Interaction of nad with rape alcohol dehydrogenase

Rape alcohol dehydrogenase is competitively inhibited with respect to NAD by nicotinamide, as well as by compounds containing adenine (adenine, adenosine, AMP, ADP, ATP). Adenine and adenosine are bound more firmly to the enzyme than nicotinamide. The two types of compound, as component parts of the NAD coenzyme, are bound to different sites on the enzyme. Adenine and adenosine compete for the adenine nucleotide bonding site, but they do not compete for the o-phenanthroline bonding site. Nicotinamide competes with o-phenanthroline for the binding site at which the metal is apparently present.     

Zinc content, metal chelator inactivation and catalytic inhibition of D-lactate dehydrogenase from the barnacle, Balanus nubilus Darwin.

Purified NAD-linked d-lactate dehydrogenase from the depressor muscle of the giant barnacle, Balanus nubilus Darwin, is inactivated when incubated with the metal chelators o-phenanthroline and EDTA. M-Phenanthroline and p-phenanthroline, which lack metal chelating ability, are ineffective in inactivating the enzyme. Inactivated enzyme can be reactivated by the addition of zinc ions to the assay mixture. Atomic absorption spectrophotometric analysis of purified B. nubilusd-lactate dehydrogenase revealed that this enzyme contains stoichiometric amounts of zinc (2 g-atoms per mol of subunit), unlike other lactate dehydrogenases, which lack zinc. Zinc appears to be required for maximal catalytic activity. Aromatic, nitrogen-containing metal chelators and their nonchelating analogs are effective instantaneous inhibitors of B. nubilusd-lactate dehydrogenase. These compounds bind at the coenzyme binding site, as the mode of inhibition is distinctly competitive with respect to NADH. The different effects of metal chelators and their nonchelator analogs suggest that time-dependent inactivation (chelation of the enzyme zinc ions) and instantaneous inhibition (competition with NADH binding) have independent mechanisms.     

Carboxymethylation of horse-liver alcohol dehydrogenase in the crystalline state. The active-site zinc region and general anion-binding site of the enzyme correlated in primary and teritiary structures.

Horse liver alcohol dehydrogenase (isozyme EE) in the crystalline state was alkylated with iodoacetate under conditions resulting in the single substitution of Cys-46, which is a ligand to the active-site zinc atom. Alkylation was facilitated by the prior formation of a complex with imidazole bound to the zinc atom. Extent and specificity of the reaction were determined by use of 14C-labelled iodoacetate and by analyses of radioactive peptides after cleavage with trypsin. Ternary complexes of the enzyme with coenzymes and inhibitors effectively protected the protein against alkylation. ADP-ribose, Pt(CN)2-/4 , 1,10-phenanthroline, Au(CN)-/2 and AMP also prevented alkylation with decreasing effectiveness. Crystallographic studies of the alkylated enzyme show that the carboyxmethylated sulfur atom of Cys-46 is still liganded to the active-site zinc atom and that the iodide ion liberated during alkylation is bound as the fourth ligand to zinc, displacing imidazole. Crystallographic analyses were also performed of the binding of AMP and Pt(CN2-/4 to the enzyme. It was found that Arg-47 interacts with the phosphate moiety of the nucleotide. Lys-228 and Arg-47 interact in the platinate complex with the bulky anion, the center of which coincides with the position of the nucleotide phosphate. Some of the cyano-ligands to platinum occupy a crevice between the coenzyme phosphate binding site and the active-site zinc atom. The results of the combined studies on primary and tertiary structures confirm previous suggestions that iodoacetate enters the active site via reversible binding to an anion-binding site. This site interacts with the negatively charged groups of the coenzyme as well as with ADP-ribose, Pt(CN2-/4 and to a lesser extent Au(CN)-/2 and AMP, which therefore prevent the reversible binding of iodoacetate. 1,10-Phenanthroline does not block the binding site but interferes with alkylation presumably by changing the coordination of zinc. Identificationof this labelled residue in both chemical and crystallographic studies correlates the primary and tertiary structures. Characterizations of the active-site zinc region and the general anion-binding site are also presented.     

Oligopeptidase B from <Emphasis Type="Italic">Serratia proteamaculans</Emphasis>. III. Inhibition analysis. Specific interactions with metalloproteinase inhibitors

Inhibition of the novel oligopeptidase B from Serratia proteamaculans (PSP) by basic pancreatic trypsin inhibitor, Zn²⁺ ions, and o- and m-phenanthroline was investigated. A pronounced effect of calcium ions on the interaction of PSP with inhibitors was demonstrated. Inversion voltamperometry and atomic absorption spectrometry revealed no zinc ions in the PSP molecule. Hydrophobic nature of the enzyme inhibition by o- and m-phenanthroline was established.     

Effect of inhibitors,redox state and isoprenoid chain length on the affinity of ubiquinone for the secondary acceptor binding site in the reaction centers of photosynthetic bacteria

Quinone and inhibitor binding to Rhodopseudomonas sphaeroides (R-26 and GA) reaction centers were studied using spectroscopic methods and by direct adsorption of reaction centers onto anion exchange filters in the presence of ¹⁴C-labelled quinone or inhibitor. These measurements show that as secondary acceptor, Q_B, ubiquinone (UQ) is tightly bound in the semiquinone form and loosely bound in the quinone and quinol forms. The quinol is probably more loosely bound than the quinone. o-Phenanthroline and terbutryn, a triazine inhibitor, compete with UQ and with each other for binding to the reaction center. Inhibition by o-phenanthroline of electron transfer from the primary to the secondary quinone acceptor (Q_A to Q_B) occurs via displacement of UQ from the Q_B binding site. Displacement of UQ by terbutryn is apparently accessory to the inhibition of electron transfer. Terbutryn binding is lowered by reduction of Q_B to Q^?_B but is practically unaffected by reduction of Q_A to Q^?_A in the absence of Q_B. UQ-9 and UQ-10 have a 5- to 6-fold higher binding affinity to the Q_B site than does UQ-1, indicating that the long isoprenoid chain facilitates the binding to the Q_B site.     

The interaction of adenine with its binding site in rabbit muscle glyceraldehyde 3-phosphate dehydrogenase studied by fluorescence decay.

The fluorescence decay mechanism of 1, N⁶-ethenoadenosine diphosphoribose bound to rabbit muscle glyceraldehyde 3-phosphate dehydrogenase markedly differs from that of the intact coenzyme analog (εNAD⁺) bound to the same enzyme. In the latter case the fluorescence is partially quenched by interactions between the ethenoadenine ring and amino acid residues in its binding site. Binding of the nicotinamide moiety of the coenzyme thus affects the relative orientation of the adenine ring within its binding site leading to the quenching interactions. The interactions of the adenine group with its binding site induce conformational changes in the enzyme which affect the binding of additional coenzyme molecules. The nicotinamide base thus determines, indirectly, the negative cooperativity found in NAD⁺ binding.     

Effect of the side chain structure of coenzyme Q on the steady state kinetics of bovine heart NADH: coenzyme Q oxidoreductase

Steady state kinetics of bovine heart NADH: coenzyme Q oxidoreductase using coenzyme Q with two isoprenoid unit (Q₂) or with a decyl group (DQ) show an ordered sequential mechanism in which the order of substrate binding and product release is NADH-Q₂ (DQ) -Q₂H₂ (DQH₂)-NAD⁺ in contrast to the order determined using Q₁ (Q₁-NADH-NAD⁺-Q₁H₂) (Nakashima et al., J. Bioenerg. Biomembr. 34, 11–19, 2002). The effect of the side chain structure of coenzyme Q suggests that NADH binding to the enzyme results in a conformational change, in the coenzyme Q binding site, which enables the site to accept coenzyme Q with a side chain significantly larger than one isoprenoid unit. The side chains of Q₂ and DQ bound to the enzyme induce a conformational change in the binding site to stabilize the substrate binding, while the side chain of Q₁ (one isoprenoid unit) is too short to induce the conformational change.     

Ion‐Exchange and Adsorption of Fe(III) by Sepia Melanin

Sepia eumelanin is associated with many metal ions, yet little is known about its metal binding capacity and the chemical nature of the binding site(s). Herein, the natural concentrations of metal ions are presented and the ability to remove metals by exposure of the melanin granules to EDTA is quantified. The results reveal that the binding constants of melanin at pH 5.8 for Mg(II), Ca(II), Sr(II) and Cu(II) are, respectively, 5, 4, 14 and 34 times greater than the corresponding binding constants of these ions with EDTA. By exposing Sepia eumelanin to aqueous solutions of FeCl₃, the content of bound Fe(III) can be increased from a natural concentration of ～180 ppm to a saturation limit of ～80 000 ppm or 1.43 mmol/g of melanin. Similar saturation limits are found for Mg(II) and Ca(II). Exposure of Sepia melanin granules to aqueous solutions containing Ca(II) results in the stoichiometric replacement of the initially bound Mg(II), arguing that these two ions occupy the same binding site(s) in the pigment. The pH‐dependent binding of Mg(II) and Ca(II) suggests coordination of these ions to carboxylic acid groups in the pigment. Mg(II) and Ca(II) can be added to a Fe(III)‐saturated melanin sample without affecting the amount of Fe(III) pre‐adsorbed, clearly establishing Fe(III) and Mg(II)/Ca(II) occupy different binding sites. Taking recent Raman spectroscopic data into account, the binding of Fe(III) is concluded to involve coordination to o‐dihydroxyl groups. The effects of metal ion content on the surface morphology were analyzed. No significant changes were found over the full range of Fe(III) concentration studied, which is supported by the Brunauer–Emmett–Teller surface area analysis. These observations imply the existence of channels within the melanin granules that can serve to transport metal ions.     

Light-induced oxidation of the acceptor-side Fe(II) of Photosystem II by exogenous quinones acting through the QB binding site. II. Blockage by inhibitors and their effects on the Fe(III) EPR spectra

Four representative inhibitors of Photosystem II (PS II) Q⁻_A to Q_B electron transfer were shown to bind, at high concentrations, to PS II reaction centers having the acceptor-side non-heme iron in the Fe(III) state. Three of the inhibitors studied, DCMU, o-phenanthroline and dinoseb, modified the EPR spectrum of the Fe(III) relative to that obtained by ferricyanide oxidation in the absence of inhibitor. o-Phenanthroline gave particularly axial symmetry, while DCMU and dinoseb gave more rhombic configurations. The herbicide inhibitor, atrazine and its analogue, terbutryn, had no effect. The dissociation constants for inhibitor binding to reaction centers in the Fe(III) state were measured directly and also estimated from shifts in the midpoint potential of the Fe(III)/Fe(II) couple and were shown to increase by factors of approx. 100, approx. 10 and 10–15 for DCMU (pH 7.5), atrazine (pH 7.0) and o-phenanthroline (pH 7.0), respectively, upon oxidation of the iron. Atrazine and o-phenanthroline, which induce the smallest changes in the midpoint potential of the Fe(III)/Fe(II) couple, were shown to inhibit light-induced oxidation of the Fe(II) by phenyl-p-BQ, described in the preceding paper (Petrouleas, V. and Diner, B.A. (1987) Biochim. Biophys. Acta 893, 126–137). The extent of inhibition was much greater than would be predicted from a simple shift in the midpoint potential for Fe(III)/Fe(II) and we conclude that phenyl-p-BQ and the other quinones, which show light-induced oxidation, act through the Q_B binding site. It is also argued that reduction and oxidation of the iron by ferro- and ferricyanide, respectively, occur through this site. The effects of these inhibitors and of various quinones on the Fe(III) environment are discussed with reference to the known contact points between the protein and o-phenanthroline and terbutryn in the Q_B binding pocket of Rhodopseudomonas viridis reaction centers (Michel, H., Epp, O. and Deisenhofer, J. (1986) EMBO J. 5, 2445–2451). The Fe(III) EPR spectrum is thus a new and sensitive probe of the contact points at which molecules bind to the Q_B binding site.     

Subunits and Sulfhydryl Groups of Beef Liver d-Glycerate Dehydrogenase

The amino acid composition of beef liver d-glycerate dehydrogenase (EC 1.1.1.29) was determined. Results of sodium dodecyl sulfate gel electrophoresis and measurements of the number of NADH bound by the enzyme and the number of the essential sulfhydryl groups suggested that the enzyme was composed of two identical subunits with the molecular weight of 36,000. Close relation between the essential sulfhydryl groups and the coenzyme binding site was also suggested. Effect of an alkylating agent (bromopyruvate) with the structure similar to the substrate was studied. Effects of iodoacetate and iodoacetamide were also studied. It was suggested that these reagents behaved as active-site-directed irreversible inhibitors of the enzyme. Bromopyruvate exhibited a high affinity to the enzyme. Iodoacetate (anionic reagent) had a higher affinity than iodoacetamide (neutral reagent).     

Differential effects of metal ligands on synaptic membrane glutamate binding and uptake systems

The high affinity, Na⁺-independentl-[³H]glutamate binding process in synaptic membranes and in the purified binding protein was shown to be inhibited to an almost equal extent by the metal ligands NaN₃, KCN, ando-phenanthroline, and by 2,4,5-trihydroxyphenylalanine (6-OH DOPA). The high affinity, Na⁺-dependent glutamate transport activity in these membranes was almost totally insensitive to NaN₃,o-phenanthroline, KCN, and 6-OH DOPA. These agents, especially 6-OH DOPA, may be useful tools in achieving a discrimination between putative physiologic receptors and uptake carrier sites forl-glutamate in synaptic membranes. The sensitivity of the glutamate binding sites to the effects of the metal ligands may be correlated to the presence of an iron-sulfur center in the purified glutamate binding protein. Some of the characteristics of this metallic center were explored by optical and paramagnetic resonance spectroscopic techniques and are described in this study.This research was supported by grants DAAG29-79-C-0156 from the Army Research Office and AA 04732 from NIAAA.     

Cation binding to β-casein. a comparison of electrostatic models

The binding of cations of β-casein at pH 6.6 was considered previously. Available for three sodium concentiations, I = 0.04, 0.08, or 0.16 M are: [1] proton releases between I and [2] for each I, as calcium activity is increased, correlated sequences of monomer net charge, proton release, site bound calcium and protein Solvation- Models for ion binding are examined. Critical considerations are the intrinsic binding constants between hydrogen[H], calcium[Ca] and sodium[Na] ions and phosphate[P] and caiboxyIate[C] sites, and the effects of electrostatic interaction between sites as influenced by spatial fixed charge distribution, ionic strength and dielectric constant [D]. Anticipated intrinsic binding constants are k_H,P^o = 3 × 10⁶, k_Ca,P^o = 120, k_Na,P^o = 1, k_H,C^o = 7 × 10⁴ and k_Ca,C^o = 5.6Distributed charge models, either surface or volume, are inadequate since any reasonable monomer size yields fixed charge densities requiring k_H,P^o and k_Ca,C^o which are too low when the maximum in D is 75. Also, with increasing calcium binding, calculated proton release is only 0.4 to 0.5 of that observed.Discrete charge models accept anticipated k^o and yield calculated sequences of calcium binding and proton release which are in good agreement with those observed provided that: (1) using the known amino acid sequence of the phosphate-containing acidic peptide portion of the molecule, pep tide fixed charge is distributed at the lowest I so as to minimize electrostatic free energy; (2) in the region of fixed charge, D is approximately 5; (3) the distances between peptide fixed charges decrease with increasing ionic strength or calcium binding and (4) while protein is in solution, the acidic peptide and the remainder of the molecule are essentially electrostatically independent.     

The stabilization by a coenzyme analog of a conformational change induced by substrate in 6-phosphogluconate dehydrogenase.

The reaction of NADP⁺ with periodate yields a coenzyme analog that can be bound to the NADP⁺ binding site of 6-phosphogluconate dehydrogenase from Candida utilis. This coenzyme analog can be irreversibly bound to the enzyme by reduction with sodium borohydride. The binding of one molecule of inhibitor to only one of the two subunits of the enzyme causes the inactivation of this subunit but does not alter the catalytic activity of the other subunit. Thus the two subunits do not have apparent catalytic interactions. When the reaction between the enzyme and the coenzyme analog is carried out in the presence of the substrate, the covalent modification of only one subunit causes the inactivation of both subunits. In this case the two subunits show an extreme negative cooperativity. It is suggested that the binding of the substrate induces in the enzyme molecule a conformational change that is stabilized by the irreversible binding of the coenzyme analog.     

Flash photolysis-electron spin resonance study of the effect of o-phenanthroline and temperature on the decay time of the ESR signal B1 in reaction-center preparations and chromatophores of mutant and wild strains of Rhodopseudomonas spheroides and Rhodospirillum rubrum

We have studied the effect of o-phenanthroline and temperature on the decay rate of Signal B1 in reaction-center preparations and in chromatophores from Rhodopseudomonas spheroides and Rhodospirillum rubrum. We have shown that o-phenanthroline binds specifically to the reaction center protein (the binding center is probably at the iron) and when so bound inhibits the transfer of electrons from primary to secondary acceptors. We have also shown that the direct return decay time (A^? → P865⁺) increases with increasing temperature above approx. 150 K. This phenomenon has been interpreted within a quantum mechanical tunnelling model in which the distance of closest approach between P865⁺ and A^? increases about 2 Å between approx. 150 and 300 K.     

STUDY ON THE INHIBITION OF BRAIN GLUTAMATE DECARBOXYLASE BY PYRIDOXAL PHOSPHATE OXIME-O-ACETIC ACID

The kinetics of the inhibition of mouse brain glutamate decarboxylase by pyri-doxaI-5′-phosphate oxime-O-acetic acid (PLPOAA) was studied. The inhibition was noncompetitive with regard to glutamic acid; it could be partially reversed by pyridoxal phosphate, but only when the concentration of the latter in the incubation medium was higher than that of pyridoxal-5′-phosphate oxime-O-acetic acid. The inhibition produced by aminooxyacetic acid, which is remarkably greater than that produced by PLPOAA, was also partially reversed only when an excess of pyridoxal phosphate was added. Both in the presence and in the absence of a saturating concentration of pyridoxal phosphate, the activity of the enzyme was decreased by PLPOAA at a 10^?4m concentration to a value of about 50 per cent of the control value obtained without added coenzyme. This activity could not be further reduced even when PLPOAA concentration was increased to 5 × 10^?3m . This same minimal activity of glutamate decarboxylase was obtained after dialysis of the enzymic preparation, or after incubation with glutamic acid in the cold followed by filtration through Sephadex G-25. The addition of pyridoxal phosphate to the dialysed or glutamic acid-treated enzyme restored the activity to almost the control values. PLPOAA did not affect the activity of glutamate decarboxylase from E. coli or that of DOPA decarboxylase and GABA transaminase from mouse brain. To account for the results obtained it is postulated that brain glutamate decarboxylase has two types of active site, one with firmly bound, non-dialysable pyridoxal phosphate and the other with loosely bound, dialysable coenzyme; PLPOAA behaves as a weak inhibitor probably because it can combine mainly with the loosely bound coenzyme site, while aminooxyacetic acid is a potent inhibitor probably because it can block both the ‘loosely bound coenzyme’ and the ‘firmly bound coenzyme’ sites.     

S1 nuclease: Immunoaffinity purification and evidence for the proximity of cysteine 25 to the substrate binding site

A simple procedure, involving heat treatment, gel filtration on Sephadex G-100 followed by chromatography on anti-S1 nuclease antibodies bound to Sepharose, was developed for purification of S1 nuclease to homogeneity with an overall yield of 72%. S1 nuclease was rapidly inactivated, at pH 6.0 and 37°C, in presence of o-phthalaldehyde. Kinetic analysis of o-phthalaldehyde mediated inactivation showed that the reaction followed pseudo-first-order kinetics and the loss of enzyme activity was due to the formation of a single isoindole derivative per molecule of the enzyme. Absorbance and fluorescence spectrophotometric data also gave similar results. The isoindole derivative formation, as a result of o-phthalaldehyde treatment is known to occur through crosslinking of the thiol group of cysteine and the ε-amino group of lysine, situated in close proximity in the native enzyme. Since, modification of only available cysteine residue (Cys 25) did not affect the catalytic activity of the enzyme, the o-phthalaldehyde mediated inactivation of S1 nuclease is due to the modification of lysine. Substrates of S1 nuclease, namely ssDNA, RNA and 3′ AMP, could protect the enzyme against o-phthalaldehyde mediated inactivation. Moreover, the modified enzyme (having very little catalytic activity) showed a significant decrease in its ability to bind 5′ AMP, a competitive inhibitor of S1 nuclease, suggesting that the modification has occurred at the substrate binding site. The above results point towards the presence of cysteine 25 in close proximity to the substrate binding site.     

Ion transport and regulation ofTetrahymena pyriformis in isotonic and hypotonic media

Summary The ion and volume regulatory mechanisms ofTetrahymena pyriformis were studied in normal or hypotonic nutrient media and in isotonic inorganic media with different Na/K ratios, in conjunction with the effects of a general metabolic inhibitor (low temperature) and a specific inhibitor (iodoacetate). For K two mechanisms of active influx were found: The first is sensitive to IAc and seems to be the basic mechanism for the maintenance of the K_i/K_o gradient. The second is sensitive to cooling and related to the function of the contractile vacuole; it is also responsible for the high intracellular levels of K. The passive K efflux seems to be a basic factor for volume regulation, together with the contractile vacuole. It increases in hypotonic media and this seems to be related to structural changes of the membranes occurring in hypotonic media. For Na two mechanisms of active transport were also found: One for active Na efflux with highK _m, which is associated with the contractile vacuole and another, for active Na influx with lowK _m, which is inhibited by high levels of intracellular K.The electrochemical potentials of Na and K and the membrane potential (Cl Nernst potential) were also studied in isotonic inorganic media. The membrane is negatively polarized, except if Na_o<5 mM when it becomes positive. In normal conditions, Na is transported outwards actively and leaks passively, while K is transported inwards actively and leaks 56 times more rapidly than Na ions.A model for the overall transport and regulation of ions inTetrahymena is proposed.Abbreviations IAc iodoacetate - PCV packed cell volume - Na _i,K _i,Cl intracellular concentrations ofNa ⁺,K ⁺,Cl ^–, respectively - Na _o,K _o, Cl_o extracellular concentrations of Na⁺, K⁺, Cl^–, respectively - DR distribution ratio - HyN hypotonic nutrient medium - IsN isotonic nutrient medium - HyS IsS hypotonic, and isotonic salt medium, respectively     

The guanosine 3',5'-bis(diphosphate) (ppGpp) cycle. Comparison of synthesis and degradation of guanosine 3',5'-bis(diphosphate) in various bacterial systems.

4-(3-Bromoacetylpyridinio)butyldiphosphoadenosine was synthesized with a [carbonyl-14C]acetyl label. The reactive coenzyme analogue inactivates alcohol dehydrogenase from Bacillus stearothermophilus by forming a covalent enzyme-coenzyme compound. The inactivation kinetics as well as the spectral properties of the modified enzyme after treatment with sodium hyposulphite suggest that the analogue is bound at the coenzyme binding site. B. stearothermophilus alcohol dehydrogenase modified with 14C-labelled coenzyme analogue and subseqeuntly carboxymethylated with unlabelled iodoacetic acid was digested with trypsin. The radioactive peptide was isolated and sequenced in parallel with the corresponding peptide similarly isolated from unmodified enzyme that had instead been carboxymethylated with iodo[14C]acetic acid. Amino acid and sequence analysis show that Cys-38 of the B. stearothermophilus alcohol dehydrogenase was modified by the reactive coenzyme analogue. This residue is homologous to Cys-43 in yeast alcohol dehydrogenase and Cys-46 in the horse liver enzyme but, unlike the latter two, Cys-38 is not reactive towards iodoacetate in the native bacterial enzyme.     

Some effects of o-phenanthroline on electron transport in chromatophores from photosynthetic bacteria

The midpoint potentials of the primary electron acceptors in chromatophores from Rhodopseudomonas spheroides and Chromatium have been studied by titrating the laser-induced P605 and cytochrome c oxidations, respectively. Both midpoint potentials are pH dependent (60 mV/pH unit).o-Phenanthroline shifts the midpoint potentials of the primary acceptors, by +40 mV in Rps spheroides and +135 mV in Chromatium. A similar though less extensive change in midpoint potential was observed in the presence of batho-phenanthroline, but not with 8-hydroxyquinoline. The shifted midpoints retain the same dependence on pH.Some of the effects of o-phenanthroline can be explained by assuming that it chelates the reduced form of the primary electron acceptor. This suggests the presence in the primary electron acceptor of a metal chelated by o- and batho-phenanthroline.In Rps spheroides chromatophores o-phenanthroline inhibits the laser- and flash-induced carotenoid shift at all redox potentials, stimulates the laser-induced P605 oxidation at redox potentials between +350 and +420 mV and slows the decay of the laser-induced cytochrome c oxidation below +180 mV. These effects show that o-phenanthroline may have more than one site of action.     

Porcine kidney -amino acid oxidase: the three-dimensional structure and its catalytic mechanism based on the enzyme–substrate complex model

The three-dimensional structure of porcine kidney -amino acid oxidase (DAO), an FAD-dependent oxidase, has been solved by X-ray crystallography. The overall structure is a dimer, subunits of which are correlated by a non-crystallographic two-fold axis. Each subunit comprises two domains, ‘αβ domain’ and ‘pseudo-barrel domain’. The coenzyme FAD is in an elongated conformation and is bound at the N-terminal βαβ dinucleotide binding motif. The active site is located in the boundary region between the two domains. The crystal structure of DAO in complex with a substrate analog, o-aminobenzoate, was also solved and is used for modeling the DAO- -leucine complex, i.e. Michaelis complex, by means of molecular mechanics simulation. The Michaelis-complex model provided structural information leading to two alternative hypothetical mechanisms for the reductive half-reaction of DAO. These two hypotheses characterize themselves by electron transfer from the lone-pair orbital of the substrate amino nitrogen to flavin C(4a) and by proton transfer from the substrate α-position to flavin N(5) which acts as a catalytic base.