Quercetinase, a dioxygenase containing copper

The case for an oxidopyrylium intermediate in the mechanism of quercetin dioxygenases

The quercetin dioxygenases (QDOs) are unusual metalloenzymes in that they display ring-opening dioxygenase activity with several different first-row transition metal ions which do not undergo redox changes during turnover. The QDOs are also unique in that the substrate binds as an η1-flavonolate rather than the η2 -bidentate mode seen in all reported model complexes. The flavonol substrates were early examples of excited state intramolecular proton transfer (ESIPT) phenomena, in which photoexcitation causes an H-atom exchange between the adjacent hydroxyl and ketone, generating an oxidopyrylium emissive state. These oxidopyryliums undergo ring-opening dioxygenations analogous to the enzymatic reactions. Our hypothesis is that lability of the divalent metal ion may allow access to a reactive oxidopyrylium intermediate via coordination switching from the oxy to ketone position, which allows reaction with O2. In this report, we use a straight-forward methylation strategy to generate a panel of flavonol and thioflavonol derivatives modeling several η1- and η2-coordination modes. Methylation of 3-hydroxythioflavone generates an air stable η1 hydroxopyrylium salt, which undergoes rapid ring-opening dioxygenation by deprotonation or photoexcitation. By comparison, the η1-methoxyflavonol does not react with O2 under any condition. We find that any of the studied flavonol derivatives, η1 or η2, which demonstrates ESIPT-like oxidopyrylium emissions undergo QDO-like ring-opening reactions with dioxygen. The implications of these results concerning the mechanism of QDOs and related dioxygenases is discussed.

Flavonol dioxygenation catalysed by cobalt(II) complexes supported with 3N(COO) and 4N donor ligands: a comparative study to assess the carboxylate effects on quercetin 2,4-dioxygenase-like reactivity

Two new cobalt(II)-acetato complexes, [CoII(L3NCOO)(OAc)]·0.5H2O (1OAc·0.5H2O) and [CoII(L4N)(OAc)](PF6) (2OAc(PF6)), were synthesised using ligands L3NCOO- (Li+L3NCOO- = lithium 2-(benzyl((6'-methyl-[2,2'-bipyridin]-6-yl)methyl)amino)acetate) and L4N (N-benzyl-1-(6'-methyl-[2,2'-bipyridin]-6-yl)-N-(pyridin-2-ylmethyl)methanamine), respectively, to mimic the functional activity of cobalt(II)-quercetin-2,4-dioxygenase (CoII-2,4-QD). Additionally, Co(II)-flavonolato ternary complexes, [CoII(L3NCOO)(fla)]·H2O (1fla·H2O) and [CoII(L4N)(fla)](PF6) (2fla(PF6)), were synthesised as enzyme-substrate models. All four complexes were thoroughly characterised by elemental analyses and spectroscopic methods. Structural characterisation was performed for 1OAc·0.5H2O, 2OAc(PF6)·CH2Cl2 and 2fla+ with a perchlorate counter anion, 2fla(ClO4)·1.5H2O. Furthermore, density functional theory (DFT) calculations, time-dependent DFT (TD-DFT) and molecular orbital (MO) analysis were performed for the flavonolato adducts 1fla and 2fla+. The catalytic activities of complexes 1OAc·0.5H2O and 2OAc(PF6) in the oxygenative degradation of flavonol (multiple-turnover reactions) were investigated at 70 °C in DMF to determine the effect of the carboxylate substituent over a pyridyl donor residue on reactivity. Complex 1OAc·0.5H2O showed a higher catalytic rate than complex 2OAc(PF6). The same reactivity order was observed for single-turnover dioxygenation reactions with ternary complexes (1fla > 2fla+). The formation constants (Kf) of 1fla and 2fla+ species are comparable, implying that catalyst-substrate adduct formation occurs in similar amounts for both catalytic reactions. Therefore, the Kf values have a similar impact on reactivities. However, the oxidation potential of the bound fla-/fla˙ couple in 1fla is considerably lower than that in 2fla+. DFT calculations predicted that the negatively charged carboxylate group of ligand L3NCOO- determines the higher reactivity of 1fla with dioxygen by decreasing the oxidation potential of the bound fla-/fla˙ couple. During the dioxygenation process, the reactive Co(II)-bound flavonoxy radical was generated via single-electron transfer from the coordinated fla- to dioxygen, simultaneously forming a superoxide ion. The anionic carboxylate group improves the stability of the bound flavonoxy radical by providing substantial electron density to the electron-deficient fla˙ through the Co(II) centre, allowing the reactive fla˙ species to accumulate at an optimal concentration for effective catalysis. EPR spectroscopy successfully detected the cobalt-bound fla˙ species formed through the dioxygenation of 1fla. NBT2+ and EPR spin-trapping experiments confirmed superoxide formation during the dioxygenation process. So, the present work describes CoII-2,4-QD model studies and clarifies the function of carboxylate in quercetinase-like reactivity.

Underlying Role of Hydrophobic Environments in Tuning Metal Elements for Efficient Enzyme Catalysis

The catalytic functions of metalloenzymes are often strongly correlated with metal elements in the active sites. However, dioxygen-activating nonheme quercetin dioxygenases (QueD) are found with various first-row transition-metal ions when metal swapping inactivates their innate catalytic activity. To unveil the molecular basis of this seemingly promiscuous yet metal-specific enzyme, we transformed manganese-dependent QueD into a nickel-dependent enzyme by sequence- and structure-based directed evolution. Although the net effect of acquired mutations was primarily to rearrange hydrophobic residues in the active site pocket, biochemical, kinetic, X-ray crystallographic, spectroscopic, and computational studies suggest that these modifications in the secondary coordination spheres can adjust the electronic structure of the enzyme-substrate complex to counteract the effects induced by the metal substitution. These results explicitly demonstrate that such noncovalent interactions encrypt metal specificity in a finely modulated manner, revealing the underestimated chemical power of the hydrophobic sequence network in enzyme catalysis.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

The effects of metal cofactors on the reactivity of quercetin 2,4-dioxygenase: synthetic model studies with M(ii)-complexes (M = Mn, Co, Ni, Cu, Zn) and assessment of the regulatory factors in catalytic efficacy

This paper demonstrates the metal ion effects on the dioxygenation of flavonol catalysed by M(ii)-complexes (M = Mn, Co, Ni, Cu, Zn) as functional models of quercetin 2,4-dioxygenase-like reactivity.

The 3-His Metal Coordination Site Promotes the Coupling of Oxygen Activation to Cysteine Oxidation in Cysteine Dioxygenase

Cysteine dioxygenase (CDO) structurally resembles cupin enzymes that use a 3-His/1-Glu coordination scheme. However, the glutamate ligand is substituted with a cysteine (Cys93) residue, which forms a thioether bond with tyrosine (Tyr157) under physiological conditions. The reversion variant, C93E CDO, was generated in order to reestablish the more common 3-His/1-Glu metal ligands of the cupin superfamily. This variant provides a framework for testing the structural and functional significance of Cys93 and the cross-link in CDO. Although dioxygen consumption was observed with C93E CDO, it was not coupled with l-cysteine oxidation. Substrate analogues (d-cysteine, cysteamine, and 3-mercaptopropionate) were not viable substrates for the C93E CDO variant, although they showed variable coordinations to the iron center. The structures of C93E and cross-linked and non-cross-linked wild-type CDO were solved by X-ray crystallography to 1.91, 2.49, and 2.30 Å, respectively. The C93E CDO variant had similar overall structural properties compared to cross-linked CDO; however, the iron was coordinated by a 3-His/1-Glu geometry, leaving only two coordination sites available for dioxygen and bidentate l-cysteine binding. The hydroxyl group of Tyr157 shifted in both non-cross-linked and C93E CDO, and this displacement prevented the residue from participating in substrate stabilization. Based on these results, the divergence of the metal center of cysteine dioxygenase from the 3-His/1-Glu geometry seen with many cupin enzymes was essential for effective substrate binding. The substitution of Glu with Cys in CDO allows for a third coordination site on the iron for bidentate cysteine and monodentate oxygen binding.

Formation and Cleavage of C-C Bonds by Enzymatic Oxidation-Reduction Reactions

Many oxidation-reduction (redox) enzymes, particularly oxygenases, have roles in reactions that make and break C-C bonds. The list includes cytochrome P450 and other heme-based monooxygenases, heme-based dioxygenases, nonheme iron mono- and dioxygenases, flavoproteins, radical S-adenosylmethionine enzymes, copper enzymes, and peroxidases. Reactions involve steroids, intermediary metabolism, secondary natural products, drugs, and industrial and agricultural chemicals. Many C-C bonds are formed via either (i) coupling of diradicals or (ii) generation of unstable products that rearrange. C-C cleavage reactions involve several themes: (i) rearrangement of unstable oxidized products produced by the enzymes, (ii) oxidation and collapse of radicals or cations via rearrangement, (iii) oxygenation to yield products that are readily hydrolyzed by other enzymes, and (iv) activation of O₂ in systems in which the binding of a substrate facilitates O₂ activation. Many of the enzymes involve metals, but of these, iron is clearly predominant.

Biosynthesis of Heptacyclic Duclauxins Requires Extensive Redox Modifications of the Phenalenone Aromatic Polyketide

Duclauxins are dimeric and heptacyclic fungal polyketides with notable bioactivities. We characterized the cascade of redox transformations in the biosynthetic pathway of duclauxin from Talaromyces stipitatus. The redox reaction sequence is initiated by a cupin family dioxygenase DuxM that performs an oxidative cleavage of the peri-fused tricyclic phenalenone and affords a transient hemiketal-oxaphenalenone intermediate. Additional redox enzymes then morph the oxaphenoalenone into either an anhydride or a dihydrocoumarin-containing monomeric building block that is found in dimeric duxlauxins. Oxidative coupling between the monomers to form the initial C-C bond was shown to be catalyzed by a P450 monooxygenase, although the enzyme responsible for the second C-C bond formation was not found in the pathway. Collectively, the number and variety of redox enzymes used in the duclauxin pathway showcase Nature's strategy to generate structural complexity during natural product biosynthesis.

Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase

QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.

Set of Fe(II)-3-Hydroxyflavonolate Enzyme-Substrate Model Complexes of Atypically Coordinated Mononuclear Non-Heme Fe(II)-Dependent Quercetin 2,4-Dioxygenase

With the aim of revealing the catalytic role of atypically coordinated (3His-1Glu) active site mononuclear non-heme Fe(II)-dependent quercetin 2,4-dioxygenase (Fe-2,4-QD) and the electronic effects of the model ligands on the reactivity toward dioxygen, a set of p/m-R-substituted carboxylate-containing ligand-supported Fe(II)-3-hydroxyflavonolate complexes, [Fe^IIL^R(fla)] (L^RH: 2-{[bis(pyridin-2-ylmethyl)amino]methyl}-p/m-R-benzoic acid; R: p-OMe (1), p-Me (2), m-Br (4), and m-NO₂ (5); fla: 3-hydroxyflavonolate), were synthesized and characterized as structural and functional models for the ES (enzyme-substrate) complexes of Fe-2,4-QD. [Fe^IIL^R(fla)] show relatively high enzyme-type reactivity (dioxygenative ring opening of the coordinated substrate fla, single-turnover reaction) at low temperatures (30-65 °C). The reaction shows a linear Hammett plot (ρ = -1.21), and electron donating groups enhance the reaction rates. The notable difference on the reactivity can be rationalized from the electronic nature of the substituent in the ligands, which could tune the reactivity via tuning Lewis acidity of the Fe(II) ion, electron density, and the redox potential of fla. The properties and the reactivity show approximately linear correlations between λ_max or E _1/2 of fla and the reaction rate constant k. This work sheds light not only on understanding of electronic effects of the ligands and the property-reactivity relationship but also on the role of the catalytic reaction by Fe-2,4-QD.

Biotransformation of quercetin by Gliocladium deliquescens NRRL 1086

With an attempt to synthesize high-value isoquercitrin (quercetin-3-O-β-D-glucopyranoside), we carried out the biotransformation of quercetin (1) by Gliocladium deliquescens NRRL 1086. Along with the aimed product quercetin 3-O-β-D-glycoside (2), three additional metabolites, 2-protocatechuoyl-phlorogucinol carboxylic acid (3), 2,4,6-trihydroxybenzoic acid (4), and protocatechuic acid (5), were also isolated. The time-course experiments revealed that there were two metabolic routes, regio-selectivity glycosylation and quercetin 2,3-dioxygenation, co-existing in the culture. Both glycosylation and oxidative cleavage rapidly took place after quercetin feeding; about 98% quercetin were consumed within the initial 8 h and the oxdized product (2-protocatechuoyl-phlorogucinol carboxylic acid) was hydrolyzed into two phenolic compounds (2,4,6-trihydroxybenzoic acid and protocatechuic acid). We also investigated the impact of glucose content and metal ions on the two reactions and found that high concentrations of glucose significantly inhibited the oxidative cleavage and improved the yield of isoquercitrin and that Ca²⁺, Fe²⁺, Mn²⁺, Mg²⁺, and Zn²⁺ inhibited glycosylation. To test the promiscuity of this culture, we selected other four flavonols as substrates; the results demonstrated its high regio-selectivity glycosylation ability towards flavonols at C-3 hydroxyl. In conclusion, our findings indicated that the versatile microbe of G. deliquescens NRRL 1086 maitained abundant enzymes, deserving further research.

The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase

Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe²⁺ or Ni²⁺) in the active site. The Fe²⁺-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni²⁺-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate. The dual chemistry of ARD was originally discovered in the bacterium Klebsiella oxytoca, but it has recently been shown that mammalian ARD enzymes (mouse and human) are also capable of catalyzing metal-dependent dual chemistry in vitro. This is particularly interesting, since carbon monoxide, one of the products of off-pathway reaction, has been identified as an antiapoptotic molecule in mammals. In addition, several biochemical and genetic studies have indicated an inhibitory role of human ARD in cancer. This comprehensive review describes the biochemical and structural characterization of the ARD family, the proposed experimental and theoretical approaches to establishing mechanisms for the dual chemistry, insights into the mechanism based on comparison with structurally and functionally similar enzymes, and the applications of this research to the field of artificial metalloenzymes and synthetic biology.

Catalytic dioxygenation of flavonol by M(II)-complexes (M = Mn, Fe, Co, Ni, Cu and Zn) - mimicking the M(II)-substituted quercetin 2,3-dioxygenase

In order to get insights into the metal ion effects and the carboxylate effects on enzymatic activity, a series of the carboxylate ligand supported transition metal complexes [M(II)L(OAc)] (M = Mn (), Fe (), Co (), Ni (), Cu () and Zn (); LH = 2-{[bis-(pyridin-2-ylmethyl)amino]methyl}-4-methoxy benzoic acid) were synthesized and characterized as structural and functional models for the active sites of various M(II)-substituted resting quercetin 2,3-dioxygenases (2,3-QD). Their structures, spectroscopic features, redox properties, as well as the catalytic reactivity toward the substrate flavonol and O2 have been investigated in detail. The model complexes show higher enzymatic reactivities in the catalytic dioxygenation (oxidative ring opening) of the substrate flavonol at lower temperatures (55-100 °C), presumably caused by the carboxylate group in the supporting model ligand, which could lower the redox potential of the bound substrate flavonolate by electron donation. The catalytic reactivity of [M(II)L(OAc)] exhibits notable differences and it is in a metal ion dependent order of Co () > Ni () > Zn () > Fe () > Mn () > Cu (). The differences in the reactivities among them could be ascribed to the redox potential of the bound substrate flavonolate, which was drastically influenced by the metal ions via tuning the electron density of flavonolate, providing important insights into the metal ion effects and the carboxylate effects on the enzymatic activity of various M(II)-substituted 2,3-QD. Our model complexes [M(II)L(OAc)] are the first examples of a series of structural and functional models of various M(II)-substituted resting 2,3-QD.

Computational Study of Catalytic Reaction of Quercetin 2,4-Dioxygenase

We present a quantum mechanics/molecular mechanics (QM/MM) and QM-only study on the oxidative ring-cleaving reaction of quercetin catalyzed by quercetin 2,4-dioxygenase (2,4-QD). 2,4-QD has a mononuclear type 2 copper center and incorporates two oxygen atoms at C2 and C4 positions of the substrate. It has not been clear whether dioxygen reacts with a copper ion or a substrate radical as the first step. We have found that dioxygen is more likely to bind to a Cu(2+) ion, involving the dissociation of the substrate from the copper ion. Then a Cu(2+)-alkylperoxo complex can be generated. Comparison of geometry and stability between QM-only and QM/MM results strongly indicates that steric effects of the protein environment contribute to maintain the orientation of the substrate dissociated from the copper center. The present QM/MM results also highlight that a prior rearrangement of the Cu(2+)-alkylperoxo complex and a subsequent hydrogen bond switching assisted by the movement of Glu73 can facilitate formation of an endoperoxide intermediate selectively.

Nickel quercetinase, a "promiscuous" metalloenzyme: metal incorporation and metal ligand substitution studies

BACKGROUND

Quercetinases are metal-dependent dioxygenases of the cupin superfamily. While fungal quercetinases are copper proteins, recombinant Streptomyces quercetinase (QueD) was previously described to be capable of incorporating Ni(2+) and some other divalent metal ions. This raises the questions of which factors determine metal selection, and which metal ion is physiologically relevant.

RESULTS

Metal occupancies of heterologously produced QueD proteins followed the order Ni > Co > Fe > Mn. Iron, in contrast to the other metals, does not support catalytic activity. QueD isolated from the wild-type Streptomyces sp. strain FLA contained mainly nickel and zinc. In vitro synthesis of QueD in a cell-free transcription-translation system yielded catalytically active protein when Ni(2+) was present, and comparison of the circular dichroism spectra of in vitro produced proteins suggested that Ni(2+) ions support correct folding. Replacement of individual amino acids of the 3His/1Glu metal binding motif by alanine drastically reduced or abolished quercetinase activity and affected its structural integrity. Only substitution of the glutamate ligand (E76) by histidine resulted in Ni- and Co-QueD variants that retained the native fold and showed residual catalytic activity.

CONCLUSIONS

Heterologous formation of catalytically active, native QueD holoenzyme requires Ni(2+), Co(2+) or Mn(2+), i.e., metal ions that prefer an octahedral coordination geometry, and an intact 3His/1Glu motif or a 4His environment of the metal. The observed metal occupancies suggest that metal incorporation into QueD is governed by the relative stability of the resulting metal complexes, rather than by metal abundance. Ni(2+) most likely is the physiologically relevant cofactor of QueD of Streptomyces sp. FLA.

Latex clearing protein-an oxygenase cleaving poly(cis-1,4-isoprene) rubber at the cis double bonds

Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O2) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH2-) and ketone (-CH2-CO-CH3) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases.

Pirin1 (PRN1) is a multifunctional protein that regulates quercetin, and impacts specific light and UV responses in the seed-to-seedling transition of Arabidopsis thaliana

Pirins are cupin-fold proteins, implicated in apoptosis and cellular stress in eukaryotic organisms. Pirin1 (PRN1) plays a role in seed germination and transcription of a light- and ABA-regulated gene under specific conditions in the model plant system Arabidopsis thaliana. Herein, we describe that PRN1 possesses previously unreported functions that can profoundly affect early growth, development, and stress responses. In vitro-translated PRN1 possesses quercetinase activity. When PRN1 was incubated with G-protein-α subunit (GPA1) in the inactive conformation (GDP-bound), quercetinase activity was observed. Quercetinase activity was not observed when PRN1 was incubated with GPA1 in the active form (GTP-bound). Dark-grown prn1 mutant seedlings produced more quercetin after UV (317 nm) induction, compared to levels observed in wild type (WT) seedlings. prn1 mutant seedlings survived a dose of high-energy UV (254 nm) radiation that killed WT seedlings. prn1 mutant seedlings grown for 3 days in continuous white light display disoriented hypocotyl growth compared to WT, but hypocotyls of dark-grown prn1 seedlings appeared like WT. prn1 mutant seedlings transformed with GFP constructs containing the native PRN1 promoter and full ORF (PRN1::PRN1-GFP) were restored to WT responses, in that they did not survive UV (254 nm), and there was no significant hypocotyl disorientation in response to white light. prn1 mutants transformed with PRN1::PRN1-GFP were observed by confocal microscopy, where expression in the cotyledon epidermis was largely localized to the nucleus, adjacent to the nucleus, and diffuse and punctate expression occurred within some cells. WT seedlings transformed with the 35S::PRN1-GFP construct exhibited widespread expression in the epidermis of the cotyledon, also with localization in the nucleus. PRN1 may play a critical role in cellular quercetin levels and influence light- or hormonal-directed early development.

Structure and function of atypically coordinated enzymatic mononuclear non-heme-Fe(II) centers

Mononuclear, non-heme-Fe(II) centers are key structures in O₂ metabolism and catalyze an impressive variety of enzymatic reactions. While most are bound via two histidines and a carboxylate, some show a different organization. A short overview of atypically coordinated O₂ dependent mononuclear-non-heme-Fe(II) centers is presented here Enzymes with 2-His, 3-His, 3-His-carboxylate and 4-His bound Fe(II) centers are discussed with a focus on their reactivity, metal ion promiscuity and recent progress in the elucidation of their enzymatic mechanisms. Observations concerning these and classically coordinated Fe(II) centers are used to understand the impact of the metal binding motif on catalysis.

Nitrosyl hydride (HNO) replaces dioxygen in nitroxygenase activity of manganese quercetin dioxygenase

Quercetin dioxygenase (QDO) catalyzes the oxidation of the flavonol quercetin with dioxygen, cleaving the central heterocyclic ring and releasing CO. The QDO from Bacillus subtilis is unusual in that it has been shown to be active with several divalent metal cofactors such as Fe, Mn, and Co. Previous comparison of the catalytic activities suggest that Mn(II) is the preferred cofactor for this enzyme. We herein report the unprecedented substitution of nitrosyl hydride (HNO) for dioxygen in the activity of Mn-QDO, resulting in the incorporation of both N and O atoms into the product. Turnover is demonstrated by consumption of quercetin and other related substrates under anaerobic conditions in the presence of HNO-releasing compounds and the enzyme. As with dioxygenase activity, a nonenzymatic base-catalyzed reaction of quercetin with HNO is observed above pH 7, but no enhancement of this basal reactivity is found upon addition of divalent metal salts. Unique and regioselective N-containing products ((14)N/(15)N) have been characterized by MS analysis for both the enzymatic and nonenzymatic reactions. Of the several metallo-QDO enzymes examined for nitroxygenase activity under anaerobic condition, only the Mn(II) is active; the Fe(II) and Co(II) substituted enzymes show little or no activity. This result represents an enzymatic catalysis which we denote nitroxygenase activity; the unique reactivity of the Mn-QDO suggests a metal-mediated electron transfer mechanism rather than metal activation of the substrate's inherent base-catalyzed reactivity.

Metal centers in the anaerobic microbial metabolism of CO and CO2

Carbon dioxide and carbon monoxide are important components of the carbon cycle. Major research efforts are underway to develop better technologies to utilize the abundant greenhouse gas, CO(2), for harnessing 'green' energy and producing biofuels. One strategy is to convert CO(2) into CO, which has been valued for many years as a synthetic feedstock for major industrial processes. Living organisms are masters of CO(2) and CO chemistry and, here, we review the elegant ways that metalloenzymes catalyze reactions involving these simple compounds. After describing the chemical and physical properties of CO and CO(2), we shift focus to the enzymes and the metal clusters in their active sites that catalyze transformations of these two molecules. We cover how the metal centers on CO dehydrogenase catalyze the interconversion of CO and CO(2) and how pyruvate oxidoreductase, which contains thiamin pyrophosphate and multiple Fe(4)S(4) clusters, catalyzes the addition and elimination of CO(2) during intermediary metabolism. We also describe how the nickel center at the active site of acetyl-CoA synthase utilizes CO to generate the central metabolite, acetyl-CoA, as part of the Wood-Ljungdahl pathway, and how CO is channelled from the CO dehydrogenase to the acetyl-CoA synthase active site. We cover how the corrinoid iron-sulfur protein interacts with acetyl-CoA synthase. This protein uses vitamin B(12) and a Fe(4)S(4) cluster to catalyze a key methyltransferase reaction involving an organometallic methyl-Co(3+) intermediate. Studies of CO and CO(2) enzymology are of practical significance, and offer fundamental insights into important biochemical reactions involving metallocenters that act as nucleophiles to form organometallic intermediates and catalyze C-C and C-S bond formations.

Biocontrol treatments confer protection against Verticillium dahliae infection of potato by inducing antimicrobial metabolites

Verticillium wilt, caused by Verticillium dahliae Kleb., is a serious potato (Solanum tuberosum L.) disease worldwide, and biocontrol represents a promising eco-friendly strategy to reduce its impact. We used extracts from Canada milk vetch (CMV) and a set of four V. dahliae-antagonistic bacterial strains to coat potato seeds at planting and examined the degree of protection provided against V. dahliae as well as accumulation of soluble phenolics as markers for induced resistance. All tested treatments were effective in reducing disease severity, and CMV showed the highest level of protection. In this treatment, flavonol-glycoside rutin was a highly abundant compound induced in potato tissues, with levels two to three times higher than those detected in noninoculated controls and V. dahliae-inoculated plants. We investigated dose-dependent effects of rutin on V. dahliae growth and sporulation in vitro and in planta. The effect of rutin on mycelial growth was inconsistent between disk assay and amended medium experiments. On the other hand, significant reduction of V. dahliae sporulation in vitro was consistently observed starting at 300 and 100 μM for isolates Vd-9 and Vd-21, respectively. We successfully detected 2-protocatechuoylphloroglucinolcarboxylic acid (2-PCPGCA) using ultra-performance liquid chromatography tandem mass spectrometry, indicating that V. dahliae dioxygenally oxidizes quercetin. Quercetin, as an aglycone, is freed from the sugar moiety by glucosidases and rhamnosidases produced by the fungus and is a substrate for quercetinases. The occurrence of quercetinases in V. dahliae provides a background to formulate a hypothesis about how by-product 2-PCPGCA may be interfering with potato defenses.

Mechanistic studies of the O2-dependent aliphatic carbon-carbon bond cleavage reaction of a nickel enolate complex

The mononuclear nickel(II) enolate complex [(6-Ph(2)TPA)Ni(PhC(O)C(OH)C(O)Ph]ClO(4) (I) was the first reactive model complex for the enzyme/substrate (ES) adduct in nickel(II)-containing acireductone dioxygenases (ARDs) to be reported. In this contribution, the mechanism of its O(2)-dependent aliphatic carbon-carbon bond cleavage reactivity was further investigated. Stopped-flow kinetic studies revealed that the reaction of I with O(2) is second-order overall and is ∼80 times slower at 25 °C than the reaction involving the enolate salt [Me(4)N][PhC(O)C(OH)C(O)Ph]. Computational studies of the reaction of the anion [PhC(O)C(OH)C(O)Ph](-) with O(2) support a hydroperoxide mechanism wherein the first step is a redox process that results in the formation of 1,3-diphenylpropanetrione and HOO(-). Independent experiments indicate that the reaction between 1,3-diphenylpropanetrione and HOO(-) results in oxidative aliphatic carbon-carbon bond cleavage and the formation of benzoic acid, benzoate, and CO:CO(2) (∼12:1). Experiments in the presence of a nickel(II) complex gave a similar product distribution, albeit benzil [PhC(O)C(O)Ph] is also formed, and the CO:CO(2) ratio is ∼1.5:1. The results for the nickel(II)-containing reaction match those found for the reaction of I with O(2) and provide support for a trione/HOO(-) pathway for aliphatic carbon-carbon bond cleavage. Overall, I is a reasonable structural model for the ES adduct formed in the active site of Ni(II)ARD. However, the presence of phenyl appendages at both C(1) and C(3) in the [PhC(O)C(OH)C(O)Ph](-) anion results in a reaction pathway for O(2)-dependent aliphatic carbon-carbon bond cleavage (via a trione intermediate) that differs from that accessible to C(1)-H acireductone species. This study, as the first detailed investigation of the O(2) reactivity of a nickel(II) enolate complex of relevance to Ni(II)ARD, provides insight toward understanding the chemical factors involved in the O(2) reactivity of metal acireductone species.

O2-dependent aliphatic carbon-carbon bond cleavage reactivity in a Ni(II) enolate complex having a hydrogen bond donor microenvironment; comparison with a hydrophobic analogue

A mononuclear Ni(II) complex having an acireductone type ligand, and supported by the bnpapa (N,N-bis((6-neopentylamino-2-pyridyl)methyl)-N-((2-pyridyl)methyl)amine) ligand, [(bnpapa)Ni(PhC(O)C(OH)C(O)Ph)]ClO(4) (14), has been prepared and characterized by elemental analysis, (1)H NMR, FTIR, and UV-vis. To gain insight into the (1)H NMR features of 14, the air stable analogue complexes [(bnpapa)Ni(CH(3)C(O)CHC(O)CH(3))]ClO(4) (16) and [(bnpapa)Ni(ONHC(O)CH(3))]ClO(4) (17) were prepared and characterized by X-ray crystallography, (1)H NMR, FTIR, UV-vis, mass spectrometry, and solution conductivity measurements. Compounds 16 and 17 are 1:1 electrolyte species in CH(3)CN. (1)H and (2)H NMR studies of 14, 16, and 17 and deuterated analogues revealed that the complexes having six-membered chelate rings for the exogenous ligand (14 and 16) do not have a plane of symmetry within the solvated cation and thus exhibit more complicated (1)H NMR spectra. Compound 17, as well as other simple Ni(II) complexes of the bnpapa ligand (e.g., [(bnpapa)Ni(ClO(4))(CH(3)CN)]ClO(4) (18) and [(bnpapaNi)(2)(mu-Cl)(2)](ClO(4))(2) (19)), exhibit (1)H NMR spectra consistent with the presence of a plane of symmetry within the cation. Treatment of [(bnpapa)Ni(PhC(O)C(OH)C(O)Ph)]ClO(4) (14) with O(2) results in aliphatic carbon-carbon bond cleavage within the acireductone-type ligand and the formation of [(bnpapa)Ni(O(2)CPh)]ClO(4) (9), benzoic acid, benzil, and CO. Use of (18)O(2) in the reaction gives high levels of incorporation (>80%) of one labeled oxygen atom into 9 and benzoic acid. The product mixture and level of (18)O incorporation in this reaction is different than that exhibited by the analogue supported the hydrophobic 6-Ph(2)TPA ligand, [(6-Ph(2)TPA)Ni(PhC(O)C(OH)C(O)Ph)]ClO(4) (2). We propose that this difference is due to variations in the reactivity of bnpapa- and 6-Ph(2)TPA-ligated Ni(II) complexes with triketone and/or peroxide species produced in the reaction pathway.

Transcriptional analysis of the queD gene coding for quercetinase of Streptomyces sp. FLA

Quercetinase, catalyzing the 2,4-dioxygenolytic cleavage of the flavonol quercetin (3,5,7,3',4'-pentahydroxyflavone) to carbon monoxide and 2-protocatechuoylphloroglucinol carboxylic acid, is encoded by the queD gene in Streptomyces sp. FLA. Because studies on the transcriptional regulation of quercetinase genes are rare, we analyzed the expression of queD in response to quercetin and other carbon compounds. RNA hybridization experiments revealed that transcription of queD is triggered by quercetin and its 3-O-rhamnosylglucoside rutin, but not by the flavonol morin (3,5,7,2',4'-pentahydroxyflavone), the presumed quercetin degradation products protocatechuate and 2,4,6-trihydroxybenzoate or the sugars rhamnose and glucose. Quercetin-induced queD expression was not influenced by the presence of Ni(II), the preferred cofactor of Streptomyces QueD. Reverse transcription-PCR analysis showed a concerted transcription of queD and two putative genes located downstream of queD, which were predicted to code for an amidohydrolase and an esterase. By determination of the transcriptional start site of the queD operon, putative -10 and -35 regions could be identified, suggesting transcription from a sigma70-dependent promoter. Sequence analysis of the queD promoter region indicated possible binding sites for an LmrA/YxaF-like repressor.

Biochemical and molecular characterization of a quercetinase from Penicillium olsonii

Quercetinase (quercetin 2,3-dioxygenase, EC 1.13.11.24) is produced by various filamentous fungi when grown on rutin as the sole carbon and energy source. From a rutin based liquid culture of Penicillium olsonii, we purified a quercetinase with a specific activity of 175U mg(-1). The enzyme is a monomeric glycoprotein of approximately 55 kDa, containing 0.9+/-0.1 copper atoms per protein. Its substrate specificity is restricted to the flavonol family of flavonoids. It is completely inhibited by diethyldithiocarbamate at a concentration of 100 nM and 1H-2-benzyl-3-hydroxy-4-oxoquinolin is a competitive inhibitor with a K(I) of 4 microM. The cDNA poquer1 was cloned and sequenced. It encodes a 365 amino acids long enzyme with a strong sequence identity with the Aspergillus japonicus quercetinase (Q7SIC2). Like the enzyme from A. japonicus, only one of the two cupin domains of the Penicillium olsonii quercetinase is able to bind a metal atom.

Piecing together the structure–function puzzle: Experiences in structure-based functional annotation of hypothetical proteins

The combination of genomic sequencing with structural genomics has provided a wealth of new structures for previously uncharacterized ORFs, more commonly referred to as hypothetical proteins. This rapid growth has been the direct result of high-throughput, automated approaches in both the identification of new ORFs and the determination of high-resolution 3-D protein structures. A significant bottleneck is reached, however, at the stage of functional annotation in that the assignment of function is not readily automatable. It is often the case that the initial structural analysis at best indicates a functional family for a given hypothetical protein, but further identification of a relevant ligand or substrate is impeded by the diversity of function in a particular structural classification of proteins family, a highly selective and specific ligand-binding site, or the identification of a novel protein fold. Our approach to the functional annotation of hypothetical proteins relies on the combination of structural information with additional bioinformatics evidence garnered from operon prediction, loose functional information of additional operon members, conservation of catalytic residues, as well as cocrystallization trials and virtual ligand screening. The synthesis of all available information for each protein has permitted the functional annotation of several hypothetical proteins from Escherichia coli and each assignment has been confirmed through generally accepted biochemical methods.

Variations of the 2-His-1-carboxylate theme in mononuclear non-heme FeII oxygenases

A facial triad of two histidine side chains and one aspartate or glutamate side chain forms the canonical metal-coordinating motif in the catalytic centers of various mononuclear non-heme Fe(II) enzymes. Although these active sites are based on totally unrelated protein folds and bring about a wide range of chemical transformations, most of them share the ability to couple dioxygen reduction with the oxygenation of an organic substrate. With the increasing number of protein structures now solved, it has become clear that the 2-His-1-carboxylate signature is less of a paradigm for non-heme Fe(II) active sites than had long been thought and that it can be replaced by alternative metal centers in various oxygenases, the structure-function relationships and proposed catalytic mechanisms of which are reviewed here. Metal coordination through three histidines and one glutamate constitutes the classical motif described for enzyme members of the cupin protein superfamily, such as aci-reductone dioxygenase and quercetin dioxygenase, multiple metal forms of which (including the Fe(II) type) are found in nature. Cysteine dioxygenase and diketone dioxygenase, which are strictly Fe(II)-dependent oxygenases based on the cupin fold, bind the catalytic metal through the homologous triad of histidines, but lack the fourth glutamate ligand. An alpha-ketoglutarate-dependent Fe(II) halogenase shows metal coordination by two histidines as the only protein-derived ligands, whilst carotene oxygenase, from a different protein fold family, features an Fe(II) site consisting of four histidine side chains. These recently discovered metallocenters are discussed with respect to their metal-binding properties and the reaction coordinates of the O(2)-dependent conversions they catalyze.

Cerium(IV)-mediated oxidation of flavonol with relevance to flavonol 2,4-dioxygenase. Direct evidence for spin delocalization in the flavonoxy radical

The cerium(IV)-mediated oxidation of 3-hydroxy-4'-methylflavone (1) proceeds by H-atom abstraction forming the flavonoxy radical (7), and the subsequent combination of its resonance forms leads to the 3-hydroxy-4'-methylflavone dehydro dimer (9). The above system serves as direct evidence for the intermediacy of the flavonoxy radical, its spin delocalization, and also indirect evidence for valence tautomerism as a key step on the substrate activation both in the quercetinase and its biomimic model system.

Pirin regulates pyruvate catabolism by interacting with the pyruvate dehydrogenase E1 subunit and modulating pyruvate dehydrogenase activity

The protein pirin, which is involved in a variety of biological processes, is conserved from prokaryotic microorganisms, fungi, and plants to mammals. It acts as a transcriptional cofactor or an apoptosis-related protein in mammals and is involved in seed germination and seedling development in plants. In prokaryotes, while pirin is stress induced in cyanobacteria and may act as a quercetinase in Escherichia coli, the functions of pirin orthologs remain mostly uncharacterized. We show that the Serratia marcescens pirin (pirin(Sm)) gene encodes an ortholog of pirin protein. Protein pull-down and bacterial two-hybrid assays followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electrospray ionization-tandem mass spectrometry analyses showed the pyruvate dehydrogenase (PDH) E1 subunit as a component interacting with the pirin(Sm) gene. Functional analyses showed that both PDH E1 subunit activity and PDH enzyme complex activity are inhibited by the pirin(Sm) gene in S. marcescens CH-1. The S. marcescens CH-1 pirin(Sm) gene was subsequently mutated by insertion-deletion homologous recombination. Accordingly, the PDH E1 and PDH enzyme complex activities and cellular ATP concentration increased up to 250%, 140%, and 220%, respectively, in the S. marcescens CH-1 pirin(Sm) mutant. Concomitantly, the cellular NADH/NAD(+) ratio increased in the pirin(Sm) mutant, indicating increased tricarboxylic acid (TCA) cycle activity. Our results show that the pirin(Sm) gene plays a regulatory role in the process of pyruvate catabolism to acetyl coenzyme A through interaction with the PDH E1 subunit and inhibiting PDH enzyme complex activity in S. marcescens CH-1, and they suggest that pirin(Sm) is an important protein involved in determining the direction of pyruvate metabolism towards either the TCA cycle or the fermentation pathways.

Evaluation of phenolics and sugars as inducers of quercetinase activity inPenicillium olsonii

Quercetinase is produced by various filamentous fungi when grown on rutin as sole carbon and energy source. We investigated on the effect of 10 phenolics and two sugars, structurally related to substrates and products of the rutin catabolic pathway, on the induction of a quercetinase activity in Penicillium olsonii. Neither the sugars (glucose and rhamnose, two constituents of rutin), nor phenolics such as protocatechuic acid, salicylic acid, 4-hydroxy-benzoic acid and phloroglucinol were inducers. Rutin (maximum activity 150 nmol/min/mL after 5 days), quercetin (70 nmol/min/mL, 3 days), phloroglucinol carboxylic acid (60 nmol/min/mL, 3 days), 2-protocatechuoylphloroglucinolcarboxylic acid (50 nmol/min/mL, 5 days), 2,6-dihydroxy-carboxylic acid (90 nmol/min/mL, 7 days) and 2,4-dihydroxy-carboxylic acid (30 nmol/min/mL, 7 days) were demonstrated to be quercetinase inducers. We propose that rutin, quercetin and 2-protocatechuoyl-phloroglucinol carboxylic acid, the product of the reaction catalysed by quercetinase, act as inducers after their catabolic transformation in phloroglucinol carboxylic acid.