes perform O(2)-dependent dehydrogenations initiated at unactivated C-H groups with the use of a diiron active site. Determination of the long-sought oxidized desaturase crystal structure facilitated structural comparison of the active sites of disparate diiron enzymes. Experiments on the castor desaturase are discussed that provide experimental support for a hypothesized ancestral oxidase enzyme in the context of the evolution of the diiron enzyme diverse functionality. We also summarize recent analysis of a castor mutant desaturase that provides valuable insights into the relationship of proposed substrate-binding modes with respect to a range of catalytic outcomes.

A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold

Chlamydia trachomatis R2c is the prototype for a recently discovered group of ribonucleotide reductase R2 proteins that use a heterodinuclear Mn/Fe redox cofactor for radical generation and storage. Here, we show that the Mycobacterium tuberculosis protein Rv0233, an R2 homologue and a potential virulence factor, contains the heterodinuclear manganese/iron-carboxylate cofactor but displays a drastic remodeling of the R2 protein scaffold into a ligand-binding oxidase. The first structural characterization of the heterodinuclear cofactor shows that the site is highly specific for manganese and iron in their respective positions despite a symmetric arrangement of coordinating residues. In this protein scaffold, the Mn/Fe cofactor supports potent 2-electron oxidations as revealed by an unprecedented tyrosine-valine crosslink in the active site. This wolf in sheep's clothing defines a distinct functional group among R2 homologues and may represent a structural and functional counterpart of the evolutionary ancestor of R2s and bacterial multicomponent monooxygenases.

Lessons from nature: unraveling biological CH bond activation

The cleavage of unactivated CH bonds is one of the most challenging reactions in chemical biology. Metalloenzymes have evolved that efficiently perform these transformations with exquisite control of selectivity; however, a proposed requirement is the generation of highly reactive intermediates that could be lethal. A thermodynamic argument involving the putative reactive species is outlined, whereby the interplay between two tunable parameters, redox potential and pK(a), may be the key to sustainable function. In addition, factors that control these parameters are also described, including hydrogen-bonding networks found within protein active sites. Synthetic examples are used to corroborate these ideas.

Spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle DFsc peptides: implications for O2 reactivity of binuclear non-heme iron enzymes

DFsc is a single chain de novo designed four-helix bundle peptide that mimics the core protein fold and primary ligand set of various binuclear non-heme iron enzymes. DFsc and the E11D, Y51L, and Y18F single amino acid variants have been studied using a combination of near-IR circular dichroism (CD), magnetic circular dichroism (MCD), variable temperature variable field MCD (VTVH MCD), and X-ray absorption (XAS) spectroscopies. The biferrous sites are all weakly antiferromagnetically coupled with mu-1,3 carboxylate bridges and one 4-coordinate and one 5-coordinate Fe, very similar to the active site of class I ribonucleotide reductase (R2) providing open coordination positions on both irons for dioxygen to bridge. From perturbations of the MCD and VTVH MCD the iron proximal to Y51 can be assigned as the 4-coordinate center, and XAS results show that Y51 is not bound to this iron in the reduced state. The two open coordination positions on one iron in the biferrous state would become occupied by dioxygen and Y51 along the O(2) reaction coordinate. Subsequent binding of Y51 functions as an internal spectral probe of the O(2) reaction and as a proton source that would promote loss of H(2)O(2). Coordination by a ligand that functions as a proton source could be a structural mechanism used by natural binuclear iron enzymes to drive their reactions past peroxo biferric level intermediates.

Alternative oxidase: an inter-kingdom perspective on the function and regulation of this broadly distributed 'cyanide-resistant' terminal oxidase

Alternative oxidase (AOX) is a terminal quinol oxidase located in the respiratory electron transport chain that catalyses the oxidation of quinol and the reduction of oxygen to water. However, unlike the cytochrome c oxidase respiratory pathway, the AOX pathway moves fewer protons across the inner mitochondrial membrane to generate a proton motive force that can be used to synthesise ATP. The energy passed to AOX is dissipated as heat. This appears to be very wasteful from an energetic perspective and it is likely that AOX fulfils some physiological function(s) that makes up for its apparent energetic shortcomings. An examination of the known taxonomic distribution of AOX and the specific organisms in which AOX has been studied has been used to explore themes pertaining to AOX function and regulation. A comparative approach was used to examine AOX function as it relates to the biochemical function of the enzyme as a quinol oxidase and associated topics, such as enzyme structure, catalysis and transcriptional expression and post-translational regulation. Hypotheses that have been put forward about the physiological function(s) of AOX were explored in light of some recent discoveries made with regard to species that contain AOX. Fruitful areas of research for the AOX community in the future have been highlighted.

Evolutionary history of a specialized p450 propane monooxygenase

The evolutionary pressures that shaped the specificity and catalytic efficiency of enzymes can only be speculated. While directed evolution experiments show that new functions can be acquired under positive selection with few mutations, the role of negative selection in eliminating undesired activities and achieving high specificity remains unclear. Here we examine intermediates along the 'lineage' from a naturally occurring C12-C20 fatty acid hydroxylase (P450BM3) to a laboratory-evolved P450 propane monooxygenase (P450PMO) having 20 heme domain substitutions compared to P450BM3. Biochemical, crystallographic, and computational analyses show that a minimal perturbation of the P450BM3 fold and substrate-binding pocket accompanies a significant broadening of enzyme substrate range and the emergence of propane activity. In contrast, refinement of the enzyme catalytic efficiency for propane oxidation (approximately 9000-fold increase in kcat/Km) involves profound reshaping and partitioning of the substrate access pathway. Remodeling of the substrate-recognition mechanisms ultimately results in remarkable narrowing of the substrate profile around propane and enables the acquisition of a basal iodomethane dehalogenase activity as yet unknown in natural alkane monooxygenases. A highly destabilizing L188P substitution in a region of the enzyme that undergoes a large conformational change during catalysis plays an important role in adaptation to the gaseous alkane. This work demonstrates that positive selection alone is sufficient to completely respecialize the cytochrome P450 for function on a nonnative substrate.

Synthesis and Characterization of a Ditriflate-Bridged, Diiron(II) Complex with Syn-N-Donor Ligands: [Fe(2)(μ-OTf)(2)(PIC(2)DET)(2)](BARF)(2)

The synthesis and characterization of the diiron(II) complex [Fe(2)(μ-OTf)(2)-(PIC(2)DET)(2)](BARF)(2) (2), where PIC(2)DET is a 2,3-diethynyltriptycene-linked dipicolinic methyl ester ligand, are described. The dication in 2, contains, [Fe(2)(μ-OTf)(2)(PIC(2)DET)(2)](2+) two symmetry-equivalent iron atoms with octahedral coordination geometries. Each metal ion has a N(2)O(4) atom donor set that includes four atoms from two picolinic ester N,O chelate rings, as well as two oxygen atoms from the bridging trifluoromethanesulfonate groups. The Fe(2)(μ-OTf)(2) core of 2 is stabilized by two PIC(2)DET ligands that bind the two metal ions in a head-to-head fashion, leading to an Fe···Fe distance of 5.173(1)Å. Molar conductivity data for 2 are consistent with Fe(2)(μ-OTf)(2)(PIC(2)DET)(2)](2+) retaining its identity in acetone solutions, where it behaves as a 2:1 electrolyte. (1)H NMR spectroscopic, solution (d(6)-acetone) and solid-state magnetic susceptibility data all indicate that the iron atoms of 2 are high-spin (S = 2). A fit of the magnetic data (2 - 300K) to a spin-only isotropic exchange Hamiltonian H = -2JS(1)·S(2) are consistent with weak antiferromagnetic coupling between the two iron atoms with J ~ -0.99(2) cm(-1) and g = 2.10(1).

Protein engineering of toluene monooxygenases for synthesis of chiral sulfoxides

Enantiopure sulfoxides are valuable asymmetric starting materials and are important chiral auxiliaries in organic synthesis. Toluene monooxygenases (TMOs) have been shown previously to catalyze regioselective hydroxylation of substituted benzenes and phenols. Here we show that TMOs are also capable of performing enantioselective oxidation reactions of aromatic sulfides. Mutagenesis of position V106 in the alpha-hydroxylase subunit of toluene ortho-monooxygenase (TOM) of Burkholderia cepacia G4 and the analogous position I100 in toluene 4-monooxygenase (T4MO) of Pseudomonas mendocina KR1 improved both rate and enantioselectivity. Variant TomA3 V106M of TOM oxidized methyl phenyl sulfide to the corresponding sulfoxide at a rate of 3.0 nmol/min/mg protein compared with 1.6 for the wild-type enzyme, and the enantiomeric excess (pro-S) increased from 51% for the wild type to 88% for this mutant. Similarly, T4MO variant TmoA I100G increased the wild-type oxidation rate by 1.7-fold, and the enantiomeric excess rose from 86% to 98% (pro-S). Both wild-type enzymes showed lower activity with methyl para-tolyl sulfide as a substrate, but the improvement in the activity and enantioselectivity of the mutants was more dramatic. For example, T4MO variant TmoA I100G oxidized methyl para-tolyl sulfide 11 times faster than the wild type did and changed the selectivity from 41% pro-R to 77% pro-S. A correlation between regioselectivity and enantioselectivity was shown for TMOs studied in this work. Using in silico homology modeling, it is shown that residue I100 in T4MO aids in steering the substrate into the active site at the end of the long entrance channel. It is further hypothesized that the main function of V106 in TOM is the proper positioning or docking of the substrate with respect to the diiron atoms. The results from this work suggest that when the substrate is not aligned correctly in the active site, the oxidation rate is decreased and enantioselectivity is impaired, resulting in products with both chiral configurations.

The biochemistry of methane oxidation

Methanotrophic bacteria oxidize methane to methanol in the first step of their metabolic pathway. Two forms of methane monooxygenase (MMO) enzymes catalyze this reaction: soluble MMO (sMMO) and membrane-bound or particulate MMO (pMMO). pMMO is expressed when copper is available, and its active site is believed to contain copper. Whereas sMMO is well characterized, most aspects of pMMO biochemistry remain unknown and somewhat controversial. This review emphasizes advances in the past two to three years related to pMMO and to copper uptake and copper-dependent regulation in methanotrophs. The pMMO metal centers have been characterized spectroscopically, and the first pMMO crystal structure has been determined. Significant effort has been devoted to improving in vitro pMMO activity. Proteins involved in sMMO regulation and additional copper-regulated proteins have been identified, and the Methylococcus capsulatus (Bath) genome has been sequenced. Finally, methanobactin (mb), a small copper chelator proposed to facilitate copper uptake, has been characterized.

The crystal structure of the ivy Delta4-16:0-ACP desaturase reveals structural details of the oxidized active site and potential determinants of regioselectivity

The multifunctional acyl-acyl carrier protein (ACP) desaturase from Hedera helix (English ivy) catalyzes the Delta(4) desaturation of 16:0-ACP and the Delta(9) desaturation of 18:0-ACP and further desaturates Delta(9)-16:1 or Delta(9)-18:1 to the corresponding Delta(4,9) dienes. The crystal structure of the enzyme has been solved to 1.95 A resolution, and both the iron-iron distance of approximately 3.2A and the presence of a mu-oxo bridge reveal this to be the only reported structure of a desaturase in the oxidized FeIII-FeIII form. Significant differences are seen between the oxidized active site and the reduced active site of the Ricinus communis (castor) desaturase; His(227) coordination to Fe2 is lost, and the side chain of Glu(224), which bridges the two iron ions in the reduced structure, does not interact with either iron. Although carboxylate shifts have been observed on oxidation of other diiron proteins, this is the first example of the residue moving beyond the coordination range of both iron ions. Comparison of the ivy and castor structures reveal surface amino acids close to the annulus of the substrate-binding cavity and others lining the lower portion of the cavity that are potential determinants of their distinct substrate specificities. We propose a hypothesis that differences in side chain packing explains the apparent paradox that several residues lining the lower portion of the cavity in the ivy desaturase are bulkier than their equivalents in the castor enzyme despite the necessity for the ivy enzyme to accommodate three more carbons beyond the diiron site.

Substrate trafficking and dioxygen activation in bacterial multicomponent monooxygenases

Non-heme carboxylate-bridged diiron centers in the hydroxylase components of the bacterial multicomponent monooxygenases process four substrates during catalysis: electrons, protons, dioxygen, and hydrocarbons. Understanding how protein-protein interactions mediate the transport of these substrates to the diiron center to achieve the selective oxidation of the hydrocarbon is a significant challenge. In this Account, we summarize our current knowledge of these processes with a focus on the methane monooxygenase system. We also describe recent results for the toluene/ o-xylene monooxygenase and phenol hydroxylase systems from Pseudomonas sporium OX1. The observation in these latter systems of a diiron(III) oxygenated intermediate having different Mössbauer parameters from analogous species in other carboxylate-bridged diiron proteins is discussed. The results indicate that the ability of the protein framework to tune the reactivity of the diiron center at structurally similar active sites is substantially more complex than previously recognized.

Structural and mechanistic insights into methane oxidation by particulate methane monooxygenase

Particulate methane monooxygense (pMMO) is an integral membrane copper-containing enzyme that converts methane to methanol. Knowledge of how pMMO selectively oxidizes methane under ambient conditions could impact the development of new catalysts. The crystal structure of Methylococcus capsulatus (Bath) pMMO reveals the composition and location of three metal centers. Spectroscopic data provide insight into the coordination environments and oxidation states of these metal centers. These results, combined with computational studies and comparisons to relevant systems, are discussed in the context of identifying the most likely site for O 2 activation.

Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O

The di-iron flavoprotein F(420)H(2) oxidase found in methanogenic Archaea catalyzes the four-electron reduction of O(2) to 2H(2)O with 2 mol of reduced coenzyme F(420)(7,8-dimethyl-8-hydroxy-5-deazariboflavin). We report here on crystal structures of the homotetrameric F(420)H(2) oxidase from Methanothermobacter marburgensis at resolutions of 2.25 A, 2.25 A and 1.7 A, respectively, from which an active reduced state, an inactive oxidized state and an active oxidized state could be extracted. As found in structurally related A-type flavoproteins, the active site is formed at the dimer interface, where the di-iron center of one monomer is juxtaposed to FMN of the other. In the active reduced state [Fe(II)Fe(II)FMNH(2)], the two irons are surrounded by four histidines, one aspartate, one glutamate and one bridging aspartate. The so-called switch loop is in a closed conformation, thus preventing F(420) binding. In the inactive oxidized state [Fe(III)FMN], the iron nearest to FMN has moved to two remote binding sites, and the switch loop is changed to an open conformation. In the active oxidized state [Fe(III)Fe(III)FMN], both irons are positioned as in the reduced state but the switch loop is found in the open conformation as in the inactive oxidized state. It is proposed that the redox-dependent conformational change of the switch loop ensures alternate complete four-electron O(2) reduction and redox center re-reduction. On the basis of the known Si-Si stereospecific hydride transfer, F(420)H(2) was modeled into the solvent-accessible pocket in front of FMN. The inactive oxidized state might provide the molecular basis for enzyme inactivation by long-term O(2) exposure observed in some members of the FprA family.

Synthesis, Molecular Structure, and Catalytic Potential of the Tetrairon Complex [Fe4(N3O2-L)4(μ-O)2]4+ (L = 1-Carboxymethyl-4,7-dimethyl-1,4,7-triazacyclononane)

The reaction of iron sulfate with 1-carboxymethyl-4,7-dimethyl-1,4,7-triazacyclononane (L) and hydrogen peroxide in aqueous ethanol gives a brown dinuclear complex considered to be [Fe2(N3O-L)2(mu-O)(mu-OOCCH3)] + (1), which converts upon standing in acetonitrile solution into the green tetranuclear complex [Fe4(N3O2-L)4(mu-O)2]4+ (2). A single-crystal X-ray structure analysis of [2][PF6]4.5MeCN reveals 2 to contain four iron(III) centers, each of which is coordinated to three nitrogen atoms of a triazacyclononane ligand and is bridged by one oxo and two carboxylato bridges, a structural feature known from the active center of methane monooxygenase. Accordingly, complex 2 was found to catalyze the oxidative functionalization of methane with hydrogen peroxide in aqueous solution to give methanol, methyl hydroperoxide, and formic acid; the total turnover numbers attain 24 catalytic cycles within 4 h. To gain more insight into the catalytic process, the catalytic potential of 2 was also studied for the oxidation of higher alkanes, cycloalkanes, and isopropanol in acetonitrile, as well as in aqueous solution. The bond selectivities of the oxidation of linear and branched alkanes suggest a ferroxy radical pathway.

X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase

Phenol hydroxylase (PH) belongs to a family of bacterial multicomponent monooxygenases (BMMs) with carboxylate-bridged diiron active sites. Included are toluene/o-xylene (ToMO) and soluble methane (sMMO) monooxygenase. PH hydroxylates aromatic compounds, but unlike sMMO, it cannot oxidize alkanes despite having a similar dinuclear iron active site. Important for activity is formation of a complex between the hydroxylase and a regulatory protein component. To address how structural features of BMM hydroxylases and their component complexes may facilitate the catalytic mechanism and choice of substrate, we determined X-ray structures of native and SeMet forms of the PH hydroxylase (PHH) in complex with its regulatory protein (PHM) to 2.3 A resolution. PHM binds in a canyon on one side of the (alphabetagamma)2 PHH dimer, contacting alpha-subunit helices A, E, and F approximately 12 A above the diiron core. The structure of the dinuclear iron center in PHH resembles that of mixed-valent MMOH, suggesting an Fe(II)Fe(III) oxidation state. Helix E, which comprises part of the iron-coordinating four-helix bundle, has more pi-helical character than analogous E helices in MMOH and ToMOH lacking a bound regulatory protein. Consequently, conserved active site Thr and Asn residues translocate to the protein surface, and an approximately 6 A pore opens through the four-helix bundle. Of likely functional significance is a specific hydrogen bond formed between this Asn residue and a conserved Ser side chain on PHM. The PHM protein covers a putative docking site on PHH for the PH reductase, which transfers electrons to the PHH diiron center prior to O2 activation, suggesting that the regulatory component may function to block undesired reduction of oxygenated intermediates during the catalytic cycle. A series of hydrophobic cavities through the PHH alpha-subunit, analogous to those in MMOH, may facilitate movement of the substrate to and/or product from the active site pocket. Comparisons between the ToMOH and PHH structures provide insights into their substrate regiospecificities.

X-ray crystal structures of manganese(II)-reconstituted and native toluene/o-xylene monooxygenase hydroxylase reveal rotamer shifts in conserved residues and an enhanced view of the protein interior

We report the X-ray crystal structures of native and manganese(II)-reconstituted toluene/o-xylene monooxygenase hydroxylase (ToMOH) from Pseudomonas stutzeri OX1 to 1.85 and 2.20 A resolution, respectively. The structures reveal that reduction of the dimetallic active site is accompanied by a carboxylate shift and alteration of the coordination environment for dioxygen binding and activation. A rotamer shift in a strategically placed asparagine 202 accompanies dimetallic center reduction and is proposed to influence protein component interactions. This rotamer shift is conserved between ToMOH and the corresponding residue in methane monooxygenase hydroxylase (MMOH). Previously unidentified hydrophobic pockets similar to those present in MMOH are assigned.