Spectroscopic and kinetic properties of recombinant choline oxidase from Arthrobacter globiformis

Ultrafast Dynamics of Fatty Acid Photodecarboxylase in Anionic Semiquinone State

Fatty acid photodecarboxylase is a newly identified blue-light driven photoenzyme that catalyzes decarboxylation of fatty acids. The catalytic reaction involves a transient anionic semiquinone of flavin cofactor (FAD^•-) as an intermediate, but photochemical properties of this anionic radical are largely unknown. Here, we have anaerobically produced the wild-type FAP in the FAD^•- state and conducted femtosecond-resolved fluorescence and absorption measurements. We have observed the multiphasic deactivation dynamics of excited states on multiple time scales from a few picoseconds even to a few nanoseconds through conical intersections between various electronic states. Interestingly, the nanosecond components can only be observed from higher electronic excited states. Our results show the complexity of the energy landscapes of various excited states and rule out the occurrence of electron or proton transfer with nearby residue(s) in the active site.

Flavoprotein Photochemistry: Fundamental Processes and Photocatalytic Perspectives

Flavins are highly versatile redox-active and colored cofactors in a large variety of proteins. These do include photoenzymes and photoreceptors, although the vast majority performs non-light-driven physiological functions. Nevertheless, electron transfer between flavins and specific nearby amino acid residues (in particular tyrosine, tryptophan, and presumably histidine and arginine) takes place upon excitation of flavin in many flavoproteins. For oxidized flavoproteins these reactions potentially have a photoprotective role. In this Perspective, we outline work on the characterization of early reaction intermediates not only in the relatively well-studied resting oxidized forms but also in the fully reduced and the intrinsically unstable semireduced forms, where ultrafast photooxidation of flavin was recently demonstrated. Along different lines, flavoprotein-based novel photocatalysts for biotechnological applications are presently emerging, employing both substrate photooxidation and photoreduction strategies. Deep insight into the fundamental flavin photochemical reactions may help in guiding and optimizing their development and in the exploration of novel photocatalytic approaches.

Ultrafast photooxidation of protein-bound anionic flavin radicals

Flavoproteins are colored proteins involved in a large variety of biochemical reactions. They can perform photochemical reactions, which are increasingly exploited for bioengineering new protein-derived photocatalysts. In particular, light-induced reduction of the resting oxidized state of the flavin by close-lying amino acids or substrates is extensively studied. Here, we demonstrate that the reverse and previously unknown reaction photooxidation of the anionic semireduced flavin radical, a short-lived reaction intermediate in many biochemical reactions, efficiently occurs in flavoprotein oxidases. We anticipate that this finding will allow photoreduction of external reactants and lead to exploration of novel photocatalytic pathways.

The photophysical properties of anionic semireduced flavin radicals are largely unknown despite their importance in numerous biochemical reactions. Here, we studied the photoproducts of these intrinsically unstable species in five different flavoprotein oxidases where they can be stabilized, including the well-characterized glucose oxidase. Using ultrafast absorption and fluorescence spectroscopy, we unexpectedly found that photoexcitation systematically results in the oxidation of protein-bound anionic flavin radicals on a time scale of less than ∼100 fs. The thus generated photoproducts decay back in the remarkably narrow 10- to 20-ps time range. Based on molecular dynamics and quantum mechanics computations, positively charged active-site histidine and arginine residues are proposed to be the electron acceptor candidates. Altogether, we established that, in addition to the commonly known and extensively studied photoreduction of oxidized flavins in flavoproteins, the reverse process (i.e., the photooxidation of anionic flavin radicals) can also occur. We propose that this process may constitute an excited-state deactivation pathway for protein-bound anionic flavin radicals in general. This hitherto undocumented photochemical reaction in flavoproteins further extends the family of flavin photocycles.

Choline oxidases

Choline oxidase catalyzes the four-electron, two-step, flavin-mediated oxidation of choline to glycine betaine. The enzyme is important both for medical and biotechnological reasons, because glycine betaine is one among a limited number of compatible solutes used by cells to counteract osmotic pressure. From a fundamental standpoint, choline oxidase has emerged as one of the paradigm enzymes for the oxidation of alcohols catalyzed by flavoproteins. Mechanistic, structural, and computational studies have elucidated the mechanism of action of the enzyme from Arthrobacter globiformis at the molecular level. Both choline and oxygen access to the active site cavity are gated and tightly controlled. Amino acid residues involved in substrate binding, and their contribution, have been identified. The mechanism of choline oxidation, with a hydride transfer reaction, an asynchronous transition state, the formation and stabilization of an alkoxide transient species, and a quantum mechanical mode of reaction, has been elucidated. The importance of nonpolar side chains for oxygen localization and of the positive charge harbored on the substrate for activation of oxygen for reaction with the reduced flavin have been recognized. Interesting phenomena, like the formation of a metastable photoinduced flavin-protein adduct, the reversible formation of a bicovalent flavoprotein, and the trapping of the enzyme in inactive conformations, have been described. This review summarizes the current status of our understanding on the structure-function-dynamics of choline oxidase.

Electrochemical micro analytical device interfaced with portable potentiostat for rapid detection of chlorpyrifos using acetylcholinesterase conjugated metal organic framework using Internet of things

An Electrochemical micro Analytical Device (EµAD) was fabricated for sensitive detection of organophosphate pesticide chlorpyrifos in the food chain. Gold microelectrode (µE) modified with Zinc based Metal Organic Framework (MOF-Basolite Z1200) and Acetylcholinesterase (AChE) enzyme served as an excellent electro-analytical transducer for the detection of chlorpyrifos. Electrochemical techniques such as Cyclic Voltammetry (CV), Electrochemical Impedance Spectroscopy (EIS) and Differential Pulse Voltammetry (DPV) were performed for electrochemical analysis of the developed EµAD. The sensor needs only 2 µL of the analyte and it was tested within the linear range of 10 to 100 ng/L. The developed EµAD’s limit of detection (LoD) and sensitivity is 6 ng/L and 0.598 µ A/ng L⁻¹/mm² respectively. The applicability of the device for the detection of chlorpyrifos from the real vegetable sample was also tested within the range specified. The fabricated sensor showed good stability with a shelf-life of 20 days. The EµAD’s response time is of 50 s, including an incubation time of 20 s. The developed EµAD was also integrated with commercially available low-cost, handheld potentiostat (k-Stat) using Bluetooth and the results were comparable with a standard electrochemical workstation.

On the use of noncompetitive kinetic isotope effects to investigate flavoenzyme mechanism

This account describes the application of kinetic isotope effects (KIEs) to investigate the mechanistic properties of flavin dependent enzymes. Assays can be conducted during steady-state catalytic turnover of the flavoenzyme with its substrate or by using rapid-kinetic techniques to measure either the reductive or oxidative half-reactions of the enzyme. Great care should be taken to ensure that the observed effects are due to isotopic substitution and not other factors such as pH effects or changes in the solvent viscosity of the reaction mixture. Different types of KIEs are described along with a physical description of their origins and the unique information each can provide about the mechanism of an enzyme. Detailed experimental techniques are outlined with special emphasis on the proper controls and data analysis that must be carried out to avoid erroneous conclusions. Examples are provided for each type of KIE measurement from references in the literature. It is our hope that this article will clarify any confusion concerning the utility of KIEs in the study of flavoprotein mechanism and encourage their use by the community.

Structure-Based Engineering of Phanerochaete chrysosporium Alcohol Oxidase for Enhanced Oxidative Power toward Glycerol

Glycerol is a major byproduct of biodiesel production, and enzymes that oxidize this compound have been long sought after. The recently described alcohol oxidase from the white-rot basidiomycete Phanerochaete chrysosporium (PcAOX) was reported to feature very mild activity on glycerol. Here, we describe the comprehensive structural and biochemical characterization of this enzyme. PcAOX was expressed in Escherichia coli in high yields and displayed high thermostability. Steady-state kinetics revealed that PcAOX is highly active toward methanol, ethanol, and 1-propanol (k_cat = 18, 19, and 11 s^–1, respectively), but showed very limited activity toward glycerol (k_obs = 0.2 s^–1 at 2 M substrate). The crystal structure of the homo-octameric PcAOX was determined at a resolution of 2.6 Å. The catalytic center is a remarkable solvent-inaccessible cavity located at the re side of the flavin cofactor. Its small size explains the observed preference for methanol and ethanol as best substrates. These findings led us to design several cavity-enlarging mutants with significantly improved activity toward glycerol. Among them, the F101S variant had a high k_cat value of 3 s^–1, retaining a high degree of thermostability. The crystal structure of F101S PcAOX was solved, confirming the site of mutation and the larger substrate-binding pocket. Our data demonstrate that PcAOX is a very promising enzyme for glycerol biotransformation.

Substitutions of S101 decrease proton and hydride transfers in the oxidation of betaine aldehyde by choline oxidase

Choline oxidase oxidizes choline to glycine betaine, with two flavin-mediated reactions to convert the alcohol substrate to the carbon acid product. Proton abstraction from choline or hydrated betaine aldehyde in the wild-type enzyme occurs in the mixing time of the stopped-flow spectrophotometer, thereby precluding a mechanistic investigation. Mutagenesis of S101 rendered the proton transfer reaction amenable to study. Here, we have investigated the aldehyde oxidation reaction catalyzed by the mutant enzymes using steady-state and rapid kinetics with betaine aldehyde. Stopped-flow traces for the reductive half-reaction of the S101T/V/C variants were biphasic, corresponding to the reactions of proton abstraction and hydride transfer. In contrast, the S101A enzyme yielded monophasic traces like wild-type choline oxidase. The rate constants for proton transfer in the S101T/C/V variants decreased logarithmically with increasing hydrophobicity of residue 101, indicating a behavior different from that seen previously with choline for which no correlation was determined. The rate constants for hydride transfer also showed a logarithmic decrease with increasing hydrophobicity at position 101, which was similar to previous results with choline as a substrate for the enzyme. Thus, the hydrophilic character of S101 is necessary not only for efficient hydride transfer but also for the proton abstraction reaction.

Automated Determination of Oxygen-Dependent Enzyme Kinetics in a Tube-in-Tube Flow Reactor

Enzyme-mediated oxidation is of particular interest to synthetic organic chemists. However, the implementation of such systems demands knowledge of enzyme kinetics. Conventionally collecting kinetic data for biocatalytic oxidations is fraught with difficulties such as low oxygen solubility in water and limited oxygen supply. Here, we present a novel method for the collection of such kinetic data using a pressurized tube-in-tube reactor, operated in the low-dispersed flow regime to generate time-series data, with minimal material consumption. Experimental development and validation of the instrument revealed not only the high degree of accuracy of the kinetic data obtained, but also the necessity of making measurements in this way to enable the accurate evaluation of high KMO enzyme systems. For the first time, this paves the way to integrate kinetic data into the protein engineering cycle.

Evidence for proton tunneling and a transient covalent flavin-substrate adduct in choline oxidase S101A

The effect of temperature on the reaction of alcohol oxidation catalyzed by choline oxidase was investigated with the S101A variant of choline oxidase. Anaerobic enzyme reduction in a stopped-flow spectrophotometer was biphasic using either choline or 1,2-[²H₄]-choline as a substrate. The limiting rate constants k_lim1 and k_lim2 at saturating substrate were well separated (k_lim1/k_lim2>9), and were >15-fold slower than for wild-type choline oxidase. Solvent deuterium kinetic isotope effects (KIEs) ~4 established that k_lim1 probes the proton transfer from the substrate hydroxyl to a catalytic base. Primary substrate deuterium KIEs ≥7 demonstrated that k_lim2 reports on hydride transfer from the choline alkoxide to the flavin. Between 15°C and 39°C the k_lim1 and k_lim2 values increased with increasing temperature, allowing for the analyses of H⁺ and H^- transfers using Eyring and Arrhenius formalisms. Temperature-independent KIE on the k_lim1 value (^H2Ok_lim1/^D2Ok_lim1) suggests that proton transfer occurs within a highly reorganized tunneling-ready-state with a narrow distribution of donor-acceptor distances. Eyring analysis of the k_lim2 value gave lines with the slope_(choline)>slope_(D-choline), suggesting kinetic complexity. Spectral evidence for the transient occurrence of a covalent flavin-substrate adduct during the first phase of the anaerobic reaction of S101A CHO with choline is presented, supporting the notion that an important role of amino acid residues in the active site of flavin-dependent enzymes is to eliminate alternative reactions of the versatile enzyme-bound flavin for the reaction that needs to be catalyzed.

Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase

Choline oxidase from Arthrobacter globiformis catalyzes the oxidation of choline to glycine betaine by using oxygen as an electron acceptor. A partially rate limiting isomerization of the reduced wild-type enzyme during the reaction with oxygen was previously detected using solvent viscosity effects. In this study, we hypothesized that the side chains of M62 and F357, located at the entrance to the active site of choline oxidase, may be related to the slow isomerization detected. We engineered a double-variant enzyme M62A/F357A. The kinetic characterization of the double-variant enzyme showed a lack of the isomerization detected in wild-type choline oxidase, and a lack of saturation with an oxygen concentration as high as 1 mM, while most other kinetic parameters were similar to those of wild-type choline oxidase. The kinetic characterization of the single-variant enzymes established that only the side chain of F357 plays a role in the isomerization of choline oxidase in the oxidative half-reaction. Molecular dynamics studies suggest that the slow isomerization related to F357 is possibly due to the participation of the phenyl ring in a newly proposed gating mechanism for a narrow tunnel, assumed to regulate the access of oxygen to the reduced cofactor.

Alcohol oxidation by flavoenzymes

This review article describes the occurrence, general properties, and substrate specificity of the flavoenzymes belonging to the glucose-methanol-choline oxidoreductase superfamily and the l-α-hydroxyacid dehydrogenase family. Most of these enzymes catalyze the oxidations of hydroxyl groups, yielding carbonyl moieties. Over the years, carbanion, hydride transfer, and radical mechanisms have been discussed for these enzymes, and the main experimental evidences supporting these mechanisms are presented here. Regardless of the chemical nature of the organic substrate (i.e., activated and non-activated alcohols), a hydride transfer mechanism appears to be the most plausible for the flavoenzymes acting on CH-OH groups. The reaction of most of these enzymes likely starts with proton abstraction from the substrate hydroxyl group by a conserved active site histidine. Among the different approaches carried out to determine the chemical mechanisms with physiological substrates, primary substrate and solvent deuterium kinetic isotope effect studies have provided the most unambiguous evidences. It is expected that the numerous studies reported for these enzymes over the years will be instrumental in devising efficient industrial biocatalysts and drugs.

Structural and kinetic studies on the Ser101Ala variant of choline oxidase: catalysis by compromise

The oxidation of choline catalyzed by choline oxidase includes two reductive half-reactions where FAD is reduced by the alcohol substrate and by an aldehyde intermediate transiently formed in the reaction. Each reductive half-reaction is followed by an oxidative half-reaction where the reduced flavin is oxidized by oxygen. Here, we have used mutagenesis to prepare the Ser101Ala mutant of choline oxidase and have investigated the impact of this mutation on the structural and kinetic properties of the enzyme. The crystallographic structure of the Ser101Ala enzyme indicates that the only differences between the mutant and wild-type enzymes are the lack of a hydroxyl group on residue 101 and a more planar configuration of the flavin in the mutant enzyme. Kinetics established that replacement of Ser101 with alanine yields a mutant enzyme with increased efficiencies in the oxidative half-reactions and decreased efficiencies in the reductive half-reactions. This is accompanied by a significant decrease in the overall rate of turnover with choline. Thus, this mutation has revealed the importance of a specific residue for the optimization of the overall turnover of choline oxidase, which requires fine-tuning of four consecutive half-reactions for the conversion of an alcohol to a carboxylic acid.

Involvement of ionizable groups in catalysis of human liver glycolate oxidase

Glycolate oxidase is a flavin-dependent, peroxisomal enzyme that oxidizes alpha-hydroxy acids to the corresponding alpha-keto acids, with reduction of oxygen to H(2)O(2). In plants, the enzyme participates in photorespiration. In humans, it is a potential drug target for treatment of primary hyperoxaluria, a genetic disorder where overproduction of oxalate results in the formation of kidney stones. In this study, steady-state and pre-steady-state kinetic approaches have been used to determine how pH affects the kinetic steps of the catalytic mechanism of human glycolate oxidase. The enzyme showed a Ping-Pong Bi-Bi kinetic mechanism between pH 6.0 and 10.0. Both the overall turnover of the enzyme (k(cat)) and the rate constant for anaerobic substrate reduction of the flavin were pH-independent at pH values above 7.0 and decreased slightly at lower pH, suggesting the involvement of an unprotonated group acting as a base in the chemical step of glycolate oxidation. The second-order rate constant for capture of glycolate (k(cat)/K(glycolate)) and the K(d)((app)) for the formation of the enzyme-substrate complex suggested the presence of a protonated group with apparent pK(a) of 8.5 participating in substrate binding. The k(cat)/K(oxygen) values were an order of magnitude faster when a group with pK(a) of 6.8 was unprotonated. These results are discussed in the context of the available three-dimensional structure of GOX.

Spectral and kinetic characterization of intermediates in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase

The flavoenzyme nikD, a 2-electron acceptor, catalyzes a remarkable aromatization of piperideine-2-carboxylate (P2C) to picolinate, an essential component of nikkomycin antibiotics. Steady-state kinetic data are indicative of a sequential mechanism where oxygen reacts with a reduced enzyme.dihydropicolinate (DHP) complex. The kinetics observed for complex formation with competitive inhibitors are consistent with a one-step binding mechanism. The anaerobic reaction with P2C involves three steps. The first step yields an enzyme.substrate charge transfer complex likely to contain the electron-rich P2C enamine. Calculated rates of formation and dissociation of the nikD.P2C complex are similar to those observed for the enzyme.1-cyclohexenoate complex. Formation of a reduced enzyme.DHP complex, (EH(2).DHP)(ini), occurs in a second step that exhibits a hyperbolic dependence on substrate concentration. The limiting rate of nikD reduction is at least 10-fold faster than the turnover rate observed with unlabeled or [4,4,5,5,6,6-D(6)]-P2C and exhibits a kinetic isotope effect (KIE = 6.4). The observed KIE on K(d apparent) (4.7) indicates that P2C is a sticky substrate. Formation of a final reduced species, (EH(2).DHP)(fin), occurs in a third step that is independent of P2C concentration and equal to the observed turnover rate. The observed KIE (3.3) indicates that the final step involves cleavage of at least one C-H bond. Tautomerization, followed by isomerization, of the initial DHP intermediate can produce an isomer that could be oxidized to picolinate in a reaction that satisfies known steric constraints of flavoenzyme reactions without the need to reposition a covalently tethered flavin or tightly bound intermediate.

Oxidation of amines by flavoproteins

Many flavoproteins catalyze the oxidation of primary and secondary amines, with the transfer of a hydride equivalent from a carbon-nitrogen bond to the flavin cofactor. Most of these amine oxidases can be classified into two structural families, the D-amino acid oxidase/sarcosine oxidase family and the monoamine oxidase family. This review discusses the present understanding of the mechanisms of amine and amino acid oxidation by flavoproteins, focusing on these two structural families.

Aryl-alcohol oxidase involved in lignin degradation: a mechanistic study based on steady and pre-steady state kinetics and primary and solvent isotope effects with two alcohol substrates

Aryl-alcohol oxidase (AAO) is a FAD-containing enzyme in the GMC (glucose-methanol-choline oxidase) family of oxidoreductases. AAO participates in fungal degradation of lignin, a process of high ecological and biotechnological relevance, by providing the hydrogen peroxide required by ligninolytic peroxidases. In the Pleurotus species, this peroxide is generated in the redox cycling of p-anisaldehyde, an extracellular fungal metabolite. In addition to p-anisyl alcohol, the enzyme also oxidizes other polyunsaturated primary alcohols. Its reaction mechanism was investigated here using p-anisyl alcohol and 2,4-hexadien-1-ol as two AAO model substrates. Steady state kinetic parameters and enzyme-monitored turnover were consistent with a sequential mechanism in which O(2) reacts with reduced AAO before release of the aldehyde product. Pre-steady state analysis revealed that the AAO reductive half-reaction is essentially irreversible and rate limiting during catalysis. Substrate and solvent kinetic isotope effects under steady and pre-steady state conditions (the latter showing approximately 9-fold slower enzyme reduction when alpha-bideuterated substrates were used, and approximately 13-fold slower reduction when both substrate and solvent effects were simultaneously evaluated) revealed a synchronous mechanism in which hydride transfer from substrate alpha-carbon to FAD and proton abstraction from hydroxyl occur simultaneously. This significantly differs from the general mechanism proposed for other members of the GMC oxidoreductase family that implies hydride transfer from a previously stabilized substrate alkoxide.

Contribution of flavin covalent linkage with histidine 99 to the reaction catalyzed by choline oxidase

The FAD-dependent choline oxidase has a flavin cofactor covalently attached to the protein via histidine 99 through an 8alpha-N(3)-histidyl linkage. The enzyme catalyzes the four-electron oxidation of choline to glycine betaine, forming betaine aldehyde as an enzyme-bound intermediate. The variant form of choline oxidase in which the histidine residue has been replaced with asparagine was used to investigate the contribution of the 8alpha-N(3)-histidyl linkage of FAD to the protein toward the reaction catalyzed by the enzyme. Decreases of 10-fold and 30-fold in the k(cat)/K(m) and k(cat) values were observed as compared with wild-type choline oxidase at pH 10 and 25 degrees C, with no significant effect on k(cat)/K(O) using choline as substrate. Both the k(cat)/K(m) and k(cat) values increased with increasing pH to limiting values at high pH consistent with the participation of an unprotonated group in the reductive half-reaction and the overall turnover of the enzyme. The pH independence of both (D)(k(cat)/K(m)) and (D)k(cat), with average values of 9.2 +/- 3.3 and 7.4 +/- 0.5, respectively, is consistent with absence of external forward and reverse commitments to catalysis, and the chemical step of CH bond cleavage being rate-limiting for both the reductive half-reaction and the overall enzyme turnover. The temperature dependence of the (D)k(red) values suggests disruption of the preorganization in the asparagine variant enzyme. Altogether, the data presented in this study are consistent with the FAD-histidyl covalent linkage being important for the optimal positioning of the hydride ion donor and acceptor in the tunneling reaction catalyzed by choline oxidase.

Crystallographic, spectroscopic, and computational analysis of a flavin C4a-oxygen adduct in choline oxidase

Flavin C4a-OO(H) and C4a-OH adducts are critical intermediates proposed in many flavoenzyme reaction mechanisms, but they are rarely detected even by rapid transient kinetics methods. We observe a trapped flavin C4a-OH or C4a-OO(H) adduct by single-crystal spectroscopic methods and in the 1.86 A resolution X-ray crystal structure of choline oxidase. The microspectrophotometry results show that the adduct forms rapidly in situ at 100 K upon exposure to X-rays. Density functional theory calculations establish the electronic structures for the flavin C4a-OH and C4a-OO(H) adducts and estimate the stabilization energy of several active site hydrogen bonds deduced from the crystal structure. We propose that the enzyme-bound FAD is reduced in the X-ray beam. The aerobic crystals then form either a C4a-OH or C4a-OO(H) adduct, but an insufficient proton inventory prevents their decay at cryogenic temperatures.

Hydride transfer made easy in the reaction of alcohol oxidation catalyzed by flavin-dependent oxidases

Choline oxidase (E.C. 1.1.3.17; choline-oxygen 1-oxidoreductase) catalyzes the two-step, four-electron oxidation of choline to glycine betaine with betaine aldehyde as enzyme-associated intermediate and molecular oxygen as final electron acceptor. Biochemical, structural, and mechanistic studies on the wild-type and a number of mutant forms of choline oxidase from Arthrobacter globiformis have recently been carried out, allowing for the delineation at molecular and atomic levels of the mechanism of alcohol oxidation catalyzed by the enzyme. First, the alcohol substrate is activated to its alkoxide species by the removal of the hydroxyl proton in the enzyme-substrate complex. The resulting activated alkoxide is correctly positioned for catalysis through electrostatic and hydrogen bonding interactions with a number of active site residues. After substrate activation and correct positioning are attained, alcohol oxidation occurs in a highly preorganized enzyme-substrate complex through quantum mechanical transfer of a hydride ion from the alpha-carbon of the chelated, alkoxide species to the N(5) atom of the enzyme-bound flavin. This mechanism in its essence is shared by another class of alcohol oxidizing enzymes that utilize a catalytic zinc to stabilize an alkoxide intermediate and NAD(P)(+) as the organic cofactor that accepts the hydride ion, whose paradigm example is alcohol dehydrogenase. It will be interesting to experimentally evaluate the attractive hypothesis of whether the mechanism of choline oxidase can be extended to other flavin-dependent enzymes as well as enzymes that utilize cofactors other than flavins in the oxidation of alcohols.

Substitution of an active site valine uncovers a kinetically slow equilibrium between competent and incompetent forms of choline oxidase

The enzymatic oxidation of choline to glycine betaine is of interest because organisms accumulate glycine betaine intracellularly in response to stress conditions. This is relevant for the genetic engineering of crops with economic interest that do not naturally possess efficient pathways for the synthesis of glycine betaine and for the potential development of drugs that target the glycine betaine biosynthetic pathway in human pathogens. To date, the best characterized choline-oxidizing enzyme is the flavin-dependent choline oxidase from Arthrobacter globiformis, for which structural, mechanistic, and biochemical data are available. Here, we have replaced a hydrophobic residue (Val464) lining the active site cavity close to the N(5) atom of the flavin with threonine or alanine to investigate its role in the reaction of choline oxidation catalyzed by choline oxidase. The reductive half-reactions of the enzyme variants containing Thr464 or Ala464 were investigated using substrate and solvent kinetic isotope effects, solvent viscosity effects, and proton inventories. Replacement of Val464 with threonine or alanine uncovered a kinetically slow equilibrium between a catalytically incompetent form of enzyme and an active species that can efficiently oxidize choline. In both variants, the active form of enzyme shows a decreased rate of hydroxyl proton abstraction from the alcohol substrate, with minimal changes in the subsequent rate of hydride ion transfer to the flavin. This study therefore establishes that a hydrophobic residue not directly participating in catalysis plays important roles in the reaction of choline oxidation catalyzed by choline oxidase.

The photoreversible fluorescent protein iLOV outperforms GFP as a reporter of plant virus infection

Fluorescent proteins (FPs) based on green fluorescent protein (GFP) are widely used throughout cell biology to study protein dynamics, and have extensive use as reporters of virus infection and spread. However, FP-tagging of viruses is limited by the constraints of viral genome size resulting in FP loss through recombination events. To overcome this, we have engineered a smaller ( approximately 10 kDa) flavin-based alternative to GFP ( approximately 25 kDa) derived from the light, oxygen or voltage-sensing (LOV) domain of the plant blue light receptor, phototropin. Molecular evolution and Tobacco mosaic virus (TMV)-based expression screening produced LOV variants with improved fluorescence and photostability in planta. One variant in particular, designated iLOV, possessed photophysical properties that made it ideally suited as a reporter of subcellular protein localization in both plant and mammalian cells. Moreover, iLOV fluorescence was found to recover spontaneously after photobleaching and displayed an intrinsic photochemistry conferring advantages over GFP-based FPs. When expressed either as a cytosolic protein or as a viral protein fusion, iLOV functioned as a superior reporter to GFP for monitoring local and systemic infections of plant RNA viruses. iLOV, therefore, offers greater utility in FP-tagging of viral gene products and represents a viable alternative where functional protein expression is limited by steric constraints or genome size.

NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: structures of closed and open forms at 1.15 and 1.90 A resolution

NikD is an unusual amino-acid-oxidizing enzyme that contains covalently bound FAD, catalyzes a 4-electron oxidation of piperideine-2-carboxylic acid to picolinate, and plays a critical role in the biosynthesis of nikkomycin antibiotics. Crystal structures of closed and open forms of nikD, a two-domain enzyme, have been determined to resolutions of 1.15 and 1.9 A, respectively. The two forms differ by an 11 degrees rotation of the catalytic domain with respect to the FAD-binding domain. The active site is inaccessible to solvent in the closed form; an endogenous ligand, believed to be picolinate, is bound close to and parallel with the flavin ring, an orientation compatible with redox catalysis. The active site is solvent accessible in the open form, but the picolinate ligand is approximately perpendicular to the flavin ring and a tryptophan is stacked above the flavin ring. NikD also contains a mobile cation binding loop.

Inhibition of choline oxidase by quinoid dyes

Choline oxidase catalyzes the oxidation of choline to glycine-betaine, with betaine-aldehyde as intermediate and molecular oxygen as primary electron acceptor. This study reports on the inhibitory effects of triarylmethanes (cationic malachite green; neutral leukomalachite green), phenoxazines (cationic, meldola blue and nile blue; neutral nile red) and a structurally-related phenothiazine (methylene blue) on choline oxidase, assayed at 25 degrees C in 50 mM MOPS buffer, pH 7, using choline as substrate. Methylene B acted as a competitive inhibitor with K(i) = 74 +/- 7.2 microM, pointing to the choline-binding site of the enzyme as a target site. Nile B caused noncompetitive inhibition of enzyme activity with K(i) = 20 +/- 4.5 microM. In contrast to methylene B and nile B, malachite G and meldola B caused complex, nonlinear inhibition of choline oxidase, with estimated K(i) values in the micromolar range. The difference in kinetic pattern was ascribed to the differential ability of the dyes to interact (and interfere) with the flavin cofactor, generating different perturbations in the steady-state balance of the catalytic process.

A novel photoreaction mechanism for the circadian blue light photoreceptor Drosophila cryptochrome

Cryptochromes are flavoproteins that are evolutionary related to the DNA photolyases but lack DNA repair activity. Drosophila cryptochrome (dCRY) is a blue light photoreceptor that is involved in the synchronization of the circadian clock with the environmental light-dark cycle. Until now, spectroscopic and structural studies on this and other animal cryptochromes have largely been hampered by difficulties in their recombinant expression. We have therefore established an expression and purification scheme that enables us to purify mg amounts of monomeric dCRY from Sf21 insect cell cultures. Using UV-visible spectroscopy, mass spectrometry, and reversed phase high pressure liquid chromatography, we show that insect cell-purified dCRY contains flavin adenine dinucleotide in its oxidized state (FAD(ox)) and residual amounts of methenyltetrahydrofolate. Upon blue light irradiation, dCRY undergoes a reversible absorption change, which is assigned to the conversion of FAD(ox) to the red anionic FAD(.) radical. Our findings lead us to propose a novel photoreaction mechanism for dCRY, in which FAD(ox) corresponds to the ground state, whereas the FAD(.) radical represents the light-activated state that mediates resetting of the Drosophila circadian clock.

Trapping choline oxidase in a nonfunctional conformation by freezing at low pH

Choline oxidase is a flavin-dependent enzyme that catalyzes the oxidation of choline to glycine-betaine, with oxygen as electron acceptor. Storage at pH 6 and -20 degrees C resulted in a change in the conformation of choline oxidase, which was associated with complete loss of catalytic activity when the enzyme was assayed at pH 6. Incubation of the inactive enzyme at pH values > or = 6.5 and 25 degrees C resulted in a fast and partial reactivation of the enzyme, which occurred with slow onset of steady state during enzymatic turnover. The rate of approaching steady state was independent of the concentrations of choline and enzyme, but increased to a limiting value with increasing pH, defining a pKa value of approximately 7.3 for an unprotonated group required for enzyme activation. Prolonged incubation of the inactive enzyme at pH 6 and temperatures > or = 20 degrees C, at which no hysteretic behavior was observed, resulted in the slow and full recovery of activity over 3 h, associated with a conformational change that reverted the enzyme to the native form. Activation of the enzyme at pH 6 was enthalpy-driven with deltaH(double dagger) and TdeltaS(double dagger) values of approximately 112 kJ mol(-1) and approximately 20 kJ mol(-1) determined at 25 degrees C. These data suggest that freezing the enzyme at low pH induces a localized and reversible conformational change that is associated with the complete and reversible loss of catalytic activity.

On the contribution of the positively charged headgroup of choline to substrate binding and catalysis in the reaction catalyzed by choline oxidase

Recent kinetic studies established that the positive charge on the trimethylammonium group of choline plays an important role in substrate binding and specificity in the reaction catalyzed by choline oxidase. In the present study, pH and solvent viscosity effects with the isosteric analogue of choline 3,3-dimethyl-butan-1-ol have been used to further dissect the contribution of the substrate positive charge to substrate binding and catalysis in the reaction catalyzed by choline oxidase. Both the kcat and kcat/Km values with 3,3-dimethyl-butan-1-ol increased to limiting values that were approximately 3- and approximately 400-times lower than those observed with choline, defining pKa values that were similar to the thermodynamic pKa value of approximately 7.5 previously determined. No effects of increased solvent viscosity were observed on the kcat and kcat/Km values with the substrate analogue at pH 8, suggesting that the chemical step of substrate oxidation is fully rate-limiting for the overall turnover and the reductive half-reaction in which the alcohol substrate is oxidized to the aldehyde. The kcat/Km value for oxygen determined with the substrate analogue was pH-independent in the pH range from 6 to 10, with an average value that was approximately 75-times lower than that previously determined with choline as substrate. These data are consistent with the positive charge headgroup of choline playing important roles for substrate binding and flavin oxidation, with minimal contribution to substrate oxidation.

Oxygen- and temperature-dependent kinetic isotope effects in choline oxidase: correlating reversible hydride transfer with environmentally enhanced tunneling

Choline oxidase catalyzes the flavin-linked oxidation of choline to glycine betaine, with betaine aldehyde as intermediate and oxygen as electron acceptor. Here, the effects of oxygen concentration and temperature on the kinetic isotope effects with deuterated choline have been investigated. The D(kcat/Km) and Dkcat values with 1,2-[(2)H4]-choline were pH-independent at saturating oxygen concentrations, whereas they decreased at high pH to limiting values that depended on oxygen concentration at < or = 0.97 mM oxygen. The kcat/Km and kcat pH profiles had similar patterns reaching plateaus at high pH. Both the limiting kcat/Km at high pH and the pKa values were perturbed to lower values with choline and < or = 0.25 mM oxygen. These data suggest that oxygen availability modulates whether the reduced enzyme-betaine aldehyde complex partitions forward to catalysis rather then reverting to the oxidized enzyme-choline alkoxide species. At saturating oxygen concentrations, the D(kcat/Km) was 10.6 +/- 0.6 and temperature independent, and the isotope effect on the preexponential factors (A(H)'/A(D)') was 14 +/- 3, ruling out a classical over-the-barrier behavior for hydride transfer. Similar enthalpies of activation (deltaH(double dagger)) with values of 18 +/- 2 and 18 +/- 5 kJ mol(-1) were determined with choline and 1,2-[(2)H4]-choline. These data suggest that the hydride transfer reaction in which choline is oxidized by choline oxidase occurs quantum mechanically within a preorganized active site, with the reactive configuration for hydride tunneling being minimally affected by environmental vibrations of the reaction coordinate other than those affecting the distance between the donor and acceptor of the hydride.

Effects of paraoxon and ethylparathion on choline oxidase from Alcaligenes species: Inhibition and denaturation

The kinetics and thermodynamics of the effects of paraoxon (POX) and ethylparathion (EPA) on choline oxidase (ChOx) were studied. Lineweaver-Burk plots of initial velocity data showed a parallel pattern indicating uncompetitive inhibition versus choline. The inhibition constant (K(I)) obtained from the secondary plots for POX and EPA were 0.14+/-0.01 and 0.48+/-0.05 mM, respectively, suggesting that POX is a more potent inhibitor of ChOx than EPA. UV absorption was used to monitor the denaturation of ChOx by POX and EPA. A decrease in FAD fluorescence associated with the interaction of POX and EPA with ChOx suggested a tertiary structural change. Interaction of the enzyme molecule with POX or EPA resulted in inhibition and subsequently denaturation of the enzyme. The results indicate that inhibition and denaturation of the enzyme by POX and EPA are linked, but not parallel events, with inhibition occurring at lower concentrations with respect to denaturation. This suggests that the loss of initial velocity of the enzyme is an active site specific effect and not due to global conformational changes induced by the inhibitors.

On the Catalytic Mechanism of Choline Oxidase

Choline oxidase catalyzes the four-electron oxidation of choline to glycine betaine, with betaine aldehyde as an intermediate. In this study, primary deuterium and solvent kinetic isotope effects have been used to elucidate the mechanism for substrate oxidation by choline oxidase using both steady-state kinetics and rapid kinetics techniques. The D(kcat/Km) value with 1,2-[2H4]-choline at saturating oxygen concentration was independent of pH in the range between 6.5 and 10, with a value of approximately 10.6, indicating that CH bond cleavage is not masked by other titratable kinetic steps belonging to the reductive half-reaction. In agreement with this conclusion, a Dkred value of approximately 8.9 was determined at pH 10 for the anaerobic reduction of the flavin by choline, irrespective of whether aqueous or deuterated solvent was used. At pH 10, both the D2(O)(kcat/Km) and the D2(O)kred values were not different from unity with choline or 1,2-[2H4]-choline, while the Dkcat and D2(O)kcat values were 7.3 and 1.1, respectively. The kcat and kred values were 133 s(-1) and 135 s(-1) with betaine aldehyde and 60 s(-1) and 93 s(-1) with choline. These data are consistent with a chemical mechanism in which the choline hydroxyl proton is not in flight in the transition state for CH bond cleavage and with chemical steps of flavin reduction by choline and betaine aldehyde being rate limiting for the overall turnover of the enzyme.

The trimethylammonium headgroup of choline is a major determinant for substrate binding and specificity in choline oxidase

Choline oxidase catalyzes the oxidation of choline to glycine betaine via two sequential flavin-linked transfers of hydride equivalents to molecular oxygen and formation of a betaine aldehyde intermediate. In the present study, choline and glycine betaine analogs were used as substrates and inhibitors for the enzyme to investigate the structural determinants that are relevant for substrate recognition and specificity. Competitive inhibition patterns with respect to choline were determined for a number of substituted amines at pH 6.5 and 25 degrees C. The Kis values for the carboxylate-containing ligands glycine betaine, N,N-dimethylglycine, and N-methylglycine increased monotonically with decreasing number of methyl groups, consistent with the trimethylammonium portion of the ligand being important for binding. In contrast, the acetate portion of glycine betaine did not contribute to binding, as suggested by lack of changes in the Kis values upon substituting glycine betaine with inhibitors containing methyl, ethyl, allyl, and 2-amino-ethyl side chains. In agreement with the inhibition data, the specificity of the enzyme for the organic substrate (kcat/Km value) decreased when N,N-dimethylethanolamine, N-methylethanolamine, and the isosteric substrate 3,3-dimethyl-1-butanol were used as substrate instead of choline; a contribution of approximately 7 kcal mol(-1) toward substrate discrimination was estimated for the interaction of the trimethylammonium portion of the substrate with the active site of choline oxidase.