Kinetic studies on a 4-methoxybenzoate O-demethylase from Pseudomonas putida

Preparation and characterization of lignin demethylated at atmospheric pressure and its application in fast curing biobased phenolic resins

Agricultural crop-based lignin was utilized to modify phenol-formaldehyde (PF) resin to prepare fast curing biobased phenolic resins by copolymerization.

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.

The trans-anethole degradation pathway in an Arthrobacter sp

A bacterial strain (TA13) capable of utilizing t-anethole as the sole carbon source was isolated from soil. The strain was identified as Arthrobacter aurescens based on its 16 S rRNA gene sequence. Key steps of the degradation pathway of t-anethole were identified by the use of t-anethole-blocked mutants and specific inducible enzymatic activities. In addition to t-anethole, strain TA13 is capable of utilizing anisic acid, anisaldehyde, and anisic alcohol as the sole carbon source. t-Anethole-blocked mutants were obtained following mutagenesis and penicillin enrichment. Some of these blocked mutants, accumulated in the presence of t-anethole quantitative amounts of t-anethole-diol, anisic acid, and 4,6-dicarboxy-2-pyrone and traces of anisic alcohol and anisaldehyde. Enzymatic activities induced by t-anethole included: 4-methoxybenzoate O-demethylase, p-hydroxybenzoate 3-hydroxylase, and protocatechuate-4,5-dioxygenase. These findings indicate that t-anethole is metabolized to protocatechuic acid through t-anethole-diol, anisaldehyde, anisic acid, and p-hydroxybenzoic acid. The protocatechuic acid is then cleaved by protocatechuate-4,5-dioxygenase to yield 2-hydroxy-4-carboxy muconate-semialdehyde. Results from inducible uptake ability and enzymatic assays indicate that at least three regulatory units are involved in the t-anethole degradation pathway. These findings provide new routes for environmental friendly production processes of valuable aromatic chemicals via bioconversion of phenylpropenoids.

Substrate and solvent isotope effects on the fate of the active oxygen species in substrate-modulated reactions of putidamonooxin

Using 4-methoxybenzoate monooxygenase from Pseudomonas putida, the substrate deuterium isotope effect on product formation and the solvent isotope effect on the stoichiometry of oxygen uptake, NADH oxidation, product and/or H2O2 (D2O2) formation for tight couplers, partial uncouplers, and uncouplers as substrates were measured. These studies revealed for the true, intrinsic substrate deuterium isotope effect on the oxygenation reaction a k1H/k2H ratio of < 2.0, derived from the inter- and intramolecular substrate isotope effects. This value favours a concerted oxygenation mechanism of the substrate. Deuterium substitution in a tightly coupling substrate initiated a partial uncoupling of oxygen reduction and substrate oxygenation, with release of H2O2 corresponding to 20% of the overall oxygen uptake. This H2O2 (D2O2) formation (oxidase reaction) almost completely disappeared when the oxygenase function was increased by deuterium substitution in the solvent. The electron transfer from NADH to oxygen, however, was not affected by deuterium substitution in the substrate and/or the solvent. With 4-trifluoromethylbenzoate as uncoupling substrate and D2O as solvent, a reduction (peroxidase reaction) of the active oxygen complex was initiated in consequence of its extended lifetime. These additional two electron-transfer reactions to the active oxygen complex were accompanied by a decrease of both NADH oxidation and oxygen uptake rates. These findings lead to the following conclusions: (a) under tightly coupling conditions the rate-limiting step must be the formation time and lifetime of an active transient intermediate within the ternary complex iron/peroxo/substrate, rather than an oxygenative attack on a suitable C-H bond or electron transfer from NADH to oxygen. Water is released after the monooxygenation reaction; (b) under uncoupling conditions there is competition in the detoxification of the active oxygen complex between its protonation (deuteronation), with formation of H2O2 (D2O2) and its further reduction to water. The additional two electron-transfer reactions onto the active oxygen complex then become rate limiting for the oxygen uptake rate.

Biodegradation of 4-nitroanisole by two Rhodococcus spp

Two Rhodococcus strains, R. opacus strain AS2 and R. erythropolis strain AS3, that were able to use 4-nitroanisole as the sole source of carbon and energy, were isolated from environmental samples. The first step of the degradation involved the O-demethylation of 4-nitroanisole to 4-nitrophenol which accumulated transiently in the medium during growth. Oxygen uptake experiments indicated the transformation of 4-nitrophenol to 4-nitrocatechol and 1,2,4-trihydroxybenzene prior to ring cleavage and then subsequent mineralization. The nitro group was removed as nitrite, which accumulated in the medium in stoichiometric amounts. In R. opacus strain AS2 small amounts of hydroquinone were produced by a side reaction, but were not further degraded.

Substrate-modulated reactions of putidamonooxin. The nature of the active oxygen species formed and its reaction mechanism

1. 4-Methoxybenzoate monooxygenase is fairly nonspecific. The enzyme system with putidamonooxin as its oxygen-activating component catalyses: (a) O-, S- and N-demethylation; (b) the oxygenation of 4-methylbenzoate and 4-methylmercaptobenzoate, with formation of 4-carboxybenzyl alcohol and 4-carboxyphenylmethyl sulfoxide, respectively, and (c) attack of the aromatic ring of 4- and 3-hydroxybenzoate and 4-aminobenzoate, yielding 3,4-dihydroxybenzoate and 4-amino-3-hydroxybenzoate, respectively. 2. Compounds which are bound by the active sites of putidamonooxin have two essential features in common: a planar aromatic ring system, and a free carboxyl group attached to it. 3. By a substrate-modulated reaction putidamonooxin can be induced to function not only as a monooxygenase but also as a peroxotransferase, i.e. it incorporates both atoms of the activated oxygen molecule into a substrate molecule. This finding supports the hypothesis that a mesomeric state of the iron.peroxo complex, [FeO2]+, is indeed the active oxygenating species of putidamonooxin. 4. The lifetime of the ternary complex consisting of enzyme.iron-peroxo-complex.substrate is significantly prolonged by uncoupling and partially uncoupling substrates, except when it is inactivated by protonation of the iron.peroxo complex by a proton transported into the active sites by a special kind of substrate (i.e. isomers of monoaminobenzoate), with the direct formation of H2O2. 5. The lifetime of the active oxygen species is determined by (a) the rate of the oxygenation reaction in the presence of tight-coupling substrates and (b) the rate of the oxygenation reaction as well as detoxification by the availability of a dissociable proton in the presence of partial uncoupling (and uncoupling) substrate analogues. 6. The rate of the oxygenation reaction depends on the lifetime of the active oxygen species, [FeO2]+, in the presence of partial uncoupling substrates. 7. The iron.peroxo complex attacks an aromatic ring system according to the empiric rules of electrophilic substitution, whereas the attack of aliphatic substituents at the aromatic ring is controlled by steric criteria.

Transformations of chloroguaiacols, chloroveratroles, and chlorocatechols by stable consortia of anaerobic bacteria

Metabolically stable consortia of anaerobic bacteria obtained by enrichment of sediment samples with 3,4,5-trimethoxybenzoate (TMBA), 3,4,5-trihydroxybenzoate (gallate [GA]), or 5-chlorovanillin (CV) were used to study the anaerobic transformation of a series of chloroveratroles, chloroguaiacols, and chlorocatechols used as cosubstrates. Experiments were carried out with growing cultures, and the following pathways were demonstrated for metabolism of the growth substrates: (i) TMBA produced GA, which was further degraded without the formation of aromatic intermediates; (ii) GA formed pyrogallol, which was stable to further transformation; and (iii) CV was degraded by a series of steps involving de-O-methylation, oxidation of the aldehyde group, and decarboxylation to 3-chlorocatechol before ring cleavage. Mono-de-O-methylation of the cosubstrates occurred rapidly in the order 4,5,6-trichloroguaiacol greater than 3,4,5-trichloroguaiacol approximately 3,4,5-trichloroveratrole approximately tetrachloroveratrole greater than tetrachloroguaiacol and was concomitant with degradation of the growth substrates. For the polymethoxy compounds--chloroveratroles, 1,2,3-trichloro-4,5,6-trimethoxybenzene, and 4,5,6-trichlorosyringol--de-O-methylation took place sequentially. The resulting chlorocatechols were stable to further transformation until the cultures had exhausted the growth substrates; selective dechlorination then occurred with the formation of 3,5-dichlorocatechol from 3,4,5-trichlorocatechol and of 3,4,6-trichlorocatechol from tetrachlorocatechol. 2,4,5-, 2,4,6-, and 3,4,5-trichoroanisole and 2,3,4,5-tetrachloroanisole were de-O-methylated, but the resulting chlorophenols were resistant to dechlorination. These results extend those of a previous study with spiked sediment samples and their endogenous microflora and illustrate some of the transformations of chloroguaiacols and chlorocatechols which may be expected to occur in anaerobic sediments.

Protein-protein interactions and antigenic relationships between the components of 4-methoxybenzoate monooxygenase and of benzene 1,2-dioxygenase from Pseudomonas putida

The investigations presented in this paper were performed on two enzyme systems from Pseudomonas putida: (a) 4-methoxybenzoate monooxygenase, consisting of a NADH: putidamonooxin oxidoreductase and putidamonooxin, the oxygen-activating component, and (b) benzene 1,2-dioxygenase, a three-component enzyme system with an NADH: ferredoxin oxidoreductase, functioning together with a plant-type ferredoxin as electron-transport chain, and an oxygen-activating component similar to putidamonooxin in its active sites. The influence of temperature, ionic strength, and pH on the activities of 4-methoxybenzoate monooxygenase and of NADH: putidamonooxin oxidoreductase were investigated. The studies revealed that the activity of 4-methoxybenzoate monooxygenase is determined by the behaviour of the reductase. Spectroscopic measurements showed that the interaction between the two components of 4-methoxybenzoate monooxygenase influences the optical-absorption behaviour of one or both components. As a criterion for the affinity between the two components of 4-methoxybenzoate monooxygenase, the Km value of the reductase for putidamonooxin was determined and found to be 31 +/- 11 microM. Antibodies against both components of 4-methoxybenzoate monooxygenase were obtained from rabbits. The antibodies against putidamonooxin inhibited the O-demethylation reaction (up to 80%) and also the reduction of putidamonooxin by the reductase (up to 40%). The antibodies against putidamonooxin did not interact with the oxygen-activating component of benzene 1,2-dioxygenase. The electron-transport chains of 4-methoxybenzoate monooxygenase and benzene 1,2-dioxygenase could not be replaced by one another without a complete loss of enzyme activity.

Mössbauer investigation of the cofactor iron of putidamonooxin

Mononuclear non-heme cofactor iron of putidamonooxin has been investigated in the binary oxidized 'enzyme X substrate' complex and in the ternary 'enzyme X substrate X NO' complex via Mössbauer spectroscopy. The experimental spectra were analyzed on the basis of the spin-Hamiltonian formalism. The resulting fine and hyperfine structure parameters are compared with literature values of similar compounds. From this comparison we conclude that in the binary complex (reduced and oxidized) the mononuclear non-heme cofactor iron has a coordination number higher than four. Additionally, the cofactor iron shows remarkable spectral similarities with iron in protocatechuate 3,4-dioxygenase, though the catalytic properties of the iron sites in the two proteins are different. The data obtained form the ternary 'enzyme X substrate X NO' complex indicate that the cofactor iron (a) is in the ferric intermediate spin state (S = 3/2) and (b) is pentacoordinated, which means that upon NO binding to the reduced cofactor iron at least one ligand has to be released. Comparing our data with literature values suggests that the cofactor iron in the binary as well as in the ternary NO complex is not directly bound to a sulfur atom, though biochemical arguments seem to indicate the opposite.

Dioxygen activation by putidamonooxin. The oxygen species formed and released under uncoupling conditions

In the presence of substrates not favourable for hydroxylation, more than 80% of the dioxygen consumed by purified, reconstituted 4-methoxybenzoate monooxygenase appears in the reaction mixture as hydrogen peroxide. We have investigated whether under these conditions (a) reduced putidamonooxin, the oxygenase of this enzyme system, either autoxidizes in the presence of dioxygen, with liberation of superoxide anion radicals which then disproportionate to H2O2 and O2, or (b) dioxygen is reduced by two sequential single-electron steps leading to the active oxygen species that forms hydrogen peroxide directly when inactivated by protonation. Quantitative estimation of O-2 radicals, with either succinylated ferricytochrome c or epinephrine used as O-2 scavengers, revealed that only about 6% of the total electron flux channelled via putidamonooxin to dioxygen led to the monovalent reduction on dioxygen. This means that not more than 3% of the hydrogen peroxide found under uncoupling conditions arises from the rapid bimolecular disproportionation of initially formed O-2 radicals. Inconsistent results were obtained when lactoperoxidase was used as an O-2 trap. Our measurements indicate that the conversion of lactoperoxidase into compound III is an inappropriate method of detecting any O-2 radicals that may be found by the uncoupled 4-methoxybenzoate monooxygenase. The stoichiometry of about 1:1 for O2 uptake: H2O2 formation indicates that under uncoupling conditions H2O is virtually not formed. The role of [FeO2]+ as the active oxygenating species of putidamonooxin is discussed.

Biologically related iron-sulfur clusters as reaction centers. Reduction of acetylene to ethylene in systems based on [Fe4S4(SR)4]3-

The possibility that clusters containing the Fe4S4 core unit found in a wide variety of proteins can effect reductive transformations of Fe-S enzyme substrates has been investigated using the reduced synthetic clusters [Fe4S4(SPh)4]3- and acetylene, an alternate nitrogenase substrate. The system [Fe4S4(SPh)4]3-/acetic acid/acetic anhydride in N-methylpyrollidinone at approximately 25 degrees was found to reduce acetylene homogeneously to ethylene, and in the presence of a deuterium source to afford as the principal stereochemical product cis-1,2-C2H2D2. No appreciable reduction was found using the oxidized cluster [Fe4S4(SPh)4]2-. The system is not catalytic and departs from the strict stoichiometry of the reaction, 2[Fe4S4(SPh)4]3- + C2H2 + 2H+ leads to 2 [Fe4S4(SPh)4]2- + C2H4, primarily because of a competing cluster oxidation reaction which could not be eliminated. Based on this reaction ca. 60% conversion of acetylene to ethylene was achieved. A reaction sequence based on absorption and 1H nmr spectral observations and product stereo-chemistry is suggested. The results demonstrate that biologically related, reduced Fe4S4 clusters can effect reduction of at least one Fe-S enzyme substrate, and raise the general possibility of substrate transformation with such clusters as reaction sites in biological systems.

Chemical and spectral properties of putidamonooxin, the iron-containing and acid-labile-sulfur-containing monooxygenase of a 4-methoxybenzoate O-demethylase from Pseudomonas putida

Gel chromatography indicates that putidamonooxin has a molecular weight of about 126,000. On the other hand, the amino acid composition and the iron-to-protein ratio point to a minimal molecular weight of 33,000 and 31,000 respectively. On sodium dodecylsulfate/polyacrylamide gel electrophoresis the enzyme migrated as a homogeneous band corresponding to a molecular weight of about 40,000. The number of spots found in the tryptic peptide map of the carboxymethylated and digested enzyme indicates that putidamonooxin is composed of three or four identical subunits. After covalent cross-linking of the subunits with dimethyl suberimidate and subsequent dodecylsulfate electrophoresis the main bands were in the molecular weight range of 40,000, 87,000 and 124,000. These findings lead us to propose that putidamonooxin is either a trimer or tetramer. The amino acid composition of putidamonooxin and related data calculated from this are given. The isoelectric point was shown by isoelectric focusing to be a pH 4.7. Low-temperature optical spectra of the reduced and oxidized enzyme as well as of three different putidamonooxin.substrate complexes are given together with those recorded at 10 degrees C. Enzyme.substrate binding spectra are observed with the oxidized putidamonooxin but not with the reduced enzyme. For the oxidized putidamonooxin a molar absorption coefficient at 455nm of 14.7mM-1 cm-1 was determined. Ks values of putidamonooxin towards different substrates and substrate analogues (i.e. tight couplers, partial uncouplers and uncouplers) are presented and possible reasons for the difference between the Ks values here obtained and the previously reported Km values are discussed.