Purification and crystallization of benzoylformate decarboxylase

Bacterial mandelic acid degradation pathway and its application in biotechnology

Mandelic acid and its derivatives are an important class of chemical synthetic blocks, which is widely used in drug synthesis and stereochemistry research. In nature, mandelic acid degradation pathway has been widely identified and analyzed as a representative pathway of aromatic compounds degradation. The most studied mandelic acid degradation pathway from Pseudomonas putida consists of mandelate racemase, S-mandelate dehydrogenase, benzoylformate decarboxylase, benzaldehyde dehydrogenase and downstream benzoic acid degradation pathways. Because of the ability to catalyze various reactions of aromatic substrates, pathway enzymes have been widely used in biocatalysis, kinetic resolution, chiral compounds synthesis or construction of new metabolic pathways. In this paper, the physiological significance and the existing range of the mandelic acid degradation pathway were introduced first. Then each of the enzymes in the pathway is reviewed one by one, including the researches on enzymatic properties and the applications in biotechnology as well as efforts that have been made to modify the substrate specificity or improving catalytic activity by enzyme engineering to adapt different applications. The composition of the important metabolic pathway of bacterial mandelic acid degradation pathway as well as the researches and applications of pathway enzymes is summarized in this review for the first time.

Cyclohexane-1,2-dione hydrolase from denitrifying Azoarcus sp. strain 22Lin, a novel member of the thiamine diphosphate enzyme family

Alicyclic compounds with hydroxyl groups represent common structures in numerous natural compounds, such as terpenes and steroids. Their degradation by microorganisms in the absence of dioxygen may involve a C-C bond ring cleavage to form an aliphatic intermediate that can be further oxidized. The cyclohexane-1,2-dione hydrolase (CDH) (EC 3.7.1.11) from denitrifying Azoarcus sp. strain 22Lin, grown on cyclohexane-1,2-diol as a sole electron donor and carbon source, is the first thiamine diphosphate (ThDP)-dependent enzyme characterized to date that cleaves a cyclic aliphatic compound. The degradation of cyclohexane-1,2-dione (CDO) to 6-oxohexanoate comprises the cleavage of a C-C bond adjacent to a carbonyl group, a typical feature of reactions catalyzed by ThDP-dependent enzymes. In the subsequent NAD(+)-dependent reaction, 6-oxohexanoate is oxidized to adipate. CDH has been purified to homogeneity by the criteria of gel electrophoresis (a single band at ∼59 kDa; calculated molecular mass, 64.5 kDa); in solution, the enzyme is a homodimer (∼105 kDa; gel filtration). As isolated, CDH contains 0.8 ± 0.05 ThDP, 1.0 ± 0.02 Mg(2+), and 1.0 ± 0.015 flavin adenine dinucleotide (FAD) per monomer as a second organic cofactor, the role of which remains unclear. Strong reductants, Ti(III)-citrate, Na(+)-dithionite, and the photochemical 5-deazaflavin/oxalate system, led to a partial reduction of the FAD chromophore. The cleavage product of CDO, 6-oxohexanoate, was also a substrate; the corresponding cyclic 1,3- and 1,4-diones did not react with CDH, nor did the cis- and trans-cyclohexane diols. The enzymes acetohydroxyacid synthase (AHAS) from Saccharomyces cerevisiae, pyruvate oxidase (POX) from Lactobacillus plantarum, benzoylformate decarboxylase from Pseudomonas putida, and pyruvate decarboxylase from Zymomonas mobilis were identified as the closest relatives of CDH by comparative amino acid sequence analysis, and a ThDP binding motif and a 2-fold Rossmann fold for FAD binding could be localized at the C-terminal end and central region of CDH, respectively. A first mechanism for the ring cleavage of CDO is presented, and it is suggested that the FAD cofactor in CDH is an evolutionary relict.

Influence of the hydrostatic pressure and pH on the asymmetric 2-hydroxyketone formation catalyzed by Pseudomonas putida benzoylformate decarboxylase and variants thereof

Benzoylformate decarboxylase (BFD) from Pseudomonas putida is a thiamine diphosphate-dependent (ThDP) enzyme that catalyzes the asymmetric C--C bond formation to (S)-2-hydroxypropiophenone [(S)-HPP] starting from benzaldehyde and acetaldehyde. The enantioselectivity of BFD was shown to be a function of temperature and substrate concentration. It can additionally be changed by site-directed mutagenesis on hot spot positions in the active site. In this article, we present the effect of hydrostatic pressure up to 250 MPa on the enantioselectivity for the recombinant wtBFD as well as for the variants BFD F464I, BFD A460I, and BFD A460I-F464I. A general tendency toward lower amounts of (S)-HPP could be observed at increasing pressures. For two of these variants an increase in pressure even caused an inversion in the enantioselectivity and thus increasing enantiomeric excesses, respectively. A pressure-induced increase in enantioselectivity could therefore be observed for the first time in biocatalysis to the best of our knowledge. Furthermore, the pH is shown to be a parameter that also significantly influences the enantioselectivity of the reaction mentioned above.

Structural and kinetic studies on native intermediates and an intermediate analogue in benzoylformate decarboxylase reveal a least motion mechanism with an unprecedented short-lived predecarboxylation intermediate

The thiamin diphosphate- (ThDP-) dependent enzyme benzoylformate decarboxylase (BFDC) catalyzes the nonoxidative decarboxylation of benzoylformic acid to benzaldehyde and carbon dioxide. To date, no structural information for a cofactor-bound reaction intermediate in BFDC is available. For kinetic analysis, a chromophoric substrate analogue was employed that produces various absorbing intermediates during turnover but is a poor substrate with a 10(4)-fold compromised kcat. Here, we have analyzed the steady-state distribution of native intermediates by a combined chemical quench/1H NMR spectroscopic approach and estimated the net rate constants of elementary catalytic steps. At substrate saturation, carbonyl addition of the substrate to the cofactor (k' approximately 500 s-1 at 30 degrees C) and elimination of benzaldehyde (k' approximately 2.400 s-1) were found to be partially rate-determining for catalysis, whereas decarboxylation of the transient 2-mandelyl-ThDP intermediate is 1 order of magnitude faster with k' approximately 16.000 s-1, the largest rate constant of decarboxylation in any thiamin enzyme characterized so far. The X-ray structure of a predecarboxylation intermediate analogue was determined to 1.6 A after cocrystallization of BFDC from Pseudomonas putida with benzoylphosphonic acid methyl ester. In contrast to the free acid, for which irreversible phosphorylation of active center Ser26 was reported, the methyl ester forms a covalent adduct with ThDP with a similar configuration at C2alpha as observed for other thiamin enzymes. The C2-C2alpha bond of the intermediate analogue is out of plane by 7degrees, indicating strain. The phosphonate part of the adduct forms hydrogen bonds with Ser26 and His281, and the 1-OH group is held in place by interactions with His70 and the 4'-amino group of ThDP. The phenyl ring accommodates in a hydrophobic pocket formed by Phe464, Phe397, Leu109, and Leu403. A comparison with the previously determined structure of BFDC in noncovalent complex with the inhibitor (R)-mandelate suggests a least motion mechanism. Binding of benzoylphosphonic acid methyl ester to BFDC was further characterized by CD spectroscopy and stopped-flow kinetics, indicating a two-step binding mechanism with a 200-fold slower carbonyl addition to ThDP than determined for benzoylformic acid, in line with the observed slight structural reorganization of Phe464 due to steric clashes with the phosphonate moiety.

Isolation and characterization of a benzoylformate decarboxylase and a NAD+/NADP+-dependent benzaldehyde dehydrogenase involved in D-phenylglycine metabolism in Pseudomonas stutzeri ST-201

Following induction with D-phenylglycine both d-phenylglycine aminotransferase activity and benzoylformate decarboxylase activity were observed in cultures of Pseudomonas stutzeri ST-201. Induction with benzoylformate, on the other hand, induced only benzoylformate decarboxylase activity. Purification of the benzoylformate decarboxylase, followed by N-terminal sequencing, enabled the design of probes for hybridization with P. stutzeri ST-201 genomic DNA libraries. Sequencing of two overlapping genomic DNA restriction fragments revealed two open reading frames which were denoted dpgB and dpgC. Sequence alignments suggested that the genes encoded a thiamin-diphosphate-dependent decarboxylase and an aldehyde dehydrogenase, respectively. Both genes were isolated and expressed in Escherichia coli. The dpgB gene product was confirmed as a benzoylformate decarboxylase while the dpgC gene product was characterized as a NAD+/NADP+-dependent benzaldehyde dehydrogenase. In keeping with their high sequence identities (both greater than 85%) the kinetic properties of the two enzymes were similar to those of the homologous enzymes in the mandelate pathway of Pseudomonas putida ATCC 12633. However, Pseudomonas stutzeri ST-201 was unable to grow on either isomer of mandelate, and sequencing indicated that the dpgB gene did not form part of an operon. Thus it appears that the two enzymes form part of a d-phenylglycine, rather than mandelate, degrading pathway.

Protein-enhanced decarboxylation of the covalent intermediate in benzoylformate decarboxylase--Desolvation or acid catalysis?

Benzoylformate decarboxylase (BFD) enhances the rate of decarboxylation of its key intermediate compared to the nonenzymic reaction by a factor of about 10(6). It has been proposed that desolvation into a hydrophobic environment will lower the reaction barrier in TDP-dependent decarboxylases. The competition of thiamin thiazolone diphosphate (TTDP) with the cofactor thiamin diphosphate (TDP) provides a dynamic indication of the relative hydrophobicity of the cofactor binding site. BFD binds the more polar TDP tightly in the presence of excess TTDP. Therefore, desolvation would not be likely to occur during catalysis. Unlike TDP enzymes that have electron acceptors as substrates, decarboxylases require protonation to produce the precursor to the aldehyde product. A mechanism involving an associated acid that traps the carbanion generated upon C-C bond breaking will permit diffusional separation of carbon dioxide and generate the appropriate precursor to the product aldehyde. This would also account for avoidance of a competitive reaction. Hasson's detailed structure of BFD shows a highly polar active site with histidines in the vicinity of the substrate. Reports of a reduction of k(cat) to near the nonenzymic rate without a large effect on Km upon specific replacement of these histidines with alanine fit this alternative. In TDP enzymes involving oxidation or condensation, an electrophilic substrate or second cofactor will be bound (and no proton will be required). This will acquire the electron density of the carbanion itself. In such cases, protonated side chains are not functional while hydrophobic environments would promote the internal transfer.

Examination of donor substrate conversion in yeast transketolase

The cleavage of the donor substrate d-xylulose 5-phosphate by wild-type and H263A mutant yeast transketolase was studied using enzyme kinetics and circular dichroism spectroscopy. The enzymes are able to catalyze the cleavage of donor substrates, the first half-reaction, even in the absence of any acceptor substrate yielding d-glyceraldehyde 3-phosphate as measured in the coupled optical test according to Kochetov (Kochetov, G. A. (1982) Methods Enzymol. 90, 209-223) and compared with the H263A variant. Overall, the H263A mutant enzyme is less active than the wild-type. However, an increase in the rate constant of the release of the enzyme-bound glycolyl moiety was observed and related to a stabilization of the "active glycolaldehyde" (alpha-carbanion) by histidine 263. Chemically synthesized dl-(alpha,beta-dihydroxyethyl)thiamin diphosphate is bound to wild-type transketolase with an apparent K(D) of 4.3 +/- 0.8 microm (racemate) calculated from titration experiments using circular dichroism spectroscopy. Both enantiomers are cleaved by the enzyme at different rates. In contrast to the enzyme-generated alpha-carbanion of (alpha,beta-dihydroxyethyl)thiamin diphosphate formed by decarboxylation of hydroxylactylthiamin diphosphate after incubation of transketolase with beta-hydroxypyruvate, the synthesized dl-(alpha,beta-dihydroxyethyl)thiamin diphosphate did not work as donor substrate when erythrose 4-phosphate is used as acceptor substrate in the coupled enzymatic test according to Sprenger (Sprenger, G. A., Schörken, U., Sprenger, G., and Sahm, H. (1995) Eur. J. Biochem. 230, 525-532).

Thiamin-dependent enzymes as catalysts in chemoenzymatic syntheses

Enzymes are increasingly being used to perform regio- and enantioselective reactions in chemoenzymatic syntheses. To utilize enzymes for unphysiological reactions and to yield novel products, a broad substrate spectrum is desirable. Thiamin diphosphate (ThDP)-dependent enzymes vary in their substrate tolerance from rather strict substrate specificity (phosphoketolases, glyoxylate carboligase) to more permissive enzymes (transketolase, dihydroxyacetone synthase, pyruvate decarboxylase) and therefore differ in their potential to be used as biocatalysts. We give an overview of the known substrate spectra of ThDP-dependent enzymes and present examples of multi-enzyme or chemoenzymatic approaches which involve ThDP-dependent enzymes as biocatalysts to obtain pharmaceutical compounds as ephedrine and glycosidase inhibitors, sex pheromones as exo-brevicomin, 13C-labeled metabolites, and other intermediates as 1-deoxyxylulose 5-phosphate, a precursor of vitamins and isoprenoids.

Application of alpha-keto acid decarboxylases in biotransformations

The advantages of using enzymes in the synthesis of organic compounds relate to their versatility, high reaction rates, and regio- and stereospecificity and the relatively mild reaction conditions involved. Stereospecificity is especially important in the synthesis of bioactive molecules, as only one of the enantiomeric forms usually manifests bioactivity, whereas the other is often toxic. Although enzymes which catalyze asymmetric carbon-carbon bond formation are of great importance in bioorganic chemistry, only a few examples are known for thiamin diphosphate (ThDP)-dependent enzymes, whereas transformations using e.g. aldolases, lipases and lyases are well documented already. The present review surveys recent work on the application of pyruvate decarboxylase and benzoylformate decarboxylase in organic synthesis. These enzymes catalyze the synthesis of chiral alpha-hydroxy ketones which are versatile building blocks for organic and pharmaceutical chemistry. Besides the substrate spectra of both enzymes amino acid residues relevant for substrate specificity and enantioselectivity of pyruvate decarboxylase have been investigated by site-directed mutagenesis.