Origin of the Regioselective Fatty‐Acid Hydroxylation versus Decarboxylation by a Cytochrome P450 Peroxygenase: What Drives the Reaction to Biofuel Production?

The cytochromes P450 are heme‐based mono‐oxygenases or peroxygenases involved in vital reaction processes for human health. A recently described P450 per‐oxygenase, OleT_JE, converts long‐chain fatty acids to terminal olefins and as such may have biotechnological relevance in biodiesel production. However, the reaction produces significant amounts of α‐ and β‐hydroxylation by‐products, and their origin are poorly understood. Herein, we elucidate through a QM/MM study on the bifurcation pathways how the three possible products are generated and show how the enzyme can be further engineered for optimum desaturase activity. The studies showed that the polarity and the solvent accessibility of the substrate in the binding pocket destabilize the OH‐rebound pathways and kinetically enable a thermodynamically otherwise unfavorable decarboxylation reaction. The origins of the bifurcation pathways are analyzed with valence‐bond models that highlight the differences in reaction mechanism.     

A different method of measuring and detecting mono-and dioxygenase activities

A spectrophotometric method of measuring oxygenase activity in cell extracts or in zymograms was developed. It is an easy and cheap method that allows spectrophotometric measurement of activity by a colored reaction and reveals activity bands in a polyacrylamide gel electrophoresis (PAGE) gel as brown bands. To prove its usefulness, we report on a study with the oxygenase present in strain YR-1, isolated from petroleum-contaminated soils, that uses hydrocarbons as its sole carbon source. Soluble oxygenase activity was detected (under our conditions of cellular homogenization) in the mycelium of a filamentous fungus strain named YR-1. Oxygenase activity from aerobically grown mycelium was detected in growth medium containing the hydrocarbons decane or hexadecane; the enzyme activity exhibited similar optimum pH for the hydroxylation of different aliphatic or aromatic substrates (decane, hexadecane, benzene, and naphthalene) to the corresponding alcohols. Zymogram analysis conducted with partially purified fractions from cell extracts from the aerobic mycelium of the YR-1 strain indicated the existence of only one oxygenase enzyme. Partially purified samples of enzyme, analyzed by sodium dodecyl sulfate PAGE, indicated the presence of one major protein band with a mol wt of 56 kDa that can be a constituent of the native enzyme. In samples of the enzyme, the 56-kDa protein gave a positive reaction in immuno-detection experiments with antibodies directed against oxygenase from soybean. The partially purified enzyme oxidized different substrates, although higher activity was displayed with benzene. K _m values obtained for benzene and decane indicated a higher affinity for the latter     

A dinuclear palladium catalyst for α-hydroxylation of carbonyls with O2

A chemo- and regioselective α-hydroxylation reaction of carbonyl compounds with molecular oxygen as oxidant is reported. The hydroxylation reaction is catalyzed by a dinuclear Pd(II) complex, which functions as an oxygen transfer catalyst, reminiscent of an oxygenase. The development of this oxidation reaction was inspired by discovery and mechanism evaluation of previously unknown Pd(III)-Pd(III) complexes.     

Conformational and thermodynamic analysis of the COXIB scaffold using quantum chemical calculations

Selective cyclo‐oxygenase‐2 inhibitors (COXIBs) are prominent members of the nonsteroidal anti‐inflammatory drugs. The neutral and protonated COXIB scaffold has been subjected to molecular computations in the gas phase and implicit solvent to measure the relative changes in the thermodynamic functions, enthalpy (H_rel), potential energy (U_rel), Gibbs free energy (G_rel) and entropy (S_rel) induced by selected substituents. Conformational analysis of the COXIB scaffold indentified four pairs of atropisomeric conformers (from I, I′ to IV, IV′) associated with a molecular structure containing a double rotor system. All conformers had similar stability. Para‐substitution with substituents that cover a wide range of Hammett sigma values did not alter the geometries of the neutral COXIB conformers; however, the protonated COXIB scaffold was showed an increase in structural and thermodynamic perturbations due to inductive effects. Flexibility and structural resilience of the COXIB scaffold under the conditions studied herein could be an important feature of the COXIBs, especially considering the previously proposed flexibility of the cyclo‐oxygenase binding site. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Oxygenase‐Catalyzed Desymmetrization of N,N‐Dialkyl‐piperidine‐4‐carboxylic Acids

γ‐Butyrobetaine hydroxylase (BBOX) is a 2‐oxoglutarate dependent oxygenase that catalyzes the final hydroxylation step in the biosynthesis of carnitine. BBOX was shown to catalyze the oxidative desymmetrization of achiral N,N‐dialkyl piperidine‐4‐carboxylates to give products with two or three stereogenic centers.     

A high-throughput digital imaging screen for the discovery and directed evolution of oxygenases.

BACKGROUND: Oxygenases catalyze the hydroxylation of a wide variety of organic substrates. An ability to alter oxygenase substrate specificities and improve their activities and stabilities using recombinant DNA techniques would expand their use in processes such as chemical synthesis and bioremediation. Discovery and directed evolution of oxygenases require efficient screens that are sensitive to the activities of interest and can be applied to large numbers of crude enzyme samples. RESULTS: Horseradish peroxidase (HRP) couples the phenolic products of hydroxylation of aromatic substrates to generate colored and/or fluorescent compounds that are easily detected spectroscopically in high-throughput screening. Coexpression of the coupling enzyme with a functional mono- or dioxygenase creates a pathway for the conversion of aromatic substrates into fluorescent compounds in vivo. We used this approach for detecting the products of the toluene-dioxygenase-catalyzed hydroxylation of chlorobenzene and to screen large mutant libraries of Pseudomonas putida cytochrome P450cam by fluorescence digital imaging. Colors generated by the HRP coupling reaction are sensitive to the site of oxygenase-catalyzed hydroxylation, allowing the screen to be used to identify catalysts with new or altered regiospecificities. CONCLUSIONS: The coupled oxygenase-peroxidase reaction system is well suited for screening oxygenase libraries to identify mutants with desired features, including higher activity or stability and altered reaction specificity. This approach should also be useful for screening expressed DNA libraries and combinatorial chemical libraries for hydroxylation catalysts and for optimizing oxygenase reaction conditions.     

The biosynthesis of teicoplanin-type glycopeptide antibiotics: assignment of p450 mono-oxygenases to side chain cyclizations of glycopeptide a47934

Streptomyces toyocaensis produces A47934, a teicoplanin-like type-IV glycopeptide with antibiotic activity against methicillin-resistant Staphylococcus aureus. A47934 differs from the type-I vancomycin glycopeptides, which possess a tricyclic peptide backbone, by the presence of an additional ring closure between the aromatic amino acids 1 and 3. To elucidate the order of crosslinking reactions, P450 mono-oxygenase-inactivation mutants (DeltastaF, DeltastaG, DeltastaH, and DeltastaJ) of the A47934 producer were generated, and the accumulated intermediates were analyzed. Thus, the formation of each crosslink could unambiguously be assigned to a specific oxygenase. The structure of the released intermediates from the wild-type nonribosomal peptide synthetase assembly line facilitated the determination of the cyclization order. Unexpectedly, the additional ring closure in A47934, catalyzed by StaG, is the second oxygenase reaction.     

(2RS,5SR,6SR)‐Methyl 4‐{cis‐2‐[3‐fluoro‐5‐(4‐methoxy‐3,4,5,6‐tetrahydro‐2H‐pyran‐4‐yl)phenoxy­methyl]‐6‐hydroxy‐3‐phenylmorpholino}­benzene­sulfinate

The title compound, C₃₀H₃₄FNO₇S, is a key inter­mediate in the design of dual 5‐LOX (5‐lipoxygenase)/COX‐2 (cyclo­oxygenase‐2) inhibitors. The compound crystallizes as a racemate. Linear hydrogen‐bonded chains are aligned along the [201] direction, and stacked π–π inter­actions and C—H⋯O contacts stabilize the crystal structure.     

On the chemistry of flavin-dependent oxygen activation III. synthesis of 1.10a-dihydroflavin and its 10.10-aring opened derivative as model chromophores for enzyme-bound intermediates

Model chromophores of 1.10-dihydroflavin and its 10.10a-ring opened derivative have been isolated. By comparison with enzymatic intermediates, reaction mechanisms of flavin-dependent oxygenase and luciferase are discussed in terms of chemical structure.     

Molecular Design of Heme Proteins for Future Application

This review surveys our recent studies on artificial heme oxygenases, which consists of two topics. The first topic is an artificial peroxidase founded on a thermally tolerant protein, which shows high thermal stability in the catalytic reaction. In the second topic, we describe ‘Decoy system’ that has been developed to transform Cytochrome P450_BSβ into a versatile oxygenase.     

Cation–π Interactions Contribute to Substrate Recognition in γ‐Butyrobetaine Hydroxylase Catalysis

γ‐Butyrobetaine hydroxylase (BBOX) is a non‐heme Fe^II‐ and 2‐oxoglutarate‐dependent oxygenase that catalyzes the stereoselective hydroxylation of an unactivated C?H bond of γ‐butyrobetaine (γBB) in the final step of carnitine biosynthesis. BBOX contains an aromatic cage for the recognition of the positively charged trimethylammonium group of the γBB substrate. Enzyme binding and kinetic analyses on substrate analogues with P and As substituting for N in the trimethylammonium group show that the analogues are good BBOX substrates, which follow the efficiency trend N⁺>P⁺>As⁺. The results reveal that an uncharged carbon analogue of γBB is not a BBOX substrate, thus highlighting the importance of the energetically favorable cation–π interactions in productive substrate recognition.     

A point mutation converts dihydroneopterin aldolase to a cofactor-independent oxygenase

Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (1) to 6-hydroxymethyl-7,8-dihydropterin (4) in the folate biosynthetic pathway. Substitution of a conserved tyrosine residue at the active site of DHNA by phenylalanine converts the enzyme to a cofactor-independent oxygenase, which generates mainly 7,8-dihydroxanthopterin (6) rather than 4. 6 is generated via the same enol intermediate as in the wild-type enzyme-catalyzed reaction, but this species undergoes an oxygenation reaction to form 6. The conserved tyrosine residue plays only a minor role in the formation of the enol reaction intermediate but a critical role in the protonation of the enol intermediate to form 4.     

Hydroxylation and Ring‐Opening Mechanism of an Unusual Flavoprotein Monooxygenase, 2‐Methyl‐3‐hydroxypyridine‐5‐carboxylic Acid Oxygenase: A Theoretical Study

Hybrid meta‐GGA density functional theory (the MPWB1K functional) was used to study the hydroxylation and ring‐opening mechanism of 2‐methyl‐3‐hydroxypyridine‐5‐carboxylic acid oxygenase (MHPCO). This enzyme catalyses the conversion of 2‐methyl‐3‐hydroxypyridine‐5‐carboxylic acid (MHPC) to α‐(N‐acetylaminomethylene)succinic acid (AAMS), which is the essential ring‐opening step in the bacterial degradation of vitamin B₆. MHPCO belongs to the flavin‐containing aromatic hydroxylases family. However, MHPCO is capable of catalysing a subsequent aromatic ring‐cleavage reaction to give acyclic products rather than hydroxylated aromatic ones. Our calculations show that the re‐aromatisation of the hydroxylated intermediate occurs spontaneously in aqueous solution; this implies that the ring‐opening process occurs inside the enzyme’s active site, in which limited water is available. The instability of the hydroxylated intermediate of MHPCO is the main reason why acyclic products are formed. Previously proposed mechanisms for the ring‐opening step were studied, and were shown to be less likely to occur (ΔΔG^≠298>35 kcal mol^?1). Two new pathways with reasonable barrier heights (ΔΔG^≠298<15 kcal mol^?1) are reported herein, which are in accordance with all experimental information present to date.     

Water-assisted oxo mechanism for heme metabolism

A mechanism of heme metabolism by heme oxygenase (HO) is discussed from B3LYP density functional theory calculations. The concerted OH group attack to the alpha-carbon by the iron-hydroperoxo species is investigated using a model with full protoporphyrin IX to confirm our previous conclusion that this species does not have sufficient oxidizing power for heme oxidation (J. Am. Chem. Soc. 2004, 126, 3672). Calculated activation energies and structures of the intermediates and transition state for this process remain unchanged from those for a small model with porphine in the previous study, which shows that the inclusion of the side chain of the porphyrin ring is not essential in describing the OH group transfer. The activation barrier for a direct oxo attack to the alpha-carbon by an iron-oxo model is calculated to be 49.8 kcal/mol, the barrier height of which looks very high for the enzymatic reaction under physiological conditions. This large activation energy is due to a highly bent porphyrin structure in the transition state. However, a bridging water molecule plays an important role in reducing the porphyrin distortion in the transition state, resulting in a remarkable decrease of the activation barrier to 13.9 kcal/mol. A whole-enzyme model with about 4000 atoms is constructed to elucidate functions of the protein environment in this enzymatic reaction using QM/MM calculations. The key water molecule is fixed in the protein environment to ensure the low-barrier and regioselective heme oxidation. A water-assisted oxo mechanism of heme oxidation by heme oxygenase is proposed from these calculational results.     

Biologically Inspired C−H and C=C Oxidations with Hydrogen Peroxide Catalyzed by Iron Coordination Complexes

The development of catalysts for the selective oxidation of readily available hydrocarbons or organic precursors into oxygenated products is a long‐standing goal in organic synthesis. In the last decade, some iron coordination complexes have shown the potential to fit this role. These catalysts can mimic the O?O activation mode of far more sophisticated iron oxygenase enzymes, generating powerful yet selective oxidants. In this review, we report state‐of‐the‐art C?H and C=C oxidations catalyzed by non‐heme iron complexes and H₂O₂ as the oxidant. Finally, we briefly describe some novel oxidative reactivity and the perspectives of this chemistry.     

Commercial Herbicides Can Trigger the Oxidative Inactivation of Acetohydroxyacid Synthase

Acetohydroxyacid synthase (AHAS) inhibitors are highly successful commercial herbicides. New kinetic data show that the binding of these compounds leads to reversible accumulative inhibition of AHAS. Crystallographic data (to a resolution of 2.17 Å) for an AHAS–herbicide complex shows that closure of the active site occurs when the herbicidal inhibitor binds, thus preventing exchange with solvent. This feature combined with new kinetic data shows that molecular oxygen promotes an accumulative inhibition leading to the conclusion that the exceptional potency of these herbicides is augmented by subversion of an inherent oxygenase side reaction. The reactive oxygen species produced by this reaction are trapped in the active site, triggering oxidation reactions that ultimately lead to the alteration of the redox state of the cofactor flavin adenine dinucleotide (FAD), a feature that accounts for the observed reversible accumulative inhibition.     

Characterization of kinetics and products of the Baeyer-Villiger oxygenase MtmOIV, the key enzyme of the biosynthetic pathway toward the natural product anticancer drug mithramycin from Streptomyces argillaceus

MtmOIV, the key oxygenase of the mithramycin biosynthetic pathway in Streptomyces argillaceus, was proven to act initially as Baeyer-Villiger monooxygenase, but may also catalyze various follow-up reaction steps. The reaction of the overexpressed pure His6-tagged enzyme with its substrate premithramycin B was studied. Various intermediates and products were isolated and physicochemically characterized, several of them being previously unknown compounds. This is the first example in which a bacterial enzyme was unequivocally proven to act as Baeyer-Villigerase with its natural substrate, that is, in its natural context.     

Mutational analysis of the enterocin favorskii biosynthetic rearrangement

[reaction: see text] A mutational analysis of the enterocin biosynthesis genes revealed that the putative oxygenase and the methyltransferase gene products EncM and EncK, respectively, jointly catalyze a biosynthetic Favorskii-like rearrangement. Inactivation of either gene terminated enterocin production and caused the accumulation of four nonrearranged, nonmethylated polyketides. The structure elucidation of the new wailupemycins E-G is reported.