Jaap A. Jongejan

The enantiomeric ratio : origin, determination and prediction

Abstract The enantiomeric ratio E =(kcatR/KmR)/(kcatS/KmS) offers a concise representation of the enantioselective properties of an enzyme in reactions that involve chiral compounds. Both as a measure of the intrinsic selectivity of the catalyst, and as a parameter to model the performance of enzymatic processes for the production of enantiopure fine-chemicals, its merits have been well-recognized. Several methods for the determination of E exist. The scope and limitations of these methods are evaluated in terms of accuracy and feasibility. There appears to be no single method that is both reliable and readily applicable in all cases. Complementary methods, however, are available. The outstanding characteristics of the enantiomeric ratio as a quantitative measure of the effects of physical and chemical conditions on the intrinsic enantioselectivity of enzymes are presented in terms of the difference in Gibbs energies of the diastereomeric enzyme-substrate transition states. The prospects of molecular modeling strategies for the prediction of E are discussed.

Distribution of amine oxidases and amine dehydrogenases in bacteria grown on primary amines and characterization of the amine oxidase from Klebsiella oxytoca

The bacteria Klebsiella oxytoca LMD 72.65 (ATCC 8724), Arthrobacter P1 LMD 81.60 (NCIB 11625), Paracoccus versutus LMD 80.62 (ATCC 25364), Escherichia coli W LMD 50.28 (ATCC 9637), E. coli K12 LMD 93.68, Pseudomonas aeruginosa PAO1 LMD 89.1 (ATCC 17933) and Pseudomonas putida LMD 68.20 (ATCC 12633) utilized primary amines as a carbon and energy source, although the range of amines accepted varied from organism to organism. The Gram-negative bacteria K. oxytoca and E. coli as well as the Gram-positive methylotroph Arthrobacter P1 used an oxidase whereas the pseudomonads and the Gram-negative methylotroph Paracoccus versutus used a dehydrogenase for amine oxidation. K. oxytoca utilized several primary amines but showed a preference for those containing a phenyl group moiety. Only a single oxidase was used for oxidation of the amines. After purification, the following characteristics of the enzyme indicated that it belonged to the group of copper-quinoprotein amine oxidase (EC 1.4.3.6): the molecular mass (172,000 Da) of the homodimeric protein; the UV/visible and EPR spectra of isolated and p-nitrophenylhydrazine-inhibited enzyme; the presence and the content of copper and topaquinone (TPQ). The amine oxidase appeared to be soluble and localized in the periplasm, but catalase and NAD-dependent aromatic aldehyde dehydrogenase, enzymes catalysing the conversion of its reaction products, were found in the cytoplasm. From the amino acid sequence of the N-terminal part as well as that of a purified peptide, it appears that K. oxytoca produces a copper-quinoprotein oxidase which is very similar to that found in other Enterobacteriaceae.

Hydrolytic activity in baker's yeast limits the yield of asymmetric 3-oxo ester reduction.

Microbial reductions of ketones hold great potential for the production of enantiopure alcohols, as long as highly selective redox enzymes are not interfered with by competing activities. During reduction of ethyl 3-oxobutanoate by bakers yeast (Saccharomyces cerevisiae) to ethyl (S)-3-hydroxybutanoate, a high enantiomeric excess (> 99%) can be obtained. However, reported yields do not exceed 50-70%. In this article, three main causes are shown to be responsible for these low to moderate yields. These are evaporation of the substrate and product esters, absorption or adsorption of the two esters by the yeast cells and hydrolysis of the two esters by yeast enzymes. The hydrolysis products are further metabolized by the yeast. By reducing the evaporation and absorption losses, the reduction yield can easily be improved to about 85%. Improvement of the efficiency of the reduction and hence the reduction/hydrolysis ratio should lead to a further increase in yield.

Catalysis of iron core formation in Pyrococcus furiosus ferritin

The hollow sphere-shaped 24-meric ferritin can store large amounts of iron as a ferrihydrite-like mineral core. In all subunits of homomeric ferritins and in catalytically active subunits of heteromeric ferritins a diiron binding site is found that is commonly addressed as the ferroxidase center (FC). The FC is involved in the catalytic Fe(II) oxidation by the protein; however, structural differences among different ferritins may be linked to different mechanisms of iron oxidation. Non-heme ferritins are generally believed to operate by the so-called substrate FC model in which the FC cycles by filling with Fe(II), oxidizing the iron, and donating labile Fe(III)–O–Fe(III) units to the cavity. In contrast, the heme-containing bacterial ferritin from Escherichia coli has been proposed to carry a stable FC that indirectly catalyzes Fe(II) oxidation by electron transfer from a core that oxidizes Fe(II). Here, we put forth yet another mechanism for the non-heme archaeal 24-meric ferritin from Pyrococcus furiosus in which a stable iron-containing FC acts as a catalytic center for the oxidation of Fe(II), which is subsequently transferred to a core that is not involved in Fe(II)-oxidation catalysis. The proposal is based on optical spectroscopy and steady-state kinetic measurements of iron oxidation and dioxygen consumption by apoferritin and by ferritin preloaded with different amounts of iron. Oxidation of the first 48 Fe(II) added to apoferritin is spectrally and kinetically different from subsequent iron oxidation and this is interpreted to reflect FC building followed by FC-catalyzed core formation.

Exploration of lipase-catalyzed direct amidation of free carboxylic acids with ammonia in organic solvents

Abstract Lipase-catalyzed direct amidation of free carboxylic acids is possible with ammonia in organic solvents. For butyric acid as a model compound the reaction proceeds well despite precipitation of ammonium butyrate, provided that the added molar amounts of butyric acid and ammonia are in the same range. The addition of ammonium salts is a convenient way to ensure suitable ammonia concentrations. Using Candida antarctica lipase B as the biocatalyst, the amidation proceeds well for various carboxylic acids and is very enantioselective in the amidation of 4-methyloctanoic acid.

Description of Hydrolase-Enantioselectivity Must be Based on the Actual Kinetic Mechanism: Analysis of the Kinetic Resolution of Glycidyl (2,3-Epoxy-1-Propyl) Butyrate by Pig Pancreas Lipase

The kinetic resolution of R,S-glycidyl (R,S-2,3-epoxy-1-propyl) butyrate catalyzed by pig pancreas lipase (PPL) was studied in monophasic and biphasic systems. The course of the resolution at ester concentrations exceeding 0.05 M or in the presence of R,S-glycidol (R,S-2,3-epoxy-1-propanol), could not be described by the equations derived for a one substrate enzyme with a minimal kinetic scheme (Chen et al., 1987). Trivial causes like heterogeneity in activity of the (crude) PPL preparation and equilibrium phenomena due to changing phase ratios could be excluded. An equation based on the kinetic mechanism of hydrolases, in which the acyl-enzyme intermediate is allowed to react with water as well as with the produced alcohol (quantified by the selectivity constant, α), was evaluated. All initial rate and conversion data could be adequately fitted with this equation, not only for PPL in the monophasic (free in solution) but also in the biphasic (adsorbed to the interface) systems where it exhibited better a...

Enantioselective acylation of α-aminonitriles catalysed by Candida antarctica lipase. An unexpected turnover-related racemisation

Abstract Candida antarctica lipase B (Novozyme 435) catalysed the enantioselective acylation of 2-amino-2-phenylacetonitrile 1 with ethyl phenylacetate affording a near enantiopure product in 47% yield. Acylation of 1 and 2-amino-4-phenylbutyronitrile with ethyl acetate yielded an unexpected partially racemised final product. The racemisation was shown to be turnover related and is ascribed to the increased acidity of the α-proton in the formation of the tetrahedral intermediate in the active site of the enzyme.

[22] Solvent effect in lipase-catalyzed racemate resolution

Publisher Summary The ability of enzymes to catalyze enantioselective and enantiospecific reactions is evident from the large variety of enantiomerically pure natural products. Their potential as catalysts for asymmetric synthesis and racemate resolution in organic synthetic applications has obtained much attention. The majority of enzymes presently used for this purpose belong to the class of hydrolases, comprising lipases, esterases, and proteases. The stereochemical features of hydrolases can be utilized both in hydrolytic and in condensation reactions. Replacing bulk water with organic solvents has been reported to affect enzymes in various ways. Changes of stability, activity, and selectivity have been observed. This chapter presents solvent effects of practical importance for the application of lipases in racemate resolutions. Thermodynamic effects of the solvent become clear when thermodynamic activities are introduced as the mass action equivalents of the concentrations of all species involved in regular rate equations. Rationalization for this choice has been given elsewhere. Also, in this case, representation of rate equations in terms of thermodynamic activities narrows the range of α-selectivities observed in the solvents studied, emphasizing the intrinsic value of this parameter.

Reinvestigation of the Steady-State Kinetics and Physiological Function of the Soluble NiFe-Hydrogenase I of Pyrococcus furiosus

Pyrococcus furiosus has two types of NiFe-hydrogenases: a heterotetrameric soluble hydrogenase and a multimeric transmembrane hydrogenase. Originally, the soluble hydrogenase was proposed to be a new type of H2 evolution hydrogenase, because, in contrast to all of the then known NiFe-hydrogenases, the hydrogen production activity at 80 degrees C was found to be higher than the hydrogen consumption activity and CO inhibition appeared to be absent. NADPH was proposed to be the electron donor. Later, it was found that the membrane-bound hydrogenase exhibits very high hydrogen production activity sufficient to explain cellular H2 production levels, and this seems to eliminate the need for a soluble hydrogen production activity and therefore leave the soluble hydrogenase without a physiological function. Therefore, the steady-state kinetics of the soluble hydrogenase were reinvestigated. In contrast to previous reports, a low Km for H2 (approximately 20 microM) was found, which suggests a relatively high affinity for hydrogen. Also, the hydrogen consumption activity was 1 order of magnitude higher than the hydrogen production activity, and CO inhibition was significant (50% inhibition with 20 microM dissolved CO). Since the Km for NADP+ is approximately 37 microM, we concluded that the soluble hydrogenase from P. furiosus is likely to function in the regeneration of NADPH and thus reuses the hydrogen produced by the membrane-bound hydrogenase in proton respiration.

The covalent structure of the small subunit from Pseudomonas putida amine dehydrogenase reveals the presence of three novel types of internal cross-linkages, all involving cysteine in a thioether bond.

Pseudomonas putida contains an amine dehydrogenase that is called a quinohemoprotein as it contains a quinone and two hemes c as redox active groups. Amino acid sequence analysis of the smallest (8.5 kDa), quinone-cofactor-bearing subunit of this heterotrimeric enzyme encountered difficulties in the interpretation of the results at several sites of the polypeptide chain. As this suggested posttranslational modifications of the subunit, the structural genes for this enzyme were determined and mass spectrometric de novo sequencing was applied to several peptides obtained by chemical or enzymatic cleavage. In agreement with the interpretation of the X-ray electronic densities in the diffraction data for the holoenzyme, our results show that the polypeptide of the small subunit contains four intrachain cross-linkages in which the sulfur atom of a cysteine residue is involved. Two of these cross-linkages occur with the β-carbon atom of an aspartic acid, one with the γ-carbon atom of a glutamic acid and the fourth with a tryptophanquinone residue, this adduct constituting the enzymes quinone cofactor, CTQ. The thioether type bond in all four of these adducts has never been found in other proteins. CTQ is a novel cofactor in the series of the recently discovered quinone cofactors.