Substrate specificity of SIRT1-catalyzed lysine N-deacetylation reaction probed with the side chain modified N-acetyl-lysine analogs

Peptides containing l-N^ε-acetyl-lysine (l-AcK) or its side chain modified analogs were prepared and assayed using SIRT1, the prototypical human silent information regulator 2 (Sir2) enzyme. While previous studies showed that the side chain acetyl group of l-AcK can be extended to bulkier acyl groups for Sir2 (including SIRT1)-catalyzed lysine N^ε-deacylation reaction, our current study suggested that SIRT1-catalyzed deacetylation reaction had a very stringent requirement for the distance between the α-carbon and the side chain acetamido group, with that found in l-AcK being optimal. Moreover, our current study showed that SIRT1 catalyzed the stereospecific deacetylation of l-AcK versus its d-isomer. The results from our current study shall constitute another piece of important information to be considered when designing inhibitors for SIRT1 and Sir2 enzymes in general.     

Mechanism-based inactivation of the flavoprotein cyclohexanone monooxygenase by S oxygenation

The FAD-dependent enzyme cyclohexanone oxygenase carries out biological Baeyer-Villiger oxidations of ketones and aldehydes with O₂ as cosubstrate. Sulfides are enzymically oxygenated to sulfoxides but thiolactones appear to be enzymically processed to acyl sulfoxides which are reactive acylating and then sulfenylating agents, inducing mechanism-based inactivation.     

Kinetics and activation thermodynamics of methane monooxygenase compound Q formation and reaction with substrates

The transient kinetics of formation and decay of the reaction cycle intermediates of the Methylosinus trichosporium OB3b methane monooxygenase (MMO) catalytic cycle are studied as a function of temperature and substrate type and deuteration. Kinetic evidence is presented for the existence of three intermediates termed compounds O, P, and P forming after the addition of O(2) to diferrous MMO hydroxylase (H(r)) and before the formation of the reactive intermediate compound Q. The Arrhenius plots for these reactions are linear and independent of substrate concentration and type, showing that substrate does not participate directly in the oxygen activation phase of the catalytic cycle. Analysis of the transient kinetic data revealed only small changes relative to the weak optical spectrum of H(r) for any of these intermediates. In contrast, large changes in the 430 nm spectral region are associated with the formation of Q. The decay reaction of Q exhibits an apparent first-order concentration dependence for all substrates tested, and the observed rate constant depends on the substrate type. The kinetics of the decay reaction of Q yield a nonlinear Arrhenius plot when methane is the substrate, and the rates in both segments of the plot increase linearly with methane concentration. Together these observations suggest that at least two reactions with a methane concentration dependence, and perhaps two methane molecules, are involved in the decay process. When CD(4) is used as the substrate, a large isotope effect and a linear Arrhenius plot are observed. Analogous plots for all other MMO substrates tested (e.g., ethane) are linear, and no isotope effect for deuterated analogues is observed. This demonstrates that a step other than C-H bond breaking is rate limiting for alternative MMO substrates. A two step Q decay mechanism is proposed that provides an explanation for the lack of an isotope effect for alternative MMO substrates and the fact that rate of oxidation of methane by Q exceeds that of many other hydrocarbons with weaker C-H bonds.     

Methane monooxygenase: purification and properties of flavoprotein component

An anaerobic procedure was developed for the purification of the flavin:NADH oxidoreductase (flavoprotein) component of methane monooxygenase to homogeneity. The molecular weight of the flavoprotein determined by gel filtration was about 40,000, and by sedimentation equilibrium analysis, about 38,000. The purified flavoprotein is a monomeric protein with a sedimentation constant (S20,W) value of about 2.1 S. The absorption spectrum of the flavoprotein has a peak at 460 nm and shoulder at 395 nm. The fluorescent excitation and emission spectra of the fluorescent component of flavoprotein had peaks at 450, 370, and 530 nm, respectively. A FAD was identified as a prosthetic group of flavoprotein by thin-layer chromatography. The flavoprotein contained about 1 mol of FAD and 2 mol each of iron and acid-labile sulfide per mole of protein. The flavoprotein was directly reduced by NADH under anaerobic conditions. The formation of neutral flavin semiquinone was detected during anaerobic titration of flavoprotein by NADH and also as a free radical signal at a g value of 2.004 by EPR spectroscopy. The iron sulfur cluster has g values of 2.04, 1.96, and 1.87, yielding a g average of 1.96, characteristic of a Fe2S2 center. Antibody prepared against the flavoprotein reacted with flavoprotein and inhibited methane monooxygenase activity.     

Covalent immobilization of a flavoprotein monooxygenase via its flavin cofactor

A generic approach for flavoenzyme immobilization was developed in which the flavin cofactor is used for anchoring enzymes onto the carrier. It exploits the tight binding of flavin cofactors to their target apo proteins. The method was tested for phenylacetone monooxygenase (PAMO) which is a well-studied and industrially interesting biocatalyst. Also a fusion protein was tested: PAMO fused to phosphite dehydrogenase (PTDH-PAMO). The employed flavin cofactor derivative, N6-(6-carboxyhexyl)-FAD succinimidylester (FAD*), was covalently anchored to agarose beads and served for apo enzyme immobilization by their reconstitution into holo enzymes. The thus immobilized enzymes retained their activity and remained active after several rounds of catalysis. For both tested enzymes, the generated agarose beads contained 3 U per g of dry resin. Notably, FAD-immobilized PAMO was found to be more thermostable (40% activity after 1 h at 60 °C) when compared to PAMO in solution (no activity detected after 1 h at 60 °C). The FAD-decorated agarose material could be easily recycled allowing multiple rounds of immobilization. This method allows an efficient and selective immobilization of flavoproteins via the FAD flavin cofactor onto a recyclable carrier.     

Studies on the specificity toward aldehyde substrates and steady-state kinetics of xanthine oxidase

The aldehyde specificity of xanthine oxidase (xanthine:oxygen oxidoreductase, EC 1.2.3.2) has been reinvestigated. The biogenic aldehydes and succinate semialdehyde are reasonable substrates for xanthine oxidase. Pyrophosphate, which binds to xanthine oxidase, does not seem to affect significantly the enzyme's catalytic activity. The steady-state parameters for the oxidation of several substrates by xanthine oxidase and oxygen have been determined. Formaldehyde differs from xanthine and other aldehydes in phi 2, the parameter describing the reaction with oxygen. Substrate inhibition has been studied at high concentrations of xanthine with oxygen as the electron acceptor. The inhibition is hyperbolic and uncompetitive with respect to oxygen. This is possibly due to rate-limiting product release from molybdenum(IV) being slower than from molybdenum(VI).     

Mechanisms of reaction of some flavoprotein enzymes with oxygen

Biochemical investigations of the properties of free flavins and of flavoproteins have shown that reduction usually occurs in two stages, with the intermediate formation of semiquinones in the case of free flavins. Flavoproteins often show spectroscopically similar intermediates, when partially reduced with substrate. These may, however, be enzyme-product complexes. Detailed investigation of individual flavoprotein enzymes has shown examples in which catalysis involves transition of the enzyme between oxidized and fully reduced forms (glucose oxidase), between oxidized and intermediate forms (D-amino acid oxidase), and intermediate and fully reduced forms (TPNH—cytochrome c reductase). Further, examples are known in which both intermediate and reduced forms react with oxygen, in which only one reacts, while in TPNH—cytochrome c reductase neither the intermediate nor the reduced form reacts with molecular oxygen. The physiological significance of these complex findings is uncertain, partly because it is not known whether purified flavoproteins occur in the same form in the tissues. It seems unlikely, however, that flavoproteins make a major contribution to the respiratory exchange of mammals.     

Substrate specificity of the flavoprotein trypanothione disulfide reductase from Crithidia fasciculata

The substrate specificity of the trypanosomatid enzyme trypanothione reductase has been studied by measuring the ability of the enzyme to reduce a series of chemically synthesized cyclic and acyclic derivatives of N1,N8-bis(glutathionyl)spermidine disulfide (trypanothione). Kinetic analysis of the enzymatic reduction of these synthetic substrates indicates that the mutually exclusive substrate specificity observed by the NADPH-dependent trypanothione disulfide reductase and the related flavoprotein glutathione disulfide reductase is due to the presence of a spermidine binding site in the substrate binding domain of trypanothione reductase. Trypanothione reductase will reduce the disulfide form of N1-monoglutathionylspermidine and also the mixed disulfide of N1-monoglutathionylspermidine and glutathione. The Michaelis constants for these reactions are 149 microM and 379 microM, respectively. Since the disulfide form of N1-monoglutathionylspermidine and the mixed disulfide of N1-monoglutathionylspermidine and glutathione could be formed in trypanosomatids, the binding constants and turnover numbers for the enzymatic reduction of these acyclic disulfides are consistent with these being potential alternative substrates for trypanothione reductase in vivo.     

Two structures of an N-hydroxylating flavoprotein monooxygenase: ornithine hydroxylase from Pseudomonas aeruginosa

The ornithine hydroxylase from Pseudomonas aeruginosa (PvdA) catalyzes the FAD-dependent hydroxylation of the side chain amine of ornithine, which is subsequently formylated to generate the iron-chelating hydroxamates of the siderophore pyoverdin. PvdA belongs to the class B flavoprotein monooxygenases, which catalyze the oxidation of substrates using NADPH as the electron donor and molecular oxygen. Class B enzymes include the well studied flavin-containing monooxygenases and Baeyer-Villiger monooxygenases. The first two structures of a class B N-hydroxylating monooxygenase were determined with FAD in oxidized (1.9 Å resolution) and reduced (3.03 Å resolution) states. PvdA has the two expected Rossmann-like dinucleotide-binding domains for FAD and NADPH and also a substrate-binding domain, with the active site at the interface between the three domains. The structures have NADP(H) and (hydroxy)ornithine bound in a solvent-exposed active site, providing structural evidence for substrate and co-substrate specificity and the inability of PvdA to bind FAD tightly. Structural and biochemical evidence indicates that NADP⁺ remains bound throughout the oxidative half-reaction, which is proposed to shelter the flavin intermediates from solvent and thereby prevent uncoupling of NADPH oxidation from hydroxylated product formation.     

Novel substrates and inhibitors of peptidylglycine alpha-amidating monooxygenase

Peptidylglycine alpha-amidating monooxygenase (PAM, EC 1.14.17.3) catalyzes the formation of alpha-amidated peptides from their glycine-extended precursors, thus playing a key role in the processing of peptide neurohormones. We now report that PAM readily catalyzes three alternate monooxygenase reactions--sulfoxidation, amine N-dealkylation, and O-dealkylation. Thus, (4-nitrobenzyl)thioacetic acid is converted to the analogous sulfoxide, N-(4-nitrobenzyl)glycine is converted to 4-nitrobenzylamine and glyoxylate, and [(4-nitrobenzyl)oxy]acetic acid is converted to 4-nitrobenzyl alcohol and glyoxylate. All these new activities display the characteristics expected for the normal PAM-catalyzed reductive oxygenation pathway and produce an equimolar amount of glyoxylate together with the heteroatom-containing dealkylation products. The ester [(4-methoxybenzoyl)oxy]acetic acid is not a PAM substrate, but is instead a good competitive inhibitor (KI = 0.48 mM). In addition, we report that the olefinic substrate analogues trans-benzoylacrylic acid and 4-phenyl-3-butenoic acid are potent time-dependent inactivators of PAM, with inactivation exhibiting the characteristics expected for mechanism-based inhibition. Monoethyl fumarate is also a time-dependent inactivator of PAM. Finally, we introduce several small non-peptide substrates for PAM by demonstrating that PAM catalyzes the transformation of hippuric acid and several ring-substituted derivatives to the corresponding benzamides and glyoxylic acid, with the most facile substrate of this class being 4-nitrohippuric acid. These compounds are the smallest amide substrates yet reported for PAM, and it is thus apparent that only the minimal structure of an acylglycine is required for PAM-catalyzed oxygenative amidation.     

The reaction of p-nitrophenyl acetate with lysine and lysine derivatives

The kinetics of the reaction of p-nitrophenyl acetate with lysine and its derivatives has been investigated in water-dioxane solutions over the pH range 8.1–10.1. The reaction was found to be second order, and the unprotonated amino group was shown to be the reactive species. Intrinsic second-order rate constants were calculated.     

Studies of the oxidative half-reaction of anthranilate hydroxylase (deaminating) with native and modified substrates

The oxidative half-reactions of anthranilate hydroxylase (EC 1.14.12.2) were examined in the presence of anthranilate and modified substrates. C(4a)-Hydroperoxyflavin (C(4a)-FlOOH) and C(4a)-hydroxyflavin (C(4a)-FlOH) intermediates were detected in oxidative reactions with all substrates. Thus, the oxygenation reactions of the enzyme are similar to those of flavoprotein hydroxylases that convert phenolic compounds to catechols. These observations support a mechanism proposed for this enzyme (Powlowski, J. B., Dagley, S., Massey, V., and Ballou, D. P. (1987) J. Biol. Chem. 262, 69-74) involving nucleophilic attack of the substrate on C(4a)-FlOOH, and formation of an imine intermediate that is subsequently hydrolyzed. Anthranilate hydroxylase is therefore a typical flavoprotein hydroxylase with the added capacity of hydrolyzing imine intermediates. Fluorine substituents on the aromatic ring decreased the rate of conversion of C(4a)-FlOOH to C(4a)-FlOH, as predicted by this mechanism. Hydroxylation of 3-fluoro- and 3-methylanthranilates resulted in the formation of nonaromatic products that appeared to stabilize the C(4a)-FlOH. No evidence was found for a high extinction intermediate (intermediate II) (Entsch, B., Ballou, D. P., and Massey, V. (1976) J. Biol. Chem. 251, 2550-2563) under conditions where it was readily detected with other flavoprotein hydroxylases. It was shown that the spectra of the nonaromatic products (which are quinonoid forms) could not be summed with the spectra of C(4a)-hydroxyflavin to obtain that of a putative intermediate II, thus ruling out that explanation for previous observations of II.