Molybdenum Active Site Research Articles

Direct catalytic electrochemistry of sulfite dehydrogenase: Mechanistic insights and contrasts with related Mo enzymes

Under hydrodynamic electrochemical conditions with slow cyclic voltammetry sweep rates we have been able to probe catalytic events at the molybdenum active site of sulfite dehydrogenase (SDH) from Starkeya novella adsorbed on an edge plane graphite electrode within a polylysine film. The electrochemically driven catalytic behaviour of SDH mirrors that seen in solution assays suggesting that the adsorbed enzyme retains its native activity. However, at high sulfite concentrations, the voltammetric waveform transforms from the expected sigmoidal profile to a peak-shaped response, similar to that reported for the molybdenum enzymes DMSO reductase and nitrate reductase (NarGHI and NapAB) where a redox reaction at the active site has been associated with a switch to lower activity at high overpotentials. This is the first time a similar phenomenon has been observed in a Mo-containing oxidase/dehydrogenase, which raises a number of interesting mechanistic problems. The potential at which the activity of SDH becomes attenuated only emerges at saturating substrate conditions and occurs at a potential (ca. + 320mV vs NHE) well removed from any known redox couple in the enzyme. These results cannot be explained by the same mechanism adopted for DMSO reductase and nitrate reductase catalysis.

Access to the Active Site of Periplasmic Nitrate Reductase: Insights from Site-Directed Mutagenesis and Zinc Inhibition Studies

The periplasmic nitrate reductase (NapAB), a member of the DMSO reductase superfamily, catalyzes the first step of the denitrification process in bacteria. In this heterodimer, a di-heme NapB subunit is associated to the catalytic NapA subunit that binds a [4Fe-4S] cluster and a bis(molybdopterin guanine dinucleotide) cofactor. Here, we report the kinetic characterization of purified mutated heterodimers from Rhodobacter sphaeroides. By combining site-directed mutagenesis, redox potentiometry, EPR spectroscopy, and enzymatic characterization, we investigate the catalytic role of two conserved residues (M153 and R392) located in the vicinity of the molybdenum active site. We demonstrate that M153 and R392 are involved in nitrate binding: the Vm measured on the M153A and R392A mutants are similar to that measured on the wild-type enzyme, whereas the Km for nitrate is increased 10-fold and 200-fold, respectively. The use of an alternative enzymatic assay led us to discover that NapAB is uncompetitively inhibited by Zn2+ ions (Ki' = 1 microM). We used this property to further probe the active site access in the mutant enzymes. It is proposed that R392 acts as a filter by preventing a direct reduction of the Mo atom by small reducing molecules and partially protecting the active site against zinc inhibition. In addition, we show that M153 is a key residue mediating this inhibition likely by coordinating Zn2+ ions via its sulfur atom. This residue is not conserved in the DMSO reductase superfamily while it is conserved in the periplasmic nitrate reductase family. Zinc inhibition is therefore likely to be specific and restricted to periplasmic nitrate reductases.

Heterodimeric nitrate reductase (NapAB) from Cupriavidus necator H16: purification, crystallization and preliminary X-ray analysis.

The periplasmic nitrate reductase from Cupriavidus necator (also known as Ralstonia eutropha) is a heterodimer that is able to reduce nitrate to nitrite. It comprises a 91 kDa catalytic subunit (NapA) and a 17 kDa subunit (NapB) that is involved in electron transfer. The larger subunit contains a molybdenum active site with a bis-molybdopterin guanine dinucleotide cofactor as well as one [4Fe-4S] cluster, while the small subunit is a di-haem c-type cytochrome. Crystals of the oxidized form of this enzyme were obtained using polyethylene glycol 3350 as precipitant. A single crystal grown at the High Throughput Crystallization Laboratory of the EMBL in Grenoble diffracted to beyond 1.5 A at the ESRF (ID14-1), which is the highest resolution reported to date for a nitrate reductase. The unit-cell parameters are a = 142.2, b = 82.4, c = 96.8 A, beta = 100.7 degrees, space group C2, and one heterodimer is present per asymmetric unit.

X-ray Absorption Spectroscopic Characterization of the Molybdenum Site of Escherichia coli Dimethyl Sulfoxide Reductase

Structural studies of dimethyl sulfoxide (DMSO) reductases were hampered by modification of the active site during purification. We report an X-ray absorption spectroscopic analysis of the molybdenum active site of Escherichia coli DMSO reductase contained within its native membranes. The enzyme in these preparations is expected to be very close to the form found in vivo. The oxidized active site was found to have four Mo-S ligands at 2.43 A, one Mo=O at 1.71 A, and a longer Mo-O at 1.90 A. We conclude that the oxidized enzyme is a monooxomolybdenum(VI) species coordinated by two molybdopterin dithiolenes and a serine. The bond lengths determined for E. coli DMSO reductase are very similar to those determined for the well-characterized Rhodobacter sphaeroides DMSO reductase, suggesting similar active site structures for the two enzymes. Furthermore, our results suggest that the form found in vivo is the monooxobis(molybdopterin) species.

Formate-reduced E. coli formate dehydrogenase H: the reinterpretation of the crystal structure suggests a new reaction mechanism

Re-evaluation of the crystallographic data of the molybdenum-containing E. coli formate dehydrogenase H (Boyington et al. Science 275:1305-1308, 1997), reported in two redox states, reveals important structural differences for the formate-reduced form, with large implications for the reaction mechanism proposed in that work. We have re-refined the reduced structure with revised protocols and found substantial rearrangement in some parts of it. The original model is essentially correct but an important loop close to the molybdenum active site was mistraced, and, therefore, catalytic relevant residues were located in wrong positions. In particular selenocysteine-140, a ligand of molybdenum in the original work, and essential for catalysis, is no longer bound to the metal after reduction of the enzyme with formate. These results are incompatible with the originally proposed reaction mechanism. On the basis of our new interpretation, we have revised and proposed a new reaction mechanism, which reconciles the new X-ray model with previous biochemical and extended X-ray absorption fine structure data.

Enzymatic and catalytic reduction of dinitrogen to ammonia: Density functional theory characterization of alternative molybdenum active sites

AbstractWe used density functional calculations to model dinitrogen reduction by a FeMo cofactor containing a central nitrogen atom and by a Mo‐based catalyst. Plausible intermediates, reaction pathways, and relative energetics in the enzymatic and catalytic reduction of N2 to ammonia at a single Mo center are explored. Calculations indicate that the binding of N2 to the Mo atom and the subsequent multiple proton–electron transfer to dinitrogen and its protonated species involved in the conversion of N2 are feasible energetically. In the reduction of N2 the Mo atom experiences a cycled oxidation state from Mo(IV) to Mo(VI) by nitrogenase and from Mo(III) to Mo(VI) by the molybdenum catalyst, respectively, tuning the gradual reduction of N2. Such a wide range of oxidation states exhibited by the Mo center is crucial for the gradual reduction process via successive proton–electron transfer. Present results suggest that the Mo atom in the N‐centered FeMo cofactor is a likely alternative active site for dinitrogen binding and reduction under mild conditions once there is an empty site available at the Mo site. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Role of Conserved Tyrosine 343 in Intramolecular Electron Transfer in Human Sulfite Oxidase

Tyrosine 343 in human sulfite oxidase (SO) is conserved in all SOs sequenced to date. Intramolecular electron transfer (IET) rates between reduced heme (Fe(II)) and oxidized molybdenum (Mo(VI)) in the recombinant wild-type and Y343F human SO were measured for the first time by flash photolysis. The IET rate in wild-type human SO at pH 7.4 is about 37% of that in chicken SO with a similar decrease in k(cat). Steady-state kinetic analysis of the Y343F mutant showed an increase in K(m)(sulfite) and a decrease in k(cat) resulting in a 23-fold attenuation in the specificity constant k(cat)/K(m)(sulfite) at the optimum pH value of 8.25. This indicates that Tyr-343 is involved in the binding of the substrate and catalysis within the molybdenum active site. Furthermore, the IET rate constant in the mutant at pH 6.0 is only about one-tenth that of the wild-type enzyme, suggesting that the OH group of Tyr-343 is vital for efficient IET in SO. The pH dependences of IET rate constants in the wild-type and mutant SO are consistent with the previously proposed coupled electron-proton transfer mechanism.

Site-Directed Mutagenesis of Dimethyl Sulfoxide Reductase from Rhodobacter capsulatus: Characterization of a Y114 → F Mutant

A system for expressing site-directed mutants of the molybdenum enzyme dimethyl sulfoxide reductase from Rhodobacter capsulatus in the natural host was constructed. This system was used to generate and express dimethyl sulfoxide reductase with a Y114F mutation. The Y114F mutant had an increased k(cat) and increased K(m) toward both dimethyl sulfoxide and trimethylamine N-oxide compared to the native enzyme, and the value of k(cat)/K(m) was lower for both substrates in the mutant enzyme. The Y114F mutant, as isolated, was able to oxidize dimethyl sulfide with phenazine ethosulfate as the electron acceptor but with a lower k(cat) than that of the native enzyme. The pH optimum of dimethyl sulfide:acceptor oxidoreductase activity in the Y114F mutant was shown to be shifted by +1 pH unit compared to the native enzyme. The Y114F mutant did not form a pink complex with dimethyl sulfide, which is characteristic of the native enzyme. The mutant enzyme showed a large increase in the K(d) for DMS. Direct electrochemistry showed that the Mo(V)/Mo(IV) couple was unaffected by the Y114F mutant, but the midpoint potential of the Mo(VI)/Mo(V) couple was raised by about 50 mV. These data confirm that the Y114 residue plays a critical role in oxidation-reduction processes at the molybdenum active site and in oxygen atom transfer associated with sulfoxide reduction.

A voltammetric study of interdomain electron transfer within sulfite oxidase.

Protein film voltammetry of chicken liver sulfite oxidase (SO) bound at the pyrolytic graphite "edge" or modified gold electrodes shows that catalytic electron transport is controlled by the inherent electrochemical characteristics of the heme b domain and conformational changes that allow intramolecular electron transfer with the molybdenum active site. In the absence of sulfite, a single nonturnover electrochemical signal is observed at +90 mV (vs SHE) that is assigned to heme b. In the presence of sulfite, this signal transforms into a catalytic wave at similar potential. The shape and negligible pH dependence of this wave indicate that catalytic turnover is controlled by the one-electron transfers through heme b. The smaller turnover numbers obtained in this experiment (k(cat) approximately 2-4 s(-1), as compared to 100 s(-1) in solution) suggest that only a small fraction of SO is bound at the electrode in a manner that permits the conformational change necessary for fast interdomain electron transfer.

The DMSO Reductase Family of Microbial Molybdenum Enzymes; Molecular Properties and Role in the Dissimilatory Reduction of Toxic Elements

The dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes is a large and diverse group that is found in bacteria and archaea. These enzymes are characterised by a bis(molybdopterin guanine dinucleotide)Mo form of the molybdenum cofactor, and they are particularly important in anaerobic respiration including the dissimilatory reduction of certain toxic oxoanions. The structural and phylogenetic relationship between the proteins of this family is discussed. High-resolution crystal structures of enzymes of the DMSO reductase family have revealed a high degree of similarity in tertiary structure. However, there is considerable variation in the structure of the molybdenum active site and it seems likely that these subtle but important differences lead to the great diversity of function seen in this family of enzymes. This diversity of catalytic capability is associated with several distinct pathways of electron transport.

The Chemical Evolution of a Nitrogenase Model, XXIII. The Nature of the Active Site and the Role of Homocitric Acid in MoFe-Nitrogenase

Abstract The iron-molybdenum cofactor (FeMo-co) of bacterial nitrogenase is a heterometallic cluster of composition MoFe7S9 that is attached to the apoprotein by a coordinative Mo-N bond to the imidazole group of hisα442, and by a Fe-S bond to cysα215. The molybdenum atom of FeMo-co in the enzyme in addition is coordinated to one molecule of homocitrate (hc), which is required for maximal N2 reducing activity. The molybdenum atom in the enzyme-bound FeMo-co thus is hexacoordinated and cannot react with substrates unless free coordination sites are made available. It is proposed that the reactions of the substrates o f nitrogenase occur at a molybdenum active site consisting of a mononuclear molybdenum homocitrate complex attached to hisα442 of the apoprotein that in the functional enzyme is generated from FeMo-co by a reversible, redox-linked dissociation of the Fe7S9-cys cluster. Studies with catalytic model systems consisting of complexes of molybdenum with imidazole and hydroxocarboxylate ligands support this proposal and provide a rationale for the specific activating effect of homocitrate in nitrogenase.

An MCD spectroscopic study of the molybdenum active site in sulfite oxidase: insight into the role of coordinated cysteine

Temperature-dependent magnetic circular dichroism (MCD) spectroscopy has been used for the first time to probe the electronic structure of the Mo active site in sulfite oxidase (SO). The enzyme was poised in the catalytically relevant [Mo(V):Fe(II)] state by anaerobic reduction of the enzyme with the natural substrate, sulfite, in the absence of the physiological oxidant cytochrome c. The [Mo(V):Fe(II)] state is of particular importance, as it is proposed to be a catalytic intermediate in the oxidative half reaction, where SO is reoxidized to the resting [Mo(VI):Fe(III)] state by two sequential one-electron transfers to cytochrome c. The MCD spectrum of the enzyme shows no charge transfer transitions below ∼17 000 cm −1. This has been interpreted to result from (1) a severe reduction in ene-1,2-dithiolate sulfur in-plane and out-of-plane p orbital mixing, (2) a decrease in the dithiolate sulfur out-of-plane p-Mo d xy orbital overlap, and (3) an orthogonal orientation between the vertical cysteine sulfur p (perpendicular to the Mo–S cys σ-bond) and Mo d xy orbitals. The spectroscopically determined cysteine sulfur p-Mo d xy bonding scheme in the [Mo(V):Fe(II)] state is consistent with the crystallographically determined O–Mo–S cys–C dihedral angle of ∼90° and precludes a covalent interaction between the vertical cysteine sulfur p orbital and Mo d xy , effectively decoupling the cysteine from an effective through-bond electron transfer pathway. We have tentatively assigned a 22 250 cm −1 positive C-term feature in the MCD as the cysteine S(σ)→Mo d xy charge transfer that becomes allowed by a combination of configuration interaction and low-symmetry; however, the orbital overlap is anticipated to be quite small due to the near orthogonality of these orbitals. Therefore, we propose that the primary role of the coordinated cysteine is to decrease the effective nuclear charge on Mo by charge donation to the metal, statically poising the active site at more negative reduction potentials during electron transfer (ET) regeneration. Finally, the results of this study are consistent with the pyranopterin ene-1,2-dithiolate acting to couple the Mo site into efficient superexchange pathways for ET regeneration following oxygen atom transfer to the substrate.

Structure and function of mononuclear molybdenum enzymes

An account of recent advances in our understanding of enzymes possessing mononuclear molybdenum active sites is presented. On the basis of a variety of structural studies, and in conjunction with comparisons among the growing number of these enzymes for which the amino acid sequences are known, it is evident that these enzymes fall into three principal families as represented by xanthine oxidase, sulfite oxidase and DMSO reductase. Structural features of the active sites of these three families are compared and contrasted, and specific mechanistic implications of the recently reported crystal structure for the aldehyde oxidoreductase from Desulfovibrio gigas are discussed.

Spectroscopic investigation of the molybdenum active sites on MoVIheterogeneous catalysts for alkene epoxidation

Spectroscopic and spectromagnetic investigations on molybdenum centres in MoO3· H2O and its polymer-supported form have been carried out. Both were tested as catalysts for cyclohexene epoxidation in a heterogeneous phase; both needed activating pretreatment before the reaction. XPS and EPR data show that the metal is mainly present as MoVI. The activation process increases the acidic character of MoVI and its efficiency depends both on the oxidizing power of the activating reactant and on the accessibility of the metal to the reactant. The steric hindrance of MoVI lowers the catalytic activity owing to the replacement of H2O by carboxylic groups of the functionalized resin.

Studies of the reductive half-reaction of milk xanthine dehydrogenase.

The reductive half-reaction of milk xanthine dehydrogenase (XDH) with NADH and with xanthine has been studied at pH 7.5, 25 degree C. NADH reduces XDH to the two-electron reduced form at a rate of 18 s-1, independent of NADH concentration over the range studied. Further reduction by NADH to the four-electron state is inhibited by excess NADH. Subsequent binding of NADH to the four-electron reduced form of the enzyme causes the redistribution of one electron from the flavin to the molybdenum center. The four-electron reduced species reached through reduction by NADH is the same as the species obtained upon reaction of NAD with fully reduced XDH. In contrast, xanthine rapidly reduces XDH to the four-electron level; further reduction is comparatively slow and is inhibited by excess xanthine. Studies using substoichiometric xanthine show that the reaction of XDH with 1 equivalent of xanthine involves rapid substrate binding and rapid reduction of the molybdenum center of the enzyme. Before the release of urate from the molybdenum active site, an electron is transferred at 15 s-1 from the reduced molybdenum center to one of the iron-sulfur centers of XDH. Urate is then released at a rate of 13 s-1, followed by a rapid electron redistribution within the protein. The reductive half-reaction of XDH with xanthine is rate-limiting in xanthine/NAD turnover, which appears to occur between the two- and four-electron reduced enzyme species. The reduction of XDH by substoichiometric amounts of the fluorescent substrate xanthopterin was also studied. This reaction, monitored by changes in both absorbance and fluorescence, was found to involve the formation of two molybdenum complexes (an Eox.S complex and an Ered.P complex) followed by the release of the product, leucopterin.

Substrate inhibition of xanthine oxidase and its influence on superoxide radical production

The influence of substrate inhibition on xanthine oxidase-intramolecular electron transport was studied by steady-state kinetic analysis. Experiments with hypoxanthine and xanthine up to 900 μM indicated an inhibition pattern which fitted an equation of the general form ν 0 = ν max · [SJ/( K m + a[S] + b[S] 2/ K i). Univalent electron flux to oxygen was favored at substrate concentrations above 50 μM. This augmentation of univalent flux percentage that appeared at a high substrate concentration was greater for hypoxanthine than xanthine and at pH 8.3 than at 9.5. Our results support a mechanism of inhibition in which a substrate-reduced enzyme, non-productive Michaelis complex was formed. It is possible that this non-productive complex favored the univalent pathway of enzyme reoxidation (superoxide production) by increasing the midpoint redox potential of the molybdenum active site.

Computer graphic study on models of the molybdenum cofactor of xanthine oxidase.

Within the scope of our molecular modeling studies on xanthine oxidase (XOD) inhibition by purine analogs we were interested to build up a three-dimensional model of the molybdenum active site. Spectroscopic data indicated that a Mo (VI)atom which is coordinated to sulfur, oxygen and/or nitrogen is clearly involved in substrate binding. In the present study, those data and X-ray crystallography data were used to reconstruct molybdenum-organic complexes from models proposed in the literature. The computer graphic-assisted modeling and evaluation of the model complexes show that the description of the molybdenum center needs further refinement.

Nonenzymatic simulation of nitrogenase reactions and the mechanism of biological nitrogen fixation.

AbstractThe development of biologically relevant model systems of nitrogenase permitted the simulation of virtually all known reactions of the nitrogen reducing enzymes under nonenzymatic conditions. On the basis of these experiments, a mechanism of biological nitrogen fixation is formulated which is in accord with the available enzymological evidence. The key reactions of the substrates of nitrogenase occur at a molybdenum active site. The non‐heme iron, which is bound to sulfur and protein‐S⊝ groups, mediates the transport of electrons to the molybdenum active site but does not participate directly in the reduction of the substrates. ATP is required for the acceleration of the reduction and activation of the molybdenum site and is hydrolyzed to ADP and inorganic phosphate. Diimine and hydrazine were detected as intermediates in the reduction of molecular nitrogen under nonenzymatic conditions.