Structure and assembly of protocatechuate 3,4-dioxygenase

Dioxygenases catalyse the cleavage of molecular oxygen with subsequent incorporation of both oxygen atoms into organic substrates. Some of the best-studied dioxygenases have been isolated from bacteria where they catalyse the critical ring-opening step in the biodegradation of aromatic compounds. These bacterial enzymes generally contain nonheme ferric iron as the sole cofactor. Protocatechuate 3,4-dioxygenase (3,4-PCD) was one of the first such enzymes recognized and catalyses the intradiol cleavage of protocatechuic acid by oxygen to produce beta-carboxy-cis,cis-muconic acid. Previous studies have shown that the 3,4-PCD found in Pseudomonas aeruginosa is an oligomer with a relative molecular mass (Mr) of 587,000 (587K) containing 12 copies each of alpha (22.3K) and beta (26.6K) subunits. The X-ray structure determination of 3,4-PCD reveals the catalytic iron environment required for oxygenolytic cleavage of aromatic rings and also provides a novel holoenzyme assembly with cubic 23(T) symmetry and first examples of mixed beta-barrel domains.

Probing structure-function relations in heme-containing oxygenases and peroxidases

Structural factors that influence functional properties are examined in the case of four heme enzymes: cytochrome P-450, chloroperoxidase, horseradish peroxidase, and secondary amine mono-oxygenase. The identity of the axial ligand, the nature of the heme environment, and the steric accessibility of the heme iron and heme edge combine to play major roles in determining the reactivity of each enzyme. The importance of synthetic porphyrin models in understanding the properties of the protein-free metal center is emphasized. The conclusions described herein have been derived from studies at the interface between biological and inorganic chemistry.

Determination of the quaternary structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa

A 2.5 A resolution data set has been collected for crystals of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa. Analysis of the data using the rotation function shows that the alpha 2 beta 2 tetramers associate to form a particle with cubic 23 (T) point group symmetry. Prior to this analysis it was believed that eight tetramers associated to form the holoenzyme. The symmetry of the crystalline holoenzyme also addresses questions concerning its iron content and substrate stoichiometry.

Enzymatic determination of veratryl alcohol

A rapid and sensitive method was developed for the measurement of veratryl alcohol--a secondary metabolite of some lignin degrading fungi. The method is based on the enzymatic oxidation of veratryl alcohol to veratraldehyde by the ligninase of Phanerochaete chrysosporium. The purified enzymes oxidized veratryl alcohol completely to veratraldehyde (75%) and some unidentified products. The enzymatic method was applied to measure veratryl alcohol in the culture filtrates of Chrysosporium pruinosum and it gave the same results as the conventional method involving extraction and separation by high-pressure liquid chromatography. Benefits and limitations of the method are discussed.

Camphor revisited: studies of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453

The oxygenating component of 2,5-diketocamphane 1,2-monooxygenase from Pseudomonas putida ATCC 17453 was purified to homogeneity by a combination of ammonium sulfate fractionation and chromatography on DEAE-cellulose and polyanion SI-17 columns. It had an Mr of 78,000, bound one molecule of nonautooxidizable flavin mononucleotide (FMN), consisted of two subunits of equal molecular weight, and existed in two electrophoretically distinguishable active forms. The oxygenating complex was constructed from equimolecular amounts of an NADH oxidase, which could be purified separately (Mr, 36,000), and the oxygenating component. Most of the NADH oxidase dissociated from the oxygenating component during purification, although traces remained, to give the final preparation of the oxygenating component significant oxygenase activity. FMN did not dissociate significantly from the oxygenating component during purification, but it was not covalently bound and could be removed under a variety of conditions. Binding between the two proteins that made up the active complex was fairly weak and freely reversible. It probably occurred through the FMN which was strongly bound to the oxygenating component and for which the NADH had a weak binding site. Iron was not present at a significant level in the oxygenating component, and in common with other characterized Baeyer Villiger monooxygenases, 2,5-diketocamphane 1,2-monooxygenase was found to be a simple flavoprotein.

EPR and Mössbauer studies of protocatechuate 4,5-dioxygenase. Characterization of a new Fe2+ environment

Protocatechuate 4,5-dioxygenase from Pseudomonas testosteroni has been purified to homogeneity and crystallized. The iron containing, extradiol dioxygenase is shown to be composed of two subunit types (alpha, Mr = 17,700 and beta, Mr = 33,800) in a 1:1 ratio; such a composition has not been observed for other extradiol dioxygenases. The 4.2 K Mössbauer spectrum of native protocatechuate 4,5-dioxygenase prepared from cells grown in 57Fe-enriched media consists of a doublet with quadrupole splitting, delta EQ = 2.22 mm/s, and isomer shift delta Fe = 1.28 mm/s, demonstrating a high spin Fe2+ site. These parameters, and the temperature dependence of delta EQ, are unique among enzymes but are strikingly similar to those reported for the reaction center of the photosynthetic bacterium Rhodopseudomonas sphaeroides R-26, suggesting very similar ligand environments. The Fe2+ of protocatechuate 4,5-dioxygenase can be oxidized, for instance by H2O2, to yield high spin Fe3+ with EPR g values around g = 6 (and g = 4.3). In the oxidized state, protocatechuate 4,5-dioxygenase is inactive; the iron, however, can be rereduced by ascorbate to yield active enzyme. Our data suggest that protocatechuate binds to Fe2+; the spectra indicate that the ligand binding is heterogenous. The Mössbauer spectra observed here are fundamentally different from those reported earlier (Zabinski, R., Münck, E., Champion, P., and Wood, J. M. (1972) Biochemistry 11, 3212-3219). The spectra of the earlier (reconstituted) preparations, which had substantially lower specific activities, probably reflect adventitiously bound Fe3+. We discuss here how adventitiously bound iron can be identified and removed. The Fe2+ which is present in native protocatechuate 4,5-dioxygenase and its complexes with substrates and inhibitors reacts quantitatively with nitric oxide to produce a species with electronic spin S = 3/2. The EPR and Mössbauer spectra of these complexes compare favorably with EDTA . Fe(II) . NO. We have studied the latter complex extensively and have analyzed the Mössbauer spectra with an S = 3/2 spin Hamiltonian. EPR spectra show that protocatechuate 4,5-dioxygenase-NO complexes with substrates or inhibitors are heterogeneous and consist of several well defined subspecies. The data show that NO, and presumably also O2, has access to the active site Fe2+ in the enzyme-substrate complex. The use of EPR-detectable NO complexes as a rapid and sensitive tool for the study of the EPR silent active site iron of extradiol dioxygenases is discussed.

Model of the extradiol-cleaving manganese(II) dioxygenase penicillamine-manganese(II) complex

The structure of the green penicillamine(Pen)-Mn(II) complex prepared under air was determined from its electronic spectra, molar ratio, ESR spectra and oxygen consumptions at various pH values and by potentiometric titration. Pen bound with Mn(II) in a molar ratio of approximately 1:1 forming coordination bonds with a thiolate and an amino group, and the complex consumed about 1 mol of oxygen at pH 9-10. Oxygen binding to this complex was found to be reversible at room temperature. The oxygen adduct complex catalysed oxidative extradiol-cleavage of catechol at pH 7.0-7.5. The Pen-Mn(II)-02 complex seems to be a simple model of extradiol-cleaving manganese(II) dioxygenase, which was recently found in Bacillus brevis.

Magnetic and natural circular dichroism of L-tryptophan 2,3-dioxygenases and indoleamine 2,3-dioxygenase. I. Spectra of ferric and ferrous high spin forms

The ferric form of L-tryptophan 2,3-dioxygenases from both Pseudomonas acidovorans (ATCC 11299b) and rat liver showed magnetic CD spectra ascribable to a high spin protohemoprotein at neutral pH, whereas the ferric indoleamine 2,3-dioxygenase from rabbit intestine exhibited a spectrum due to a mixture of high and low spin states under comparable conditions. Upon addition of L-tryptophan, the spectra of the former enzymes changed to another type of high spin spectra, while the latter showed a marked increase in the low spin component. From these findings and effects of pH on the spectra, it is suggested that the sixth ligand of ferric L-tryptophan 2,3-dioxygenases is water at a neutral pH and that for the ferric indoleamine 2,3-dioxygenase is a strong field ligand such as an imidazole nitrogen. The mixed spin state observed for the latter enzyme was ascribable to a thermal equilibrium between high and low spin states as judged by low temperature spectroscopy. With the ferrous form, the Soret magnetic CD spectra of these enzymes were all similar, giving those of a typical high spin ferrous protohemoprotein, whereas visible spectra were different from one another, suggesting differences in the electronic structure of the heme and its vicinity. The natural CD spectra of both ferric and ferrous forms of each enzyme showed negative Cotton effects in the Soret region. Their intensities were different from one another, presumably due to some differences in the interaction of the heme with nearby aromatic amino acid residue(s).

Perinatal development of cytochrome P-450, NADPH-cytochrome c reductase and ethoxycoumarin deethylase in rat liver nuclear membranes

Perinatal development of rat liver nuclear membrane enzymatic activities was investigated with respect to the metabolism of xenobiotica. The qualitative pattern observed was very close to that reported for microsomal enzymes during development. Cytochrome P-450, NADPH-cytochrome c reductase and ethoxycoumarin deethylase are already present in fetuses at 18 days of gestational age. Phenobarbital pretreatment appears to be effective as an inducing agent for all the enzymes studied, but only after birth. The pattern of induction of cytochrome P-450 showed a peak at the 38th day of life three times higher than basal values at that age. NADPH-cytochrome c reductase presented a constant elevation to about twice basal activity throughout the period taken into consideration. Ethoxycoumarin deethylase activity took only 17 days to reach the basal value observed later in adult animals. This enzyme proved highly inducible by phenobarbital (5-fold) early after birth but the increase dropped to 3-fold from the 24th day of life.

Immobilization of metapyrocatechase and its properties in comparison with the soluble enzyme

Metapyrocatechase [catechol : oxygen 2,3-oxidoreductase, EC 1.13.11.2] was immobilized with cyanogen bromide-activated agarose with a coupling yield of 78% of the protein added. The immobilized enzyme showed a specific activity of 77 mumol/min/mg protein, which is about 30% of that of the native enzyme. The immobilization enhanced the stability of the enzyme against inactivation by heat, acid or alkaline pH, and various denaturing agents. However, like the native enzyme, the immobilized enzyme was rapidly inactivated by oxidants such as oxygen or hydrogen peroxide, and the inactivation was completely prevented in the presence of low concentrations of organic solvents. The pH profile for the activity and the substrate specificity were slightly changed by the immobilization.

Preliminary crystallographic study of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa

The enzyme protocatechuate 3,4-dioxygenase (EC 1.13.11.3) from Pseudomonas aeruginosa consisting of eight identical subunits (total Mr = 783,100) crystallizes in the monoclinic space group 12 with unit cell dimensions a = 204, b = 129, c = 137 A, and beta = 97.5 degrees. The measured density is 1.26 g ml-1. The Matthews coefficient is 2.27 A3/dalton. The large rod-like crystals diffract to about 2.5 A resolution. The asymmetric unit contains one-half of the enzyme and the enzyme contains an exact 2-fold axis of symmetry.

[Cytochrome P-450 dependent enzymatic activity in the liver of patients with porphyria cutanea tarda (author's transl)]

In the liver of 12 patients with porphyria cutanea tarda (PCT) the following parameters were measured: protein-content, NADPH-cytochrome c-reductase, 7-ethoxycoumarin-deethylase. The results were compared with the findings of patients with chronic liver disease (chronic hepatitis or cirrhosis) and patients without any liver affection. In addition the in vitro inhibition of 7-ethoxycoumarin-deethylase by metyrapone (phenobarbital induced cytochrome P-450) or naphthoflavone (benzo[a]pyrene induced cytochrome P-448) was estimated. No differences were found between the various groups. It is assumed that the induction of the mixed function monooxygenases is not an essential condition for the development or the persistence of the human porphyria cutanea tarda.

The effect of hepatic microsomal monooxygenase induction on the metabolism and toxicity of the organophosphorus insecticide chlorfenvinphos

The induction of rat liver microsomal monooxygenase by pretreatment of rats with dieldrin affords a 10-fold protection against the acute toxic effects of the organophosphorus insecticide, chlorfenvinphos. Metabolism studies were carried out to confirm that the protection was due to an enhanced rate of detoxification (via oxidative deethylation). At low doses of chlorfenvinphos (2.5 mg . kg-1), dieldrin pretreatment caused minimal changes in the metabolic profiles. However, at a higher dose (13.2 mg . kg-1), giving clinical signs of intoxication in the control animals, the dieldrin pretreated rats produced 5 times more deethylchlorofenvinphos than did the control animals. The results support the conclusion that the effect of enzyme induction on the metabolism of substrates of that enzyme are dose-dependent. Alterations in metabolism, therefore, are not an automatic consequence of enzyme induction.

The complete amino acid sequence of the beta-subunit of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa

The complete amono aicd sequence of the beta-subunit of protocatechuate 3,4-dioxygenase is presented. The beta-subunit contained 237 amino acid residues, 4 of which were methionines. Accordingly, cyanogen bromide cleavage of the S-carboxymethylated beta-subunit produced five peptides. The sequences of these peptides were determined by analyses of the peptides obtained by tryptic, staphyloccal protease and thermolysin digestions. The alignment of the cyanogen bromide peptides was deduced by the use of overlapping peptides containing methionine which were obtained by tryptic digestion of the S-carboxymethylated beta-subunit. The calculated molecular weight was 26,588, which is close to the value estimated by acrylamide gel electrophoresis in the presence of sodium dodecyl sulfate.

The primary structure of the alpha subunit of protocatechuate 3,4-dioxygenase. II. Isolation and sequence of overlap peptides and complete sequence

The complete primary structure of the alpha subunit of protocatechuate 3,4-dioxygenase has been determined by automated Edman degradation and carboxypeptidase digestionof the intact alpha chain and of peptides derived from trypsin (N.A. Kohlmiller and J.B. Howard (1979) J. Biol. Chem. 254, 7302-7308) and Staphylococcus aureus protease digestion, and from hydroxylamine and dilute acid cleavage. The alpha chain was found to consist of 200 residues in the following sequence from the NH2-terminal end: (formula: see text).

The primary structure of the alpha subunit of protocatechuate 3,4-dioxygenase. I. Isolation and sequence of the tryptic peptides

The carboxymethylated alpha subunit of protocatechuate 3,4-dioxygenase was digested with trypsin. The 14 tryptic peptides were isolated by ion exchange chromatography on DEAE-Sephadex and by gel filtration chromatography. Automated Edman degradation and carboxypeptidase Y and B digestion were used to establish the sequence of these peptides. Further fragmentation of two tryptic peptides, T3 and T5, by Staphylococcus aureus protease and cyanogen bromide, respectively, was necessary to complete the sequences. The tryptic peptides accounted for a minimum of 199 residues out of a total of 202 residues predicted by amino acid analysis.