Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron

Retuning Rieske-type oxygenases to expand substrate range

Rieske-type oxygenases are promising biocatalysts for the destruction of persistent pollutants or for the synthesis of fine chemicals. In this work, we explored pathways through which Rieske-type oxygenases evolve to expand their substrate range. BphAE(p4), a variant biphenyl dioxygenase generated from Burkholderia xenovorans LB400 BphAE(LB400) by the double substitution T335A/F336M, and BphAE(RR41), obtained by changing Asn(338), Ile(341), and Leu(409) of BphAE(p4) to Gln(338), Val(341), and Phe(409), metabolize dibenzofuran two and three times faster than BphAE(LB400), respectively. Steady-state kinetic measurements of single- and multiple-substitution mutants of BphAE(LB400) showed that the single T335A and the double N338Q/L409F substitutions contribute significantly to enhanced catalytic activity toward dibenzofuran. Analysis of crystal structures showed that the T335A substitution relieves constraints on a segment lining the catalytic cavity, allowing a significant displacement in response to dibenzofuran binding. The combined N338Q/L409F substitutions alter substrate-induced conformational changes of protein groups involved in subunit assembly and in the chemical steps of the reaction. This suggests a responsive induced fit mechanism that retunes the alignment of protein atoms involved in the chemical steps of the reaction. These enzymes can thus expand their substrate range through mutations that alter the constraints or plasticity of the catalytic cavity to accommodate new substrates or that alter the induced fit mechanism required to achieve proper alignment of reaction-critical atoms or groups.

Flavonoids biotransformation by bacterial non-heme dioxygenases, biphenyl and naphthalene dioxygenase

This review details recent progresses in the flavonoid biotransformation by bacterial non-heme dioxygenases, biphenyl dioxygenase (BDO), and naphthalene dioxygenase (NDO), which can initially activate biphenyl and naphthalene with insertion of dioxygen in stereospecfic and regiospecific manners. Flavone, isoflavone, flavanone, and isoflavanol were biotransformed by BDO from Pseudomonas pseudoalcaligenes KF707 and NDO from Pseudomonas sp. strain NCIB9816-4, respectively. In general, BDO showed wide range of substrate spectrum and produced the oxidized products, whereas NDO only metabolized flat two-dimensional substrates of flavone and isoflavone. Furthermore, biotransformation of B-ring skewed substrates, flavanone and isoflavanol, by BDO produced the epoxide products, instead of dihydrodiols. These results support the idea that substrate-driven reactivity alteration of the Fe-oxo active species may occur in the active site of non-heme dioxygenases. The study of flavonoid biotransformation by structurally-well defined BDO and NDO will provide the substrate structure and reactivity relationships and eventually establish the production of non-plant-originated flavonoids by means of microbial biotechnology.

X-ray absorption spectroscopy and reactivity of thiolate-ligated Fe(III)-OOR complexes

The reaction of a series of thiolate-ligated iron(II) complexes [Fe(II)([15]aneN(4))(SC(6)H(5))]BF(4) (1), [Fe(II)([15]aneN(4))(SC(6)H(4)-p-Cl)]BF(4) (2), and [Fe(II)([15]aneN(4))(SC(6)H(4)-p-NO(2))]BF(4) (3) with alkylhydroperoxides at low temperature (-78 °C or -40 °C) leads to the metastable alkylperoxo-iron(III) species [Fe(III)([15]aneN(4))(SC(6)H(5))(OOtBu)]BF(4) (1a), [Fe(III)([15]aneN(4))(SC(6)H(4)-p-Cl)(OOtBu)]BF(4) (2a), and [Fe(III)([15]aneN(4))(SC(6)H(4)-p-NO(2))(OOtBu)]BF(4) (3a), respectively. X-ray absorption spectroscopy (XAS) studies were conducted on the Fe(III)-OOR complexes and their iron(II) precursors. The edge energy for the iron(II) complexes (∼7118 eV) shifts to higher energy upon oxidation by ROOH, and the resulting edge energies for the Fe(III)-OOR species range from 7121-7125 eV and correlate with the nature of the thiolate donor. Extended X-ray absorption fine structure (EXAFS) analysis of the iron(II) complexes 1-3 in CH(2)Cl(2) show that their solid state structures remain intact in solution. The EXAFS data on 1a-3a confirm their proposed structures as mononuclear, 6-coordinate Fe(III)-OOR complexes with 4N and 1S donors completing the coordination sphere. The Fe-O bond distances obtained from EXAFS for 1a-3a are 1.82-1.85 Å, significantly longer than other low-spin Fe(III)-OOR complexes. The Fe-O distances correlate with the nature of the thiolate donor, in agreement with the previous trends observed for ν(Fe-O) from resonance Raman (RR) spectroscopy, and supported by optimized geometries obtained from density functional theory (DFT) calculations. Reactivity and kinetic studies on 1a- 3a show an important influence of the thiolate donor.

Absolute configuration-dependent epoxide formation from isoflavan-4-ol stereoisomers by biphenyl dioxygenase of Pseudomonas pseudoalcaligenes strain KF707

Biphenyl dioxygenase from Pseudomonas pseudoalcaligenes strain KF707 expressed in Escherichia coli was found to exhibit monooxygenase activity toward four stereoisomers of isoflavan-4-ol. LC-MS and LC-NMR analyses of the metabolites revealed that the corresponding epoxides formed between C2' and C3' on the B-ring of each isoflavan-4-ol substrate were the sole products. The relative reactivity of the stereoisomers was found to be in the order: (3S,4S)-cis-isoflavan-4-ol > (3R,4S)-trans-isoflavan-4-ol > (3S,4R)-trans-isoflavan-4-ol > (3R,4R)-cis-isoflavan-4-ol and this likely depended upon the absolute configuration of the 4-OH group on the isoflavanols, as explained by an enzyme-substrate docking study. The epoxides produced from isoflavan-4-ols by P. pseudoalcaligenes strain KF707 were further abiotically transformed into pterocarpan, the molecular structure of which is commonly found as part of plant-protective phytoalexins, such as maackiain from Cicer arietinum and medicarpin from Medicago sativa.

Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution

The biphenyl dioxygenase of Burkholderia xenovorans LB400 is a multicomponent Rieske-type oxygenase that catalyzes the dihydroxylation of biphenyl and many polychlorinated biphenyls (PCBs). The structural bases for the substrate specificity of the enzyme's oxygenase component (BphAE(LB400)) are largely unknown. BphAE(p4), a variant previously obtained through directed evolution, transforms several chlorobiphenyls, including 2,6-dichlorobiphenyl, more efficiently than BphAE(LB400), yet differs from the parent oxygenase at only two positions: T335A/F336M. Here, we compare the structures of BphAE(LB400) and BphAE(p4) and examine the biochemical properties of two BphAE(LB400) variants with single substitutions, T335A or F336M. Our data show that residue 336 contacts the biphenyl and influences the regiospecificity of the reaction, but does not enhance the enzyme's reactivity toward 2,6-dichlorobiphenyl. By contrast, residue 335 does not contact biphenyl but contributes significantly to expansion of the enzyme's substrate range. Crystal structures indicate that Thr335 imposes constraints through hydrogen bonds and nonbonded contacts to the segment from Val320 to Gln322. These contacts are lost when Thr is replaced by Ala, relieving intramolecular constraints and allowing for significant movement of this segment during binding of 2,6-dichlorobiphenyl, which increases the space available to accommodate the doubly ortho-chlorinated congener 2,6-dichlorobiphenyl. This study provides important insight about how Rieske-type oxygenases can expand substrate range through mutations that increase the plasticity and/or mobility of protein segments lining the catalytic cavity.

Crystallographic snapshots of the reaction of aromatic C-H with O(2) catalysed by a protein-bound iron complex

Chemical reactions inside single crystals are quite rare because crystallinity is difficult to retain owing to atomic rearrangements. Protein crystals in general have a high solvent content. This allows for some molecular flexibility, which makes it possible to trap reaction intermediates of enzymatic reactions without disrupting the crystal lattice. A similar approach has not yet been fully implemented in the field of inorganic chemistry. Here, we have combined model chemistry and protein X-ray crystallography to study the intramolecular aromatic dihydroxylation by an arene-containing protein-bound iron complex. The bound complex was able to activate dioxygen in the presence of a reductant, leading to the formation of catechol as the sole product. The structure determination of four of the catalytic cycle intermediates and the end product showed that the hydroxylation reaction implicates an iron peroxo, generated by reductive O(2) activation, an intermediate already observed in iron monooxygenases. This strategy also provided unexpected mechanistic details such as the rearrangement of the iron coordination sphere on metal reduction.

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.

The Catalytic Function of Nonheme Iron (III) Complex for Hydrocarbon Oxidation

A detailed catalytic study of LFe(III)Cl (where L = 3-{2-[2-(3-hydroxy-1,3-diphenyl-allylideneamino)-ethylamino]-ethylimino}-1,3-diphenyl-propen-1-ol) for hydrocarbon oxidation was carried out, focusing on the role of solvent, atmospheric dioxygen, and oxidant on catalytic efficiency. The data showed that LFe(III)Cl catalyst was efficient in homogeneous hydrocarbon oxidations providing significant yields. Moreover, tert-BuOOH provided comparable oxidation yields with H(2)O(2), slightly favoring the formation of alcohols and ketones versus epoxides. Dioxygen intervened in the catalytic reaction, influencing the nature of oxidation products. The polarity of solvent strongly influenced the reaction rates and the nature of oxidation products. A mechanistic model is postulated assuming that LFe(III)Cl functions via the formation of iron-hydroperoxo-species, followed by a radical-based mechanistic path.

Metal-dioxygen and metal-dinitrogen complexes: where are the electrons?

Transition-metal complexes of O(2) and N(2) play an important role in the environment, chemical industry, and metalloenzymes. This Perspective compares and contrasts the binding modes, reduction levels, and electronic influences on the nature of the bound O(2) or N(2) group in these complexes. The charge distribution between the metal and the diatomic ligand is variable, and different models for describing the adducts have evolved. In some cases, single resonance structures (e.g. M-superoxide = M-O(2)(-)) are accurate descriptions of the adducts. Recent studies have shown that the magnetic coupling in certain N(2)(2-) complexes differs between resonance forms, and can be used to distinguish experimentally between resonance structures. On the other hand, many O(2) and N(2) complexes cannot be described well with a simple valence-bond model. Defining the situations where ambiguities occur is a fertile area for continued study.

Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1

The Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1 have been implicated in the initial oxidation of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs), forming cis-dihydrodiols. To clarify how these two RHOs are functionally different with respect to the degradation of HMW PAHs, we investigated their substrate specificities to 13 representative aromatic substrates (toluene, m-xylene, phthalate, biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, carbazole, and dibenzothiophene) by enzyme reconstitution studies of Escherichia coli. Both Nid systems were identified to be compatible with type V electron transport chain (ETC) components, consisting of a [3Fe-4S]-type ferredoxin and a glutathione reductase (GR)-type reductase. Metabolite profiles indicated that the Nid systems oxidize a wide range of aromatic hydrocarbon compounds, producing various isomeric dihydrodiol and phenolic compounds. NidAB and NidA3B3 showed the highest conversion rates for pyrene and fluoranthene, respectively, with high product regiospecificity, whereas other aromatic substrates were converted at relatively low regiospecificity. Structural characteristics of the active sites of the Nid systems were investigated and compared to those of other RHOs. The NidAB and NidA3B3 systems showed the largest substrate-binding pockets in the active sites, which satisfies spatial requirements for accepting HMW PAHs. Spatially conserved aromatic amino acids, Phe-Phe-Phe, in the substrate-binding pockets of the Nid systems appeared to play an important role in keeping aromatic substrates within the reactive distance from the iron atom, which allows each oxygen to attack the neighboring carbons.

A profile of ring-hydroxylating oxygenases that degrade aromatic pollutants

Numerous aromatic compounds are pollutants to which exposure exists or is possible, and are of concern because they are mutagenic, carcinogenic, or display other toxic characteristics. Depending on the types of dioxygenation reactions of which microorganisms are capable, they utilize ring-hydroxylating oxygenases (RHOs) to initiate the degradation and detoxification of such aromatic compound pollutants. Gene families encoding for RHOs appear to be most common in bacteria. Oxygenases are important in degrading both natural and synthetic aromatic compounds and are particularly important for their role in degrading toxic pollutants; for this reason, it is useful for environmental scientists and others to understand more of their characteristics and capabilities. It is the purpose of this review to address RHOs and to describe much of their known character, starting with a review as to how RHOs are classified. A comprehensive phylogenetic analysis has revealed that all RHOs are, in some measure, related, presumably by divergent evolution from a common ancestor, and this is reflected in how they are classified. After we describe RHO classification schemes, we address the relationship between RHO structure and function. Structural differences affect substrate specificity and product formation. In the alpha subunit of the known terminal oxygenase of RHOs, there is a catalytic domain with a mononuclear iron center that serves as a substrate-binding site and a Rieske domain that retains a [2Fe-2S] cluster that acts as an entity of electron transfer for the mononuclear iron center. Oxygen activation and substrate dihydroxylation occurring at the catalytic domain are dependent on the binding of substrate at the active site and the redox state of the Rieske center. The electron transfer from NADH to the catalytic pocket of RHO and catalyzing mechanism of RHOs is depicted in our review and is based on the results of recent studies. Electron transfer involving the RHO system typically involves four steps: NADH-ferredoxin reductase receives two electrons from NADH; ferredoxin binds with NADH-ferredoxin reductase and accepts electron from it; the reduced ferredoxin dissociates from NADH-ferredoxin reductase and shuttles the electron to the Rieske domain of the terminal oxygenase; the Rieske cluster donates electrons to O2 through the mononuclear iron. On the basis of crystal structure studies, it has been proposed that the broad specificity of the RHOs results from the large size and specific topology of its hydrophobic substrate-binding pocket. Several amino acids that determine the substrate specificity and enantioselectivity of RHOs have been identified through sequence comparison and site-directed mutagenesis at the active site. Exploiting the crystal structure data and the available active site information, engineered RHO enzymes have been and can be designed to improve their capacity to degrade environmental pollutants. Such attempts to enhance degradation capabilities of RHOs have been made. Dioxygenases have been modified to improve the degradation capacities toward PCBs, PAHs, dioxins, and some other aromatic hydrocarbons. We hope that the results of this review and future research on enhancing RHOs will promote their expanded usage and effectiveness for successfully degrading environmental aromatic pollutants.

Location of flavone B-ring controls regioselectivity and stereoselectivity of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4

Naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 incorporated dioxygen at the C7 and C8 positions on the A-rings of flavone and isoflavone with different stereoselectivity, resulting in the formation of (7S,8S)-dihydroxy-2-phenyl-7,8-dihydro-4H-chromen-4-one (flavone-cis-(7S,8S)-dihydrodiol) and (7R,8R)-dihydroxy-3-phenyl-7,8-dihydro-4H-chromen-4-one (isoflavone-cis-(7R,8R)-dihydrodiol), respectively. In addition, NDO was shown to incorporate dioxygen at the C5 and C6 positions on the A-ring and the C2' and C3' positions on the B-ring of isoflavone, resulting in the production of (5S,6R)-dihydroxy-3-phenyl-5,6-dihydro-4H-chromen-4-one (isoflavone-cis-(5S,6R)-dihydrodiol) and 3-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]-4H-chromen-4-one (isoflavone-cis-(2'R,3'S)-dihydrodiol), respectively. The metabolites were identified by LC/MS, (1)H, and (13)C NMR analyses and TD-SCF calculations combined with CD spectroscopy. In the case of flavone biotransformation, formation of flavone-(7S,8S)-dihydrodiol is likely to be the result of hydrogen bond interactions between the substrate and the active site of the dioxygenase. On the contrary, regioselective dioxygenation of isoflavone was found not to occur, and this may be due to the fact that the same hydrogen bonds that occur in the case of the flavone reaction cannot be established due to steric hindrance caused by the position of the B-ring. It is therefore proposed that the regioselectivity and stereoselectivity of NDO from strain NCIB 9816-4 are controlled by the position of the phenyl ring on flavone molecules.

Structures and thermodynamics of biphenyl dihydrodiol stereoisomers and their metabolites in the enzymatic degradation of arene xenobiotics

A key step in the metabolic degradation of biphenyl xenobiotics is catechol formation upon dehydrogenation of cis- and trans-dihydrodiols in prokaryotic and eukaryotic pathways, respectively. Structure and thermodynamics of stereoisomers of cis-, trans-2,3-biphenyl-dihydrodiols (I) and their dehydrogenation products (hydroxyketones, II), as well as final catechol (2,3-biphenyldiol, III) are studied by means of ab initio MP2/6-311++G(2df,2p)//MP2/6-311G(d,p) calculations. Formation of stereoisomers I and II is exothermic and endergonic, whereas III is enthalpically and entropically driven. Dehydrogenations are endothermic (DeltaHR0 approximately 1.5-4 kcal mol(-1)) and exergonic (DeltaGR0 approximately -5 to -7.5 kcal mol(-1)) without noticeable differences between cis and trans pathways, although the same keto stereoisomer II-(2S) is found to be the more favored product from both cis- and trans-I. The final II --> III tautomerization is thermodynamically enhanced (DeltaHR0 approximately -27, DeltaGR0 approximately -28 kcal mol(-1)) but the process is shown to have a large activation energy if it had to occur via unimolecular path. Although this tautomerization is generally assumed to be a nonenzymatic process as it involves rearomatization of an oxygenated ring, proton transfer with an anionic intermediate might be a more probable process.

Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment

Understanding the relationship between gene diversity and function for important environmental processes are major ecological research goals. We applied gene-targeted-metagenomics and pyrosequencing to aromatic dioxygenase genes to obtain greater sequence depth than possible by other methods. A PCR primer set designed to target a 524 bp region that confers substrate specificity of biphenyl dioxygenases yielded 2000 and 604 sequences from 5′ and 3′ ends of the PCR products, respectively, that passed our validity criteria. Sequence alignment showed three known conserved residues as well as another seven conserved residues not previously reported. Ninety-five and 41% of the valid sequences were assigned to 22 and 3 novel clusters in that they did not include any previously reported sequences at 0.6 distance by Complete Linkage Clustering for the sequenced regions. The greater diversity revealed by this gene-targeted approach provides deeper insights into genes potentially important in environmental processes to better understand their ecology, functional differences and evolutionary origins. We also provide criteria for primer design for this approach as well as guidance for data processing of diverse functional genes since gene databases for most genes of environmental relevance are limited.

Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation

Dicamba (3,6-dichloro-2-methoxybenzoic acid) is a widely used herbicide that is efficiently degraded by soil microbes. These microbes use a novel Rieske nonheme oxygenase, dicamba monooxygenase (DMO), to catalyze the oxidative demethylation of dicamba to 3,6-dichlorosalicylic acid (DCSA) and formaldehyde. We have determined the crystal structures of DMO in the free state, bound to its substrate dicamba, and bound to the product DCSA at 2.10-1.75 A resolution. The structures show that the DMO active site uses a combination of extensive hydrogen bonding and steric interactions to correctly orient chlorinated, ortho-substituted benzoic-acid-like substrates for catalysis. Unlike other Rieske aromatic oxygenases, DMO oxygenates the exocyclic methyl group, rather than the aromatic ring, of its substrate. This first crystal structure of a Rieske demethylase shows that the Rieske oxygenase structural scaffold can be co-opted to perform varied types of reactions on xenobiotic substrates.

Distal end of 105-125 loop--a putative reductase binding domain of phthalate dioxygenase

The phthalate dioxygenase system consists of the dioxygenase, PDO, which contains a Rieske [2Fe-2S] center and a Fe(II)-mononuclear center, and the reductase, PDR. Involvement of the distal end of the 105-125 loop of PDO in its interaction with PDR was tested by substituting charged residues in the loop with alanines and by replacing the conserved tryptophan-94. Compared to wild-type PDO, all variants had lower catalytic activity and the Rieske centers were reduced more slowly by reduced PDR. The rates of oxidation of the Rieske centers by oxygen, which represent electron transfer between the Rieske and mononuclear centers, were essentially unaffected. These results suggest that positively charged residues of the distal end of the 105-125 loop are collectively involved in PDR binding with the PDO. Contrary to expectations, Trp94 variants were not directly involved in electron transfer between PDR and PDO. The tryptophan appears to have mainly a structural role, apparently preserving the hydrophilic environment of the Rieske center.

Peroxo and oxo intermediates in mononuclear nonheme iron enzymes and related active sites

Fe(III)OOH and Fe(IV)O intermediates have now been documented in a number of nonheme iron active sites. In this Current Opinion we use spectroscopy combined with electronic structure calculations to define the frontier molecular orbitals (FMOs) of these species and their contributions to reactivity. For the low-spin Fe(III)OOH species in activated bleomycin we show that the reactivity of this nonheme iron intermediate is very different from that of the analogous Compound 0 of cytochrome P450. For Fe(IV)O S=1 model species we experimentally define the electronic structure and its contribution to reactivity, and computationally evaluate how this would change for the Fe(IV)O S=2 intermediates found in nonheme iron enzymes.

Crystallographic, spectroscopic, and computational analysis of a flavin C4a-oxygen adduct in choline oxidase

Flavin C4a-OO(H) and C4a-OH adducts are critical intermediates proposed in many flavoenzyme reaction mechanisms, but they are rarely detected even by rapid transient kinetics methods. We observe a trapped flavin C4a-OH or C4a-OO(H) adduct by single-crystal spectroscopic methods and in the 1.86 A resolution X-ray crystal structure of choline oxidase. The microspectrophotometry results show that the adduct forms rapidly in situ at 100 K upon exposure to X-rays. Density functional theory calculations establish the electronic structures for the flavin C4a-OH and C4a-OO(H) adducts and estimate the stabilization energy of several active site hydrogen bonds deduced from the crystal structure. We propose that the enzyme-bound FAD is reduced in the X-ray beam. The aerobic crystals then form either a C4a-OH or C4a-OO(H) adduct, but an insufficient proton inventory prevents their decay at cryogenic temperatures.

Characterization of 3-ketosteroid 9{alpha}-hydroxylase, a Rieske oxygenase in the cholesterol degradation pathway of Mycobacterium tuberculosis

KshAB (3-Ketosteroid 9alpha-hydroxylase) is a two-component Rieske oxygenase (RO) in the cholesterol catabolic pathway of Mycobacterium tuberculosis. Although the enzyme has been implicated in pathogenesis, it has largely been characterized by bioinformatics and molecular genetics. Purified KshB, the reductase component, was a monomeric protein containing a plant-type [2Fe-2S] cluster and FAD. KshA, the oxygenase, was a homotrimer containing a Rieske [2Fe-2S] cluster and mononuclear ferrous iron. Of two potential substrates, reconstituted KshAB had twice the specificity for 1,4-androstadiene-3,17-dione as for 4-androstene-3,17-dione. The transformation of both substrates was well coupled to the consumption of O(2). Nevertheless, the reactivity of KshAB with O(2) was low in the presence of 1,4-androstadiene-3,17-dione, with a k(cat)/K(m)(O(2)) of 2450 +/- 80 m(-1) s(-1). The crystallographic structure of KshA, determined to 2.3A(,) revealed an overall fold and a head-to-tail subunit arrangement typical of ROs. The central fold of the catalytic domain lacks all insertions found in characterized ROs, consistent with a minimal and perhaps archetypical RO catalytic domain. The structure of KshA is further distinguished by a C-terminal helix, which stabilizes subunit interactions in the functional trimer. Finally, the substrate-binding pocket extends farther into KshA than in other ROs, consistent with the large steroid substrate, and the funnel accessing the active site is differently orientated. This study provides a solid basis for further studies of a key steroid-transforming enzyme of biotechnological and medical importance.

Structures of the multicomponent Rieske non-heme iron toluene 2,3-dioxygenase enzyme system

Bacterial Rieske non-heme iron oxygenases catalyze the initial hydroxylation of aromatic hydrocarbon substrates. The structures of all three components of one such system, the toluene 2,3-dioxygenase system, have now been determined. This system consists of a reductase, a ferredoxin and a terminal dioxygenase. The dioxygenase, which was cocrystallized with toluene, is a heterohexamer containing a catalytic and a structural subunit. The catalytic subunit contains a Rieske [2Fe-2S] cluster and mononuclear iron at the active site. This iron is not strongly bound and is easily removed during enzyme purification. The structures of the enzyme with and without mononuclear iron demonstrate that part of the structure is flexible in the absence of iron. The orientation of the toluene substrate in the active site is consistent with the regiospecificity of oxygen incorporation seen in the product formed. The ferredoxin is Rieske type and contains a [2Fe-2S] cluster close to the protein surface. The reductase belongs to the glutathione reductase family of flavoenzymes and consists of three domains: an FAD-binding domain, an NADH-binding domain and a C-terminal domain. A model for electron transfer from NADH via FAD in the reductase and the ferredoxin to the terminal active-site mononuclear iron of the dioxygenase is proposed.

Protein engineering on biphenyl dioxygenase for conferring activity to convert 7-hydroxyflavone and 5,7-dihydroxyflavone (chrysin)

A central part (amino-acid position 268-397 of 458 amino-acid residues) of the biphenyl dioxygenase large (alpha) subunit, BphA1, from Pseudomonas pseudoalcaligenes strain KF707 was exchanged with the corresponding part of BphA1 from another biphenyl-degrading bacterium, Pseudomonas putida strain KF715, to construct hybrid BphA1, BphA1 (715-707). When expressed in Escherichia coli together with the bphA2A3A4BC genes from strain KF707, this enzyme was shown to possess activity for degrading both 1-phenylnaphthalene and 2-phenylnaphthalene. Between central parts of BphA1 from strains KF707 and KF715, the difference of amino-acid residues resided only in position 324-325. An attempt was made to improve the substrate preference of BphA1 by applying random amino-acid substitutions at these positions to BphA1 (715-707). After screening the mutant library to bioconvert several flavonoids, BphA1 (1-22; T324A and I325L) and BphA1 (2-2; T324L and I325I) were selected. When expressed in E. coli together with bphA2A3A4B from strain KF707, both BphA1 (1-22) and BphA1 (2-2) bioconverted the refractory flavonoids, 7-hydroxyflavone and 5,7-dihydroxyflavone (chrysin), which were hardly converted by any unmodified and artificially-modified shuffled biphenyl dioxygeneses, into their vicinal diol forms, i.e., 2-(2,3-dihydroxyphenyl)-7-hydroxy-chromen-4-one and 2-(2,3-dihydroxyphenyl)-5,7-dihydroxy-chromen-4-one, respectively. In addition, trans-chalcone was converted into 3-(2,3-dihydroxyphenyl)-1-phenylpropan-1-one and further into 1,3-bis-(2,3-dihydroxyphenyl)-propan-1-one. The antioxidative activity of these generated compounds was markedly higher than that of the original substrates used.

Mechanism of extradiol aromatic ring-cleaving dioxygenases

The extradiol aromatic ring-cleaving dioxygenases activate molecular oxygen by binding both O(2) and the catecholic substrate to a reduced active site metal, generally Fe(II). Progress has been made in understanding the mechanism of this reaction through the combined use of kinetic, computational, biomimetic, structural, and diagnostic chemical approaches. It appears that O(2) is activated by accepting an electron transferred from the substrate through the metal, thereby simultaneously activating oxygen and substrate for reaction with each other.

Bio-inspired arene cis-dihydroxylation by a non-haem iron catalyst modeling the action of naphthalene dioxygenase

Reported in this paper is the first example of a biomimetic iron complex, ([Fe(II)(TPA)(NCMe)(2)](2+) (TPA = tris(2-pyridylmethyl)amine), that catalyses the cis-dihydroxylation of an aromatic double bond, mimicking the action of the non-haem iron enzyme naphthalene dioxygenase and shedding light on its possible mechanism of action.

A putative Fe2+-bound persulfenate intermediate in cysteine dioxygenase

The common reactions of dioxygen, superoxide, and hydroperoxides with thiolates are thought to proceed via persulfenate intermediates, yet these have never been visualized. Here we report a 1.4 A resolution crystal structure of the Fe(2+)-dependent enzyme cysteine dioxygenase (CDO) containing this putative intermediate trapped in its active site pocket. The complex raises the possibility that, distinct from known dioxygenases and proposed CDO mechanisms, the Fe-proximal oxygen atom may be involved in the primary oxidation event yielding a unique three-membered Fe-S-O cyclic intermediate. A nonpolar environment of the distal oxygen would facilitate isomerization of the persulfenate to the sulfinate product.

Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria

The anaerobic biodegradation of naphthalene, an aromatic hydrocarbon in tar and petroleum, has been repeatedly observed in environments but scarcely in pure cultures. To further explore the relationships and physiology of anaerobic naphthalene-degrading microorganisms, sulfate-reducing bacteria (SRB) were enriched from a Mediterranean sediment with added naphthalene. Two strains (NaphS3, NaphS6) with oval cells were isolated which showed naphthalene-dependent sulfate reduction. According to 16S rRNA gene sequences, both strains were Deltaproteobacteria and closely related to each other and to a previously described naphthalene-degrading sulfate-reducing strain (NaphS2) from a North Sea habitat. Other close relatives were SRB able to degrade alkylbenzenes, and phylotypes enriched anaerobically with benzene. If in adaptation experiments the three naphthalene-grown strains were exposed to 2-methylnaphthalene, this compound was utilized after a pronounced lag phase, indicating that naphthalene did not induce the capacity for 2-methylnaphthalene degradation. Comparative denaturing gel electrophoresis of cells grown with naphthalene or 2-methylnaphthalene revealed a striking protein band which was only present upon growth with the latter substrate. Peptide sequences from this band perfectly matched those of a protein predicted from genomic libraries of the strains. Sequence similarity (50% identity) of the predicted protein to the large subunit of the toluene-activating enzyme (benzylsuccinate synthase) from other anaerobic bacteria indicated that the detected protein is part of an analogous 2-methylnaphthalene-activating enzyme. The absence of this protein in naphthalene-grown cells together with the adaptation experiments as well as isotopic metabolite differentiation upon growth with a mixture of d(8)-naphthalene and unlabelled 2-methylnaphthalene suggest that the marine strains do not metabolize naphthalene by initial methylation via 2-methylnaphthalene, a previously suggested mechanism. The inability to utilize 1-naphthol or 2-naphthol also excludes these compounds as free intermediates. Results leave open the possibility of naphthalene carboxylation, another previously suggested activation mechanism.