Molybdenum-containing Enzymes Research Articles

Determination of the Metal−Dithiolate Fold Angle in Mononuclear Molybdenum(V) Centers by EPR Spectroscopy

The active sites of mononuclear molybdenum-containing enzymes contain a low-symmetry Mo(V)-dithiolene intermediate whose structure can be probed using electron paramagnetic resonance (EPR). The relationship between experimental EPR spectra and the electronic and geometric structure of the active site can be difficult to establish, not least because of the low molecular symmetry. When density functional theory is used, it is possible to assess this relationship by systematically varying the geometric structure and comparing the theoretical EPR parameters with those obtained experimentally. We employed this approach to examine the relationship between the metal-dithiolate fold angle and the monoclinic spin Hamiltonian parameters (g, A, beta) of a prototypical mononuclear molybdenyl model complex. By comparing the experimental EPR parameters with these results, we show that the metal-dithiolate fold angle of the complex in solution may be obtained from the non-coincidence angle beta that transforms the principal axes of g to those of A. This will provide a useful method for probing the structure of the Mo(V) intermediate of mononuclear molybdenum enzymes, where the electronic structure of the active site is modulated by the fold angle of the dithiolate ligand (the "metal-dithiolate folding effect").

Inhibition studies of bovine xanthine oxidase by luteolin, silibinin, quercetin, and curcumin.

Xanthine oxidoreductase (XOR) is a molybdenum-containing enzyme that under physiological conditions catalyzes the final two steps in purine catabolism, ultimately generating uric acid for excretion. Here we have investigated four naturally occurring compounds that have been reported to be inhibitors of XOR in order to examine the nature of their inhibition utilizing in vitro steady-state kinetic studies. We find that luteolin and quercetin are competitive inhibitors and that silibinin is a mixed-type inhibitor of the enzyme in vitro, and, unlike allopurinol, the inhibition is not time-dependent. These three natural products also decrease the production of superoxide by the enzyme. In contrast, and contrary to previous reports in the literature based on in vivo and other nonmechanistic studies, we find that curcumin did not inhibit the activity of purified XO nor its superoxide production in vitro.

Theoretical Study of the Oxidation Reaction and Electron Spin Resonance Parameters Involving Sulfite Oxidase

We present a density functional theory (DFT) study on the conversion of sulfite to sulfate with a model complex representing the active site of the molybdenum-containing enzyme sulfite oxidase (SO). This study considers the attack of the sulfur lone pair from SO(3)(2-) on the equatorial oxo ligand of the model complex as the initial step in the oxidation process. The good agreement between our energy profile and data derived from experimental kinetic parameters provides some support for the reaction mechanism of the oxidative half-reaction of SO proposed in this study. The enzymatic reductive half-reaction involves the formation of an Electron Spin Resonance (ESR) active Mo(V) species. Experimentally, differences in ESR parameters (g-values and (1)H hyperfine coupling constant) of the low- and high-pH forms of the enzyme have been found. The current study also presents DFT-based calculations on ESR parameters for three model complexes representing the paramagnetic center Mo(V) of SO in its possible low- and high-pH forms. We provide an analysis of the magnetic orbital coupling responsible for the calculated g-values. Finally, we suggest how the conformation and hydrogen bonding interactions of the hydroxyl ligand can explain the different ESR parameters at low- and high-pH.

Dedicated Metallochaperone Connects Apoenzyme and Molybdenum Cofactor Biosynthesis Components

The biogenesis of molybdenum-containing enzymes is a sophisticated process involving the insertion of a complex molybdenum cofactor into competent apoproteins. As for many molybdoenzymes, the maturation of trimethylamine-oxide reductase TorA requires a private chaperone. This chaperone (TorD) interacts with the signal peptide and the core of apo-TorA. Using random mutagenesis, we established that alpha-helix 5 of TorD plays a key role in the core binding and that this binding drives the maturation of TorA. In addition, we showed for the first time that TorD interacts with molybdenum cofactor biosynthesis components, including MobA, the last enzyme of cofactor synthesis, and Mo-molybdopterin, the precursor form of the cofactor. Finally we demonstrated that TorD also binds the mature molybdopterin-guanine dinucleotide form of the cofactor. We thus propose that TorD acts as a platform connecting the last step of the synthesis of the molybdenum cofactor just before its insertion into the catalytic site of TorA.

Symadex™, a FLT3 kinase inhibitor, is metabolized by aldehyde oxidase

Symadex™ (C‐1311) is a potent inhibitor of FMS‐like tyrosine kinase 3 (FLT3). This imidazoacridinone class compound has started development for oncology indications and is being investigated as a therapy for autoimmune diseases. A major circulating metabolite is an oxygenated species (+16 amu) that is found in plasma and urine after oral and intravenous administration.Aldehyde oxidase (AO) is a molybdenum‐containing enzyme present in liver that catalyzes the oxidation of a wide variety of nitrogen containing heterocycles. Data are presented from in vitro incubations with microsomes, liver cytosol, inhibitors specific for AO, and an isotopic labelling experiment to confirm the role of AO in the oxidation of Symadex™.The proposed metabolite was synthesized and its structure verified by NMR. It was shown to have similar chromatography, spectroscopy, and MS/MS fragmentation compared to the in vitro and in vivo derived metabolite. The structure was consistent with an oxidation catalyzed by AO.This non‐CYP mediated transformation is important for the metabolism of imidazoacridinones and likely plays a significant role in the metabolism of other tyrosine kinase inhibitors with imidazole and related susceptible heterocyclic scaffolds. This work presents a comprehensive investigation into this novel route of drug metabolism.

Biologically relevant O,S-donor compounds. Synthesis, molybdenum complexation and xanthine oxidase inhibition

Two O,S-donor ligands, hydroxythiopyrone and hydroxythiopyridinone derivatives, were developed and studied, as well as the corresponding O,O-derivatives, with a view to their potential pharmacological applications as xanthine oxidase (XO) inhibitors. The biological assays revealed that the O,S-ligands present high inhibitory activity towards XO (nanomolar order, close to that of the pharmaceutical drug allopurinol), in contrast to the corresponding O,O-analogues. Due to the biomedical relevance of this molybdenum-containing enzyme, the corresponding Mo(VI) complexes were studied both in solution and in the solid state, aimed at identifying the source of the biological properties. The solution studies showed that, in comparison with the O,O-analogues, the Mo(VI) complexes with the O,S-ligands present some stabilization, which is even more pronounced for the reduced Mo(IV) species. The crystal structures of the Mo(VI) complexes with the hydroxythiopyrone revealed good flexibility of the coordination modes, with two structural isomers and two polymorphic forms for a mononuclear and a binuclear species, respectively. These results give some support to mechanistic proposals for the XO inhibition involving the interaction of the thione group with the molybdenum cofactor, thus indicating a role of the sulfur atom in the XO inhibition.

Oxidation Reaction by Xanthine Oxidase. Theoretical Study of Reaction Mechanism

The oxidation process by molybdenum-containing enzyme, xanthine oxidase, is theoretically studied with a model complex representing the reaction center and a typical benchmark substrate, formamide. Comparisons were systematically made among reaction mechanisms proposed previously. In the concerted and stepwise mechanisms that were theoretically discussed previously, the oxidation reaction takes place with a moderate activation barrier. However, the product is less stable than the reactant complex, which indicates that these mechanisms are unlikely. Moreover, the product of the concerted mechanism is not consistent with the isotope experimental result. In addition to those mechanisms, another mechanism initiated by the deprotonation of the active site was newly investigated here. In the transition state of this reaction, the carbon atom of formamide interacts with the oxo ligand of the Mo center and the hydrogen atom is moving from the carbon atom to the thioxo ligand. This reaction takes place with a moderate activation barrier and considerably large exothermicity. Furthermore, the product by this mechanism is consistent with the isotope experimental result. Also, our computations clearly show that the deprotonation of the active site occurs with considerable exothermicity in the presence of glutamic acid and substrate. The intermediate of the stepwise mechanism could not be optimized in the case of the deprotonated active site. From all these results, it should be concluded that the one-step mechanism with the deprotonated active site is the most plausible.

Molecular Basis of Intramolecular Electron Transfer in Sulfite-oxidizing Enzymes Is Revealed by High Resolution Structure of a Heterodimeric Complex of the Catalytic Molybdopterin Subunit and a c-Type Cytochrome Subunit

Sulfite-oxidizing molybdoenzymes convert the highly reactive and therefore toxic sulfite to sulfate and have been identified in insects, animals, plants, and bacteria. Although the well studied enzymes from higher animals serve to detoxify sulfite that arises from the catabolism of sulfur-containing amino acids, the bacterial enzymes have a central role in converting sulfite formed during dissimilatory oxidation of reduced sulfur compounds. Here we describe the structure of the Starkeya novella sulfite dehydrogenase, a heterodimeric complex of the catalytic molybdopterin subunit and a c-type cytochrome subunit, that reveals the molecular mechanism of intramolecular electron transfer in sulfite-oxidizing enzymes. The close approach of the two redox centers in the protein complex (Mo-Fe distance 16.6 A) allows for rapid electron transfer via tunnelling or aided by the protein environment. The high resolution structure of the complex has allowed the identification of potential through-bond pathways for electron transfer including a direct link via Arg-55A and/or an aromatic-mediated pathway. A potential site of electron transfer to an external acceptor cytochrome c was also identified on the SorB subunit on the opposite side to the interaction with the catalytic SorA subunit.

In Vitro Molybdenum Ligation to Molybdopterin Using Purified Components

We have previously shown that Escherichia coli MoeA and MogA are required in vivo for the final step of molybdenum cofactor biosynthesis, the addition of the molybdenum atom to the dithiolene of molybdopterin. MoeA was also shown to facilitate the addition of molybdenum in an assay using crude extracts from E. coli moeA(-) cells. The experiments detailed in this report utilized an in vitro assay for MoeA-mediated molybdenum ligation to de novo synthesized molybdopterin using only purified components and monitoring the reconstitution of human aposulfite oxidase. In this assay, maximum activation was achieved by delaying the addition of aposulfite oxidase to allow for adequate molybdenum coordination to occur. Tungsten, which substitutes for molybdenum in hyperthermophilic organisms, could also be ligated to molybdopterin using this system, though not as efficiently as molybdenum. Addition of thiol compounds to the assay inhibited activity. Addition of MogA also inhibited the reaction. However, in the presence of ATP and magnesium, addition of MogA to the assay increased the level of aposulfite oxidase reconstitution beyond that observed with MoeA alone. This effect was not observed in the absence of MoeA. The results presented here demonstrate that MoeA is responsible for mediating molybdenum ligation to molybdopterin, whereas MogA stimulates this activity in an ATP-dependent manner.

Resonance Raman Studies of Xanthine Oxidase: the Reduced Enzyme−Product Complex with Violapterin

A study of the molecular, electronic, and vibrational characteristics of the molybdenum-containing enzyme complex xanthine oxidase with violapterin has been carried out using density functional theory calculations and resonance Raman spectroscopy. The electronic structure calculations were carried out on a model consisting of the enzyme molybdopterin cofactor [in the four-valent, reduced state; Mo(IV)O(SH)] covalently linked to violapterin (1H,3H,8H-pteridine-2,4,7-trione in the neutral form) via an oxygen bridge, Mo-O-C7. Full geometry optimizations were performed for all models using the SDD basis set and the three-parameter exchange functional of Becke combined with the Lee, Yang, and Parr correlational functional. Harmonic vibrational frequencies were determined for a variety of isotopes in an attempt to correlate experimentally observed shifts upon 18O-labeling of the Mo-OR bridge to bound product as well as shifts seen upon substitution of solvent-exchangeable protons in samples prepared in D2O. The theoretical vibrational frequencies compared favorably with experimentally observed vibrational modes in the resonance Raman spectra of the reduced xanthine oxidase-violapterin complex prepared in H2O and D2O and with 18O-labeled product. Correlating the isotopic shifts from the calculations with those from the resonance Raman experiments resulted in complete normal mode assignments for all modes observed in the 350-1750 cm(-1) range. The present work demonstrates that a model in which the violapterin is coordinated to the molybdenum of the active site in a simple end-on manner via the hydroxyl group introduced by an enzyme accurately predicts the observed resonance Raman spectrum of the complex. Given the numerous modes involving the bridging oxygen, a side-on binding mode can be eliminated.

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase

By using a bioinformatics screen of the Escherichia coli genome for potential molybdenum-containing enzymes, we have identified a novel oxidoreductase conserved in the majority of Gram-negative bacteria. The identified operon encodes for a proposed heterodimer, YedYZ in Escherichia coli, consisting of a soluble catalytic subunit termed YedY, which is likely anchored to the membrane by a heme-containing trans-membrane subunit termed YedZ. YedY is uniquely characterized by the presence of one molybdenum molybdopterin not conjugated by an additional nucleotide, and it represents the only molybdoenzyme isolated from E. coli characterized by the presence of this cofactor form. We have further characterized the catalytic subunit YedY in both the molybdenum- and tungsten-substituted forms by using crystallographic analysis. YedY is very distinct in overall architecture from all known bacterial reductases but does show some similarity with the catalytic domain of the eukaryotic chicken liver sulfite oxidase. However, the strictly conserved residues involved in the metal coordination sphere and in the substrate binding pocket of YedY are strikingly different from that of chicken liver sulfite oxidase, suggesting a catalytic activity more in keeping with a reductase than that of a sulfite oxidase. Preliminary kinetic analysis of YedY with a variety of substrates supports our proposal that YedY and its many orthologues may represent a new type of membrane-associated bacterial reductase.

Kinetics and specificity of guinea pig liver aldehyde oxidase and bovine milk xanthine oxidase towards substituted benzaldehydes.

Molybdenum-containing enzymes, aldehyde oxidase and xanthine oxidase, are important in the oxidation of N-heterocyclic xenobiotics. However, the role of these enzymes in the oxidation of drug-derived aldehydes has not been established. The present investigation describes the interaction of eleven structurally related benzaldehydes with guinea pig liver aldehyde oxidase and bovine milk xanthine oxidase, since they have similar substrate specificity to human molybdenum hydroxylases. The compounds under test included mono-hydroxy and mono-methoxy benzaldehydes as well as 3,4-dihydroxy-, 3-hydroxy-4-methoxy-, 4-hydroxy-3-methoxy-, and 3,4-dimethoxy-benzaldehydes. In addition, various amines and catechols were tested with the molybdenum hydroxylases as inhibitors of benzaldehyde oxidation. The kinetic constants have shown that hydroxy-, and methoxy-benzaldehydes are excellent substrates for aldehyde oxidase (Km values 5x10(-6) M to 1x10(-5) M) with lower affinities for xanthine oxidase (Km values around 10(-4) M). Therefore, aldehyde oxidase activity may be a significant factor in the oxidation of the aromatic aldehydes generated from amines and alkyl benzenes during drug metabolism. Compounds with a 3-methoxy group showed relatively high Vmax values with aldehyde oxidase, whereas the presence of a 3-hydroxy group resulted in minimal Vmax values or no reaction. In addition, amines acted as weak inhibitors, whereas catechols had a more pronounced inhibitory effect on the aldehyde oxidase activity. It is therefore possible that aldehyde oxidase may be critical in the oxidation of the analogous phenylacetaldehydes derived from dopamine and noradrenaline.

Kinetics and specificity of guinea pig liver aldehyde oxidase and bovine milk xanthine oxidase towards substituted benzaldehydes.

Molybdenum-containing enzymes, aldehyde oxidase and xanthine oxidase, are important in the oxidation of N-heterocyclic xenobiotics. However, the role of these enzymes in the oxidation of drug-derived aldehydes has not been established. The present investigation describes the interaction of eleven structurally related benzaldehydes with guinea pig liver aldehyde oxidase and bovine milk xanthine oxidase, since they have similar substrate specificity to human molybdenum hydroxylases. The compounds under test included mono-hydroxy and mono-methoxy benzaldehydes as well as 3,4-dihydroxy-, 3-hydroxy-4-methoxy-, 4-hydroxy-3-methoxy-, and 3,4-dimethoxy-benzaldehydes. In addition, various amines and catechols were tested with the molybdenum hydroxylases as inhibitors of benzaldehyde oxidation. The kinetic constants have shown that hydroxy-, and methoxy-benzaldehydes are excellent substrates for aldehyde oxidase (Km values 5x10(-6) M to 1x10(-5) M) with lower affinities for xanthine oxidase (Km values around 10(-4) M). Therefore, aldehyde oxidase activity may be a significant factor in the oxidation of the aromatic aldehydes generated from amines and alkyl benzenes during drug metabolism. Compounds with a 3-methoxy group showed relatively high Vmax values with aldehyde oxidase, whereas the presence of a 3-hydroxy group resulted in minimal Vmax values or no reaction. In addition, amines acted as weak inhibitors, whereas catechols had a more pronounced inhibitory effect on the aldehyde oxidase activity. It is therefore possible that aldehyde oxidase may be critical in the oxidation of the analogous phenylacetaldehydes derived from dopamine and noradrenaline.

In Rhodobacter sphaeroides respiratory nitrate reductase, the kinetics of substrate binding favors intramolecular electron transfer.

The respiratory nitrate reductase (NapAB) from Rb. sphaeroides is a periplasmic molybdenum-containing enzyme which belongs to the DMSO reductase family. We report a study of NapAB by protein film voltammetry (PFV), and we present the first quantitative interpretation of the complex redox-state dependence of activity that has also been observed with other related enzymes. The model we use to fit the data assumes that binding of substrate partly limits turnover and is faster and weaker when the Mo ion is in the V oxidation state than when it is fully reduced. We explain how the presence in the catalytic cycle of such slow chemical steps coupled to electron transfer to the active site decreases the driving force required to reduce the MoV ion and makes exergonic the last intramolecular electron-transfer step (between the proximal cubane and the Mo cofactor). Importantly, comparison is made with all Mo enzymes for which PFV data are available, and we emphasize general features of the energetics of the catalytic cycles in enzymes of the DMSO reductase family.

Studies on the mechanism of action of xanthine oxidase

Recent studies of the reaction mechanism of the molybdenum-containing enzyme xanthine oxidase are presented. The pH-dependence of both the steady-state and rapid reaction kinetics of the enzyme exhibits is bell-shaped, with pKas for the acid and alkaline limbs of 6.6 and 7.4, respectively. These are assigned to ionizations of an active site base and substrate, respectively, with the implication that enzyme acts on the neutral rather than monoanionic form of the purine substrate. A computational study provides evidence that in the course of the reaction tautomerization of substrate occurs, with a proton moving from N-3 to N-9 in the course of the reaction – enzyme facilitation of this tautomerization may contribute as much as 24 kcal/mol in transition state stabilization for the reaction. Electron spin echo (ESEEM) and electron-nuclear double resonance (ENDOR) studies of the so-called “very rapid” Mo(V) intermediate of the reaction, the latter work using a newly synthesized form of the substrate 2-hydroxy-6-methylpurine that has been selectively isotopically labeled at C-8, indicates that product is bound to the molybdenum of the active site in a simple, end-on fashion, consistent with a reaction mechanism involving nucleophilic attack of a (deprotonated) Mo–OH on the C-8 position of substrate. A kinetic study using a series of purines has failed to identify a correlation between the one-electron reduction potential for substrate and catalytic effectiveness, indicating that a reaction mechanism initiated by one-electron, outer-sphere electron transfer is unlikely. Finally, a consideration of the active site structure in the context of the above work suggests specific amino acid residues to target for site-directed mutagenesis studies. Preliminary experiments with two such mutants are entirely consistent with the proposed catalytic roles of two active site glutamate residues.

Molybdenum Cofactor-Containing Oxidoreductase Family in Plants

Recent investigations on plant molybdenum-containing enzymes that include xanthine dehydrogenase (EC 1.1.1.204) and xanthine oxidase (EC 1.1.3.22), nitrate reductase (EC 1.7.1.1-3), aldehyde oxidase (EC 1.2.3.1), and sulfite oxidase (EC 1.8.3.1) are reviewed. The enzymes belong to closely related protein family and share common structural features. Special attention is being paid to the recently solved crystal structures their implications for the substrate binding and catalytic mechanism.

Plant molybdoenzymes and their response to stress

Molybdenum-containing enzymes catalyse basic reactions in the nitrogen, sulphur and carbon metabolism. Mo-enzymes contain at their catalytic sites an organometallic structure termed the molybdenum cofactor or Moco. In higher plants, Moco is incorporated into the apoproteins of four enzymes: nitrate reductase (EC 1.6.6.1-3; NR), xanthine dehydrogenase (EC 1.1.1.204; XDH), aldehyde oxidase (EC 1.2.3.1; AO) and sulphite oxidase (EC1.8.3.1; SO). Molybdoenzymes in plants are key enzymes in nitrate assimilation, purine metabolism, hormone biosynthesis, and most probably in sulphite detoxification. They are considered to be involved in stress acclimation processes and, therefore, elucidation of the mechanisms of their response to environmental stress conditions is of agricultural importance for the improvement of plant stress tolerance. Here we would like to give a brief functional and biochemical characteristic of the four plant molybdoenzymes and to focus mainly on their sensitivity to environmental stress factors.

Intramolecular electron transfer in a bacterial sulfite dehydrogenase.

Sulfite dehydrogenase (SDH) from Starkeya novella, a sulfite-oxidizing molybdenum-containing enzyme, has a novel tightly bound alphabeta-heterodimeric structure in which the Mo cofactor and the c-type heme are located on different subunits. Flash photolysis studies of intramolecular electron transfer (IET) in SDH show that the process is first-order, independent of solution viscosity, and not inhibited by sulfate, which strongly indicates that IET in SDH proceeds directly through the protein medium and does not involve substantial movement of the two subunits relative to each other. The IET results for SDH contrast with those for chicken and human sulfite oxidase (SO) in which the molybdenum domain is linked to a b-type heme domain through a flexible loop, and IET shows a remarkable dependence on sulfate concentration and viscosity that has been ascribed to interdomain docking. The results for SDH provide additional support for the interdomain docking hypothesis in animal SO and clearly demonstrate that dependence of IET on viscosity and sulfate is not an inherent property of all sulfite-oxidizing molybdenum enzymes.

Ziprasidone metabolism, aldehyde oxidase, and clinical implications.

Ziprasidone (Geodon, Zeldox), a recently approved atypical antipsychotic agent for the treatment of schizophrenia, undergoes extensive metabolism in humans with very little (<5%) of the dose excreted as unchanged drug. Two enzyme systems have been implicated in ziprasidone metabolism: the cytosolic enzyme, aldehyde oxidase, catalyzes the predominant reductive pathway, and cytochrome P4503A4 (CYP3A4) is responsible for two alternative oxidation pathways. The involvement of two competing pathways in ziprasidone metabolism greatly reduces the potential for pharmacokinetic interactions between ziprasidone and other drugs. Because CYP3A4 only mediates one third of ziprasidone metabolism, the likelihood of interactions between ziprasidone and CYP3A4 inhibitors/ substrates is low. Furthermore, aldehyde oxidase activity does not appear to be altered when drugs or xenobiotics are coadministered. Aldehyde oxidase, a molybdenum-containing enzyme, catalyzes the oxidation of N-heterocyclic drugs such as famciclovir and zaleplon, in addition to reducing some agents such as zonisamide. Both reactions can occur simultaneously. Although in vitro inhibitors of aldehyde oxidase have been identified, there are no reported clinical interactions with aldehyde oxidase inhibitors or inducers. There is no evidence of genetic polymorphism in aldehyde oxidase, and thus it not surprising that ziprasidone exposure demonstrates unimodality in humans. Aldehyde oxidase is unrelated to the similarly named enzyme aldehyde dehydrogenase, which is predominantly responsible for the oxidation of acetaldehyde during ethanol metabolism. Consequently, it is unlikely that there would be any pharmacokinetic interaction between ethanol and ziprasidone.

In vivo detection of molybdate-binding proteins using a competition assay with ModE in Escherichia coli.

Molybdenum is an important trace element as it forms the essential part of the active site in all molybdenum-containing enzymes. We have designed an assay for the in vivo detection of molybdate binding to proteins in Escherichia coli. The assay is based on (i). the molybdate-dependent transcriptional regulation of the moa operon by the ModE protein, and (ii). the competition for molybdate between ModE and other molybdate-binding proteins in the cytoplasm of E. coli. We were able to verify in vivo molybdate binding to three different bacterial proteins that are known to bind molybdate. This sensitive in vivo system allows the testing of different proteins for molybdate binding under in vivo conditions and will facilitate the identification of other cellular factors needed for molybdate binding. As a first example, we examined the eukaryotic protein Cnx1 that is involved in the last step of molybdenum cofactor biosynthesis in plants, and show that it is able to compete with ModE for molybdate in a molybdopterin-dependent fashion.