Biochemistry and molecular genetics of poly-gamma-glutamate synthesis

Current research into poly-gamma-glutamate (PGA) and its biosynthesis is reviewed. In PGA-producing Bacillus subtilis, glutamate racemase supplies abundant DL-glutamate, the substrate for PGA synthesis. The pgsBCA genes of PGA-producing B. subtilis, which encode the membrane-associated PGA synthetase complex PgsBCA, were characterized and the enzyme complex was suggested to be an atypical amide ligase based on its structure and function. A novel reaction mechanism of PGA synthesis is proposed.

Isolation of Bacillus subtilis (chungkookjang), a poly-gamma-glutamate producer with high genetic competence

A bacterium with high poly-gamma-glutamate (PGA) productivity was isolated from the traditional Korean seasoning, Chung-Kook-Jang. This bacterium could be classified as a Bacillus subtilis, but sporulation in culture was infrequent in the absence of Mn2+. It was judged to be a variety of B. subtilis and designated B. subtilis (chungkookjang). L-Glutamate significantly induced PGA production, and highly elongated PGAs were synthesized. The volumetric yield reached 13.5 mg ml(-1) in the presence of 2% L-glutamate. The D-glutamate content was over 50% in every PGA produced under the conditions used. During PGA production, glutamate racemase activity was found in the cells, suggesting that the enzyme is involved in the D-glutamate supply. Molecular sizes of PGAs were changed by the salt concentration in the medium; PGAs with comparatively low molecular masses were produced in culture media containing high concentrations of NaCl. B. subtilis (chungkookjang) harbors no plasmid and is the first B. subtilis strain reported with both naturally high PGA productivity and high genetic competence.

Physiological and biochemical characteristics of poly gamma-glutamate synthetase complex of Bacillus subtilis

An enzymatic system for poly gamma-glutamate (PGA) synthesis in Bacillus subtilis, the PgsBCA system, was investigated. The gene-disruption experiment showed that the enzymatic system was the sole machinery of PGA synthesis in B. subtilis. We succeeded in achieving the enzymatic synthesis of elongated PGAs with the cell membrane of the Escherichia coli clone producing PgsBCA in the presence of ATP and D-glutamate. The enzyme preparation solubilized from the membrane with 8 mM Chaps catalyzed ADP-forming ATP hydrolysis only in the presence of glutamate; the D-enantiomer was the best cosubstrate, followed by the L-enantiomer. Each component of the system, PgsB, PgsC, and PgsA, was translated in vitro and the glutamate-dependent ATPase reaction was kinetically analyzed. The PGA synthetase complex, PgsBCA, was suggested to be an atypical amide ligase.

High catalytic activity of alanine racemase from psychrophilic Bacillus psychrosaccharolyticus at high temperatures in the presence of pyridoxal 5'-phosphate

We examined the effect of the pyridoxal 5'-phosphate (PLP) cofactor on the activity and stability of the psychrophilic alanine racemase, having a high catalytic activity at low temperature, from Bacillus psychrosaccharolyticus at high temperatures. The decrease in the enzyme activity at incubation temperatures over 40 degrees C was consistent with the decrease in the amount of bound PLP. Unfolding of the enzyme at temperatures above 40 degrees C was suppressed in the presence of PLP. In the presence of 0.125 mM PLP, the specific activity of the psychrophilic enzyme was higher than that of a thermophilic alanine racemase, having a high catalytic activity at high temperature, from Bacillus stearothermophilus even at 60 degrees C.

Biochemical evidence that Escherichia coli hyi (orf b0508, gip) gene encodes hydroxypyruvate isomerase

We found a significant activity of hydroxypyruvate isomerase in Escherichia coli clone cells harboring an E. coli gene (called orf b0508 or gip), which is located downstream of the glyoxylate carboligase gene. We newly designated the gene hyi. The enzyme was purified from cell extracts of the E. coli clone. The enzyme had a molecular mass of 58 kDa and was composed of two identical subunits. The optimum pH for the isomerization of hydroxypyruvate was 6.8-7.2. The enzyme required no cofactor. It exclusively catalyzed the isomerization between hydroxypyruvate and tartronate semialdehyde. The apparent K(m) value for hydroxypyruvate was 12.5 mM. The amino acid sequence of E. coli hydroxypyruvate isomerase is highly similar to those of glyoxylate-induced proteins, Gip, found widely from prokaryotes to eukaryotes.

A poly-gamma-glutamate synthetic system of Bacillus subtilis IFO 3336: gene cloning and biochemical analysis of poly-gamma-glutamate produced by Escherichia coli clone cells

Three genes encoding a poly-gamma-glutamate synthetic system of Bacillus subtilis IFO 3336 (Bacillus natto) were cloned and expressed in Escherichia coli. The E. coli clone produced poly-gamma-glutamate extracellularly. The genes, newly designated as pgsBCA, were homologous with capBCA genes of Bacillus anthracis. All of pgsB, pgsC, and pgsA genes were essential for the polymer production. Addition of Mn(2+), instead of Mg(2+), to the polymer-synthesis medium resulted in an increase in the polymer yield. Co-expression of glutamate racemase gene in E. coli cells harboring pgsBCA genes increased both the polymer production and D-glutamate content in the polymer. The polymer produced by the E. coli clone was higher in average molecular size than that produced by B. subtilis IFO 3336.

Characterization of yrpC gene product of Bacillus subtilis IFO 3336 as glutamate racemase isozyme

Glr, the glutamate racemase of Bacillus subtilis (formerly Bacillus natto) IFO 3336 encoded by the glr gene, and YrpC, a protein encoded by the yrpC gene, which is located at a different locus from that of the glr gene in the B. subtilis genome, share a high sequence similarity. The yrpC gene complemented the D-glutamate auxotrophy of Escherichia coli WM335 cells defective in the glutamate racemase gene. Glutamate racemase activity was found in the extracts of E. coli WM335 clone cells harboring a plasmid, pYRPC1, carrying its gene. Thus, the yrpC gene encodes an isozyme of glutamate racemase of B. subtilis IFO 3336. YrpC is mostly found in an inactive inclusion body in E. coli JM109/pYRPC1 cells. YrpC was solubilized readily, but glutamate racemase activity was only slightly restored. We purified YrpC from the extracts of E. coli JM109/pYRPC2 cells using a Glutathione S-transferase Gene Fusion System to characterize it. YrpC is a monomeric protein and contains no cofactors, like Glr. Enzymological properties of YrpC, such as the substrate specificity and optimum pH, are also similar to those of Glr. The thermostability of YrpC, however, is considerably lower than that of Glr. In addition, YrpC showed higher affinity and lower catalytic efficiency for L-glutamate than Glr. This is the first example showing the occurrence and properties of a glutamate racemase isozyme.

Alanine dehydrogenase from Enterobacter aerogenes: purification, characterization, and primary structure

Alanine dehydrogenase [EC 1. 4. 1. 1] was purified to homogeneity from a crude extract of Enterobacter aerogenes ICR 0220. The enzyme had a molecular mass of about 245 kDa and consisted of six identical subunits. The enzyme showed maximal activity at about pH 10.9 for the deamination of L-alanine and at about pH 8.7 for the amination of pyruvate. The enzyme required NAD+ as a coenzyme. Analogs of NAD+, deamino-NAD+ and nicotinamide guanine dinucleotide served as coenzymes. Initial-velocity and product inhibition studies suggested that the deamination of L-alanine proceeded through a sequential ordered binary-ternary mechanism. NAD+ bound first to the enzyme, followed by L-alanine, and the products were released in the order of ammonia, pyruvate, and NADH. The Km were 0.47 mM for L-alanine, 0.16 mM for NAD+, 0.22 mM for pyruvate, 0.067 mM for NADH, and 66.7 mM for ammonia. The Km for L-alanine was the smallest in the alanine dehydrogenases studied so far. The enzyme gene was cloned into Escherichia coli JM109 cells and the nucleotides were sequenced. The deduced amino acid sequence was very similar to that of the alanine dehydrogenase from Bacillus subtilis. However, the Enterobacter enzyme has no cysteine residue. In this respect, the Enterobacter enzyme is different from other alanine dehydrogenases.

Nucleotide sequence, cloning, and overexpression of the D-threonine dehydrogenase gene from Pseudomonas cruciviae

D-Threonine dehydrogenase (EC 1.1.1) catalyses the oxidation of the 3-hydroxyl group of D-threonine. The nucleotide sequence of the structural gene, dtdS, for this enzyme from Pseudomonas cruciviae IFO 12047 was determined. The dtdS gene encodes a 292 amino acid polypeptide. The enzyme was overproduced in Escherichia coli cells; the activity was found in cell extracts of the clone. The enzyme showed high sequence similarity to 3-hydroxyisobutyrate dehydrogenases. This is the first example showing the primary structure of an enzyme catalysing the NADP(+)-dependent dehydrogenation of D-threo-3-hydroxyamino acids.

Properties of glutamate racemase from Bacillus subtilis IFO 3336 producing poly-gamma-glutamate

We found glutamate racemase activity in cell extracts of Bacillus subtilis IFO 3336, which abundantly produces poly-gamma-glutamate. The highest activity was obtained in the early stationary phase of growth. The racemase was purified to homogeneity. The enzyme was a monomer with a molecular mass of about 30 kDa and required no cofactor. It almost exclusively catalyzed the racemization of glutamate; other amino acids, including alanine and aspartate but not homocysteinesulfinate, were inactive as either substrates or inhibitors. Although the Vmax value of the enzyme for L-glutamate is 21-fold higher than that for D-glutamate, the Vmax/Km value for L-glutamate is almost equal to that for the D-enantiomer. The racemase gene, glr, was cloned into Escherichia coli cells and sequenced. The racemase was overproduced in the soluble fraction of the E. coli clone cells with the substitution of ATG for TTG, the initial codon of the glr gene. D-Amino acid aminotransferase activity was not detected in Bacillus subtilis IFO 3336 cells. B. subtilis CU741, a leuC7 derivative of B. subtilis 168, showed lower glutamate racemase activity and lower productivity of poly-gamma-glutamate than B. subtilis IFO 3336. These results suggest that the glutamate racemase is mainly concerned in D-glutamate synthesis for poly-gamma-glutamate production in B. subtilis IFO 3336.

The GLY1 gene of Saccharomyces cerevisiae encodes a low-specific L-threonine aldolase that catalyzes cleavage of L-allo-threonine and L-threonine to glycine--expression of the gene in Escherichia coli and purification and characterization of the enzyme

The GLY1 gene of Saccharomyces cerevisiae is required for the biosynthesis of glycine for cell growth [McNeil, J. B., McIntosh, E. V., Taylor, B. V., Zhang, F-R., Tang, S. & Bognar, A. L. (1994) J. Biol. Chem. 269, 9155-9165], but its gene product has not been identified. We have found that the GLY1 protein is similar in primary structure to L-allo-threonine aldolase of Aeromonas jandiae DK-39, which stereospecifically catalyzes the interconversion of L-allo-threonine and glycine. The GLY1 gene was amplified by PCR, with a designed ribosome-binding site, cloned into pUC118, and expressed in Escherichia coli cells. The enzyme was purified to homogeneity, as judged by polyacrylamide gel electrophoresis. The enzyme has a molecular mass of about 170 kDa and consists of four subunits identical in molecular mass. The enzyme contains 2 mol pyridoxal 5'-phosphate/4 mol of subunit as a cofactor, and its absorption spectrum exhibits maxima at 280 nm and 420 nm. The enzyme catalyzes the cleavage of not only L-allo-threonine to glycine but also L-threonine. We have termed the enzyme a low-specific L-threonine aldolase to distinguish it from L-allo-threonine aldolase.

A novel NADP(+)-dependent serine dehydrogenase from Agrobacterium tumefaciens

NADP(+)-dependent serine dehydrogenase [EC 1.1.1.-], which catalyzes the oxidation of the hydroxyl group of serine to form 2-aminomalonate semialdehyde, was purified to homogeneity from a crude extract of Agrobacterium tumefaciens ICR 1600. The enzyme had a molecular mass of about 100 kDa and consisted of four identical subunits. In addition to L-serine, D-serine, L-glycerate, D-glycerate, and 2-methyl-DL-serine were substrates. However, O-methyl-DL-serine and L-threonine were inert. The enzyme showed maximal activity at about pH 9 for the oxidation of L-serine. The enzyme required NADP+ as a coenzyme, NAD+ was inert. The enzyme was not inhibited by EDTA, o-phenanthroline, or alpha,alpha'-dipyridyl, but was inhibited by HgCl2, p-chloromercuribenzoate, L-cysteine, D-cysteine, malonate, 2-methylmalonate, and tartronate. The Michaelis constants for L-serine, D-serine, and NADP+ were 42, 44, and 0.029 mM, respectively.

3-Hydroxyisobutyrate dehydrogenase from Pseudomonas putida E23: purification and characterization

The NAD(+)-dependent 3-hydroxyisobutyrate dehydrogenase [EC 1.1.1.31] was purified to homogeneity from Pseudomonas putida E23. The enzyme was a tetramer (molecular mass, 120 kDa) consisted of identical subunits (molecular mass, 30 kDa). The enzyme was specific for NAD+ (Km, 0.44 mM). The maximal activity was obtained at about pH 10. The enzyme was specific for the L-isomer of 3-hydroxyisobutyrate. In addition to L-3-hydroxyisobutyrate, L-serine, 2-methyl-DL-serine, and 3-hydroxypropionate were substrates. The Km for L-3-hydroxyisobutyrate, L-serine, 2-methyl-DL-serine, and 3-hydroxypropionate were 0.12, 18, 44, and 83 mM, respectively. The enzyme was inhibited by p-chloromercuribenzoate, HgCl2, and AgNO3, but not by EDTA, alpha,alpha'-dipyridyl, and o-phenanthroline. The N-terminal 26 amino acid sequence was compared with the sequences deduced from the enzyme genes of rat liver and Pseudomonas aeruginosa.

A novel phenylserine dehydratase from Pseudomonas pickettii PS22: purification, characterization, and sequence of its phosphopyridoxyl peptide

A novel phenylserine dehydratase [EC 4.2.1.-], which catalyzes the deamination of L-threo-3-phenylserine to yield phenylpyruvate and ammonia, was purified to homogeneity from a crude extract of Pseudomonas pickettii PS22 isolated from soil. The enzyme was a monomer having a molecular mass of about 38 kDa and contained 1 mol of pyridoxal 5'-phosphate per mol of enzyme. The enzyme exhibited absorption maxima at 279 and 416 nm. No appreciable spectral change was observed over the pH range of 6.0 to 8.0. The maximal reactivity was obtained at about pH 7.5. The enzyme was highly specific for L-threo-3-phenylserine (Km, 0.21 mM). L-erythro-3-Phenylserine, L-threonine, L-serine, and D-serine were inert. The enzyme was inhibited by phenylhydrazine, hydroxylamine, p-chloromercuribenzoate, and HgCl2, but not by L-isoleucine, L-threonine, or L-serine. AMP, ADP, and ATP did not affect the enzyme activity. The N-terminal amino acid sequence was not similar to those of biosynthetic and biodegradative L-threonine dehydratases and L-serine dehydratases. The isolated tryptic phosphopyridoxyl peptide, however, contained a pyridoxal 5'-phosphate-binding consensus amino acid sequence of amino acid dehydratases.

Gene cloning, purification, and characterization of thermostable and halophilic leucine dehydrogenase from a halophilic thermophile, Bacillus licheniformis TSN9

A halophilic and thermophilic isolate from the sand of Tottori Dune was found to produce a thermostable and halophilic leucine dehydrogenase (EC 1.4.1.9). It was identified to be a new strain of Bacillus licheniformis. The enzyme gene was cloned into Escherichia coli JM109 with a vector plasmid pUC18. The enzyme was purified to homogeneity from the clone cell extract by ion-exchange column chromatography with a yield of 31%. The enzyme was found to be composed of eight subunits identical in relative molecular mass (43,000). The amino acid sequence of the enzyme, deduced from the nucleotide sequence of the gene, showed an identity of 84.6% with that of the B. stearothermophilus enzyme [Nagata S, Tanizawa K, Esaki N, Sakamoto Y, Oshima T, Tanaka H, Soda K (1988) Biochemistry 27:9056-9062], although both enzymes were similar to each other in various enzymological properties such as thermostability, substrate and coenzyme specificities, and stereospecificity for hydrogen transfer from the C-4 of NADH. However, they were markedly distinct from each other in halophilicity; the B. licheniformis enzyme was much more stable than the other in the presence of high concentrations of salts.

An inducible NADP(+)-dependent D-phenylserine dehydrogenase from Pseudomonas syringae NK-15: purification and biochemical characterization

An inducible NADP(+)-dependent D-phenylserine dehydrogenase [EC 1.1.1.-], which catalyzes the oxidation of the hydroxyl group of D-threo-beta-phenylserine, was purified to homogeneity from a crude extract of Pseudomonas syringae NK-15 isolated from soil. The enzyme consisted of two subunits identical in molecular weight (about 31,000). In addition to D-threo-beta-phenylserine, it utilized D-threo-beta-thienylserine, D-threo-beta-hydroxynorvaline, and D-threonine as substrates but was inert towards other isomers of beta-phenylserine and threonine. It showed maximal activity at pH 10.4 for the oxidation of D-threo-beta-phenylserine, and it required NADP+ as a natural coenzyme. NAD+ showed a slight coenzyme activity. The enzyme was inhibited by p-chloromercuribenzoate, HgCl2, and monoiodoacetate but not by the organic acids such as tartronate. The Michaelis constants for D-threo-beta-phenylserine and NADP+ were 0.44 mM and 29 microM, respectively. The N-terminal 27 amino acids sequence was determined. It suggested that the NADP(+)-binding site was located in the N-terminal region of the enzyme.

NADP(+)-dependent D-threonine dehydrogenase from Pseudomonas cruciviae IFO 12047

NADP(+)-dependent D-threonine dehydrogenase (EC 1.1.1.-), which catalyzes the oxidation of the 3-hydroxyl group of D-threonine, was purified to homogeneity from a crude extract of Pseudomonas cruciviae IFO 12047. The enzyme had a molecular mass of about 60,000 Da and consisted of two identical subunits. In addition to D-threonine, D-threo-3-phenylserine, D-threo-3-thienylserine, and D-threo-3-hydroxynorvaline were also substrates. However, the other isomers of threonine and 3-phenylserine were inert. The enzyme showed maximal activity at pH 10.5 for the oxidation of D-threonine. The enzyme required NADP+. NAD+ showed only slight activity. The enzyme was not inhibited by EDTA, o-phenanthroline, alpha,alpha'-dipyridyl, HgCl2, or p-chloromercuribenzoate but was inhibited by tartronate, malonate, pyruvate, and DL-2-hydroxybutyrate. The inhibition by these organic acids was competitive against D-threonine. Initial-velocity and product inhibition studies suggested that the oxidation proceeded through a sequential ordered Bi Bi mechanism. The Michaelis constants for D-threonine and NADP+ were 13 and 0.12 mM, respectively.

Characterization of the half and overall reactions catalyzed by L-lysine:2-oxoglutarate 6-aminotransferase

Significant differences were found in the reaction rate, and the substrate and reaction specificities between the half reactions and the overall reactions catalyzed by L-lysine: 2-oxoglutarate 6-aminotransferase. The half reactions between an amino donor and the enzyme-bound pyridoxal 5'-phosphate, and also between an amino acceptor and the bound pyridoxamine 5'-phosphate followed first order reaction kinetics. The extrapolated first order rate constants and dissociation constants of the substrates were determined for the half reactions: lysine, 0.87 min-1 and 5.5 mM; glutamate, 1.1 min-1 and 10.5 mM; alanine, 0.66 min-1 and 6.6 mM; 6-aminohexanoate, 0.43 min-1 and 13.3 mM; and 2-oxoglutarate, 0.33 min-1 and 2.5 mM. As compared with the values reported for the overall reactions [Soda, K., Misono, H., & Yamamoto, T. (1968) Biochemistry 7, 4102-4109], the reactivity of the inherent substrates was lower by over 4 orders in the half reaction than that in the overall reaction, and the reactivity of alanine with the bound pyridoxal 5'-phosphate was reduced to 10% of that in the overall reaction. The substrate specificity in the half reaction was much lower than that in the overall reaction, which was re-examined in a reaction system containing the same concentration of the enzyme as that for the half reactions. Lysine 6-aminotransferase catalyzes the transfer of only the terminal amino group of lysine to 2-oxoglutarate in the overall reaction. However, in the half reaction, the 2-amino group as well as the terminal one was transferred to the bound pyridoxal 5'-phosphate. The ratio of reactivity of the 2-amino group to that of the 6-amino group was considerably influenced by the pH of the reaction mixture.(ABSTRACT TRUNCATED AT 250 WORDS)

Cloning and expression of endo-beta-1,3-glucanase gene from Flavobacterium dormitator in Escherichia coli and characterization of the gene product

The beta-1,3-glucanase (1,3-beta-D-glucan glucanohydrolase, EC 3.2.1.6) gene from Flavobacterium dormitator var. glucanolyticae was cloned into Escherichia coli C600 with a vector plasmid, pBR322. The E. coli cells carrying a recombinant plasmid, pKU beta G1 (8.2 kb), showed a high beta-1,3-glucanase activity and a lytic activity on viable yeast cells. These activities were found in the periplasmic space of E. coli clone cells. Southern hybridization analysis showed that the cloned gene was derived from F. dormitator chromosomal DNA. The gene products were purified from the periplasmic fraction of E. coli by ammonium sulfate fractionation and ion-exchange chromatography. The purified enzymes were demonstrated to be identical with a lytic endo-beta-1,3-glucanase II and a nonlytic endo-beta-1,3-glucanase I from F. dormitator from their enzymological and immunological properties. In the E. coli cells, endo-beta-1,3-glucanase I was also formed by a proteolytic digestion of endo-beta-1,3-glucanase II during the cultivation as in F. dormitator. Thus, the only endo-beta-1,3-glucanase II was coded for in the cloned gene.

Leucine dehydrogenase from Corynebacterium pseudodiphtheriticum: purification and characterization

Leucine dehydrogenase [EC 1.4.1.9] was purified to homogeneity from Corynebacterium pseudodiphtheriticum ICR 2210. The enzyme consisted of a single polypeptide with a molecular weight of about 34,000. Stepwise Edman degradation provided the N-terminal sequence of the first 24 amino acids, and carboxypeptidase Y digestion provided the C-terminal sequence of the last 2 amino acids. Although the enzyme catalyzed the reversible deamination of various branched-chain L-amino acids, L-valine was the best substrate for oxidative deamination at pH 10.9 and the saturated concentration. The enzyme, however, had higher reactivity for L-leucine, and the kcat/Km value for L-leucine was higher than that for L-valine. The enzyme required NAD+ as a natural coenzyme. The NAD+ analogs 3-acetylpyridine-NAD+ and deamino-NAD+ were much better coenzymes than NAD+. The enzyme activity was significantly reduced by sulfhydryl reagents and pyridoxal 5'-phosphate. D-Enantiomers of the substrate amino acids competitively inhibited the oxidation of L-valine.

Selective determination of L-lysine with L-lysine epsilon-dehydrogenase

Simple and sensitive spectrophotometric methods were developed for the selective determination of L-lysine. The assay methods were based on the spectrophotometric determination of NADH formed in the reaction catalyzed by L-lysine epsilon-dehydrogenase (Procedure A) or the formazan produced on coupling of the dehydrogenase reaction with the reduction of a tetrazolium salt (Procedure B). Procedure B was applicable to the direct determination of L-lysine in rabbit serum.

Stereospecific abstraction of epsilon-pro-R-hydrogen of L-lysine by L-lysine epsilon-dehydrogenase from Agrobacterium tumefaciens

The stereochemical aspects of the L-lysine epsilon-dehydrogenase reaction were examined with (6R)-L-[6-3H]lysine and (6S)-DL-[6-3H]lysine. When (6S)-DL-[6-3H]lysine was used as a substrate, the tritium was found in the product, delta 1-piperideine-6-carboxylate. In contrast, the radioactivity from (6R)-L-[6-3H]lysine was not retained in the product. Thus, the pro-R hydrogen at the prochiral C-6 carbon of L-lysine is specifically abstracted by the enzyme: the enzyme behaves stereochemically as an amino acid D-dehydrogenase.

Activation of L-lysine epsilon-dehydrogenase from Agrobacterium tumefaciens by several amino acids and monocarboxylates

The activation of lysine epsilon-dehydrogenase [EC 1.4.1.] by L-lysine was dependent on lysine concentration and was accompanied by association of the dimeric enzymes to a tetramer. The lysine concentration required for the half-maximal activation was 0.28 mM, which was lower than the Km value for L-lysine. In addition to L-lysine, several compounds, which were neither substrates nor inhibitors, activated the enzyme. The compounds which activated the enzyme have common structural characteristics: they have both a carboxyl group and a hydrophobic side chain. These activators also induced the association of the enzyme. The activation of the enzyme occurred well over the pH range 5.0 to 7.5, and the maximal activation was obtained by preincubation for 5 min at 30 degrees C and pH 7.4, when 5 mM L-lysine or 6-aminocaproate was used as an activator. NADH binding experiments indicated that about 2 mol of NADH bind to 1 mol of the tetrameric enzyme: the dimeric enzyme has one catalytic site. Binding experiments with n-[1-14C]heptanoate and L-[U-14C]lysine showed that approximately 2 mol of ligands bind to 1 mol of the dimeric enzyme and L-lysine could not bind to the catalytic site of the enzyme in the absence of NAD+. These results indicate the presence of one catalytic site and two activator binding binding sites in the dimeric enzyme.

Properties of L-lysine epsilon-dehydrogenase from Agrobacterium tumefaciens

Lysine epsilon-dehydrogenase, which has been purified to homogeneity from the extract of Agrobacterium tumefaciens ICR 1600, had a molecular weight of approximately 78,000 and consisted of two subunits identical in molecular weight (about 39,000). The enzyme showed a high substrate specificity. In addition to L-lysine, S-(beta-aminoethyl)-L-cysteine was deaminated by the enzyme, but to a far lesser extent. NAD+ and some NAD+ analogs (deamino-NAD+ and 3-acetylpyridine-NAD+) served as a cofactor. The pH optimum was at about 9.7 for the deamination of L-lysine. Although the NAD+ saturation curve was hyperbolic, a sigmoid saturation curve for L-lysine was obtained with the diluted enzyme solution, in which the dimeric enzyme was predominant. The reversible association of the enzyme to the tetramer was induced either by increasing the enzyme concentration or by addition of L-lysine. The preincubation of the enzyme with 5 mM L-lysine resulted in a 2-fold increase in the activity and gave a hyperbolic saturation curve for L-lysine. Upon modification of SH groups of the enzyme with DTNB, neither the interconversion between the dimer and the tetramer nor the activation by L-lysine occurred. These results indicated that the dimeric enzyme was activated by L-lysine and the activation resulted from the association of two dimeric enzymes to form a tetramer.

Thermostable alanine dehydrogenase of Bacillus sp. DSM730: gene cloning, purification, and characterization

We have cloned the thermostable alanine dehydrogenase (EC 1.4.1.1) gene from a thermophile, Bacillus sp. DSM730, into Escherichia coli C600 with a vector plasmid, pBR322. The enzyme was overproduced by the transformed cells, and purified to homogeneity with a yield of 69% by heat treatment and another step. The enzyme has a molecular weight of about 250,000 and consists of 6 subunits identical in molecular weight (43,000). It is not inactivated by heat treatment at 75 degrees C for 60 min, or incubation in the pH range of 5.5-10.5 at 55 degrees C for 10 min. The enzyme ctalyzes the oxidative deamination of L-serine in addition to L-alanine. The oxo analogue of serine is as reactive as pyruvate. Thus, the enzyme differs markedly from alanine dehydrogenases so far studied.

Purification and characterization of a dimeric phenylalanine dehydrogenase from Rhodococcus maris K-18

NAD+-dependent phenylalanine dehydrogenase (EC 1.4.1.) was purified to homogeneity from a crude extract of Rhodococcus maris K-18 isolated from soil. The enzyme had a molecular mass of about 70,000 daltons and consisted of two identical subunits. The enzyme catalyzed the oxidative deamination of L-phenylalanine and several other L-amino acids and the reductive amination of phenylpyruvate and p-hydroxyphenylpyruvate. The enzyme required NAD+ as a natural coenzyme. The NAD+ analog 3-acetylpyridine-NAD+ showed much greater coenzyme activity than did NAD+. D-Phenylalanine, D-tyrosine, and phenylethylamine inhibited the oxidative deamination of L-phenylalanine. The enzyme reaction was inhibited by p-chloromercuribenzoate and HgCl2. Initial-velocity and product inhibition studies showed that the reductive amination proceeded through a sequential ordered ternary-binary mechanism. NADH bound first to the enzyme, followed by phenylpyruvate and then ammonia, and the products were released in the order L-phenylalanine and NAD+. The Michaelis constants were as follows: L-phenylalanine, 3.8 mM; NAD+, 0.25 mM; NADH, 43 microM; phenylpyruvate, 0.50 mM; and ammonia, 70 mM.

Occurrence of L-lysine epsilon-dehydrogenase in Agrobacterium tumefaciens

A novel amino acid dehydrogenase catalyzing the oxidative deamination of the epsilon-amino group of l-lysine was found in the crude extract of Agrobacterium tumefaciens ICR 1660. The enzyme required NAD(+) and was specific for l-lysine. The enzyme was optimally active at about pH 9.7.

Stereochemistry of proton abstraction catalyzed by lysine and ornithine omega-aminotransferases

(6R)-L-[6-3H]Lysine and (6S)-L-[6]3H]lysine were prepared to investigate the stereochemical aspects of the reaction catalyzed by bacterial L-lysine epsilon-aminotransferase. When (6R)-L-[6-3H]lysine was used as a substrate, the tritium label was retained in the product, delta 1-piperideine-6-carboxylate. In contrast, the radioactivity from (6S)-L-[6-3H]lysine was found in the solvent. Thus, the pro-S hydrogen at the prochiral C-6 carbon of L-lysine is specifically abstracted by L-lysine epsilon-aminotransferase. The proton exchange was observed by proton nuclear magnetic resonance analysis in the reaction of bacterial L-ornithine delta-aminotransferase with L-ornithine in 2H2O. The isolated L-[5-2H]ornithine was converted to dextrorotatory 4-phthalimido[4-2H]butyrate. This indicates that L-ornithine delta-aminotransferase catalyzes the stereospecific exchange of the pro-S hydrogen at the prochiral C-5 carbon of L-ornithine with the solvent.

Stereochemistry of meso-alpha,epsilon-diaminopimelate decarboxylase reaction: the first evidence for pyridoxal 5'-phosphate dependent decarboxylation with inversion of configuration

The stereochemistry of the decarboxylation of meso-alpha,epsilon-diaminopimelate catalyzed by meso-alpha,epsilon-diaminopimelate decarboxylase (EC 4.1.1.20) of Bacillus sphaericus was determined by stereochemical analyses of [6-2H]-L-lysine produced by the reaction in D2O. The product [6-2H]-L-lysine was converted to levorotatory methyl 5-phthalimido[5-2H]valerate by the reactions not affecting the absolute configuration of the asymmetric carbon atom. By contrast, methyl 5-phthalimido[5-2H]valerate derived from [2,6-2H2]-L-lysine, which was produced from [2,6-2H2]diaminopimelate by decarboxylation in H2O, was dextrorotatory. The authentic methyl (R)-5-phthalimido[5-2H]valerate prepared from L-glutamate with glutamate decarboxylase was levorotatory. These results indicate that the meso-alpha,epsilon-diaminopimelate decarboxylase reaction proceeds in an inversion mode. The deuterium label in [6-2H]-L-lysine was fully conserved during the conversion into pelletierine through [1-2H]cadaverine by the stereospecific diamine oxidase reaction. Thus, the enzymatic decarboxylation of meso-alpha,epsilon-diaminopimelate occurs with inversion of configuration in contrast to the other amino acid decarboxylase reported so far.

Properties of crystalline L-ornithine: alpha-ketoglutarate delta-aminotransferase from Bacillus sphaericus

The distribution of bacterial L-ornithine: alpha-ketoglutarate delta-aminotransferase (L-ornithine:2-oxo-acid aminotransferase [EC 2.6.1.13]) was investigated, and Bacillus sphaericus (IFO 3525) was found to have the highest activity of the enzyme, which was inducibly formed by addition of L-ornithine or L-arginine to the medium. L-Ornithine:alpha-ketoglutarate delta-aminotransferase, purified to homogeneity and crystallized from B. sphaericus, had a molecular weight of about 80,000 and consisted of two subunits identical in molecular weight (41,000) and in amino-terminal residue (threonine). The enzyme exhibited absorption maxima at 278,343, and 425 nm and contained 1 mol of pyridoxal 5'-phosphate per mol of enzyme. The formyl group of pyridoxal 5'-phosphate was bound through an aldimine linkage to the epsilon-amino group of a lysine residue of the protein. The enzyme-bound pyridoxal 5'-phosphate, absorbing at 425 nm, was released by incubation with phenylhydrazine to yield the catalytically inactive form. The inactive enzyme, which was reactivated by addition of pyridoxal 5'-phosphate, still had a 343-nm peak and contained 1 mol of a vitamin B6 compound. The holoenzyme showed positive circular dichroic bands at 340 and 425 nm, whereas the inactive form had no band at 425 nm. The enzyme was highly specific for L-ornithine and alpha-ketoglutarate and catalyzed delta-transamination between them to produce L-glutamate and L-glutamate-gamma-semialdehyde, which as spontaneously converted to delta 1-pyrroline-5-carboxylate. The enzyme activity was significantly affected by nonsubstrate amino acids, amines, and carbonyl reagents.

Properties of meso-alpha,epsilon-diaminopimelate D-dehydrogenase from Bacillus sphaericus

meso-alpha,epsilon-Diaminopimelate D-dehydrogenase, which has been purified to homogeneity from the extract of Bacillus sphaericus IFO 3525, has a molecular weight of about 80,000 and consists of two subunits identical in molecular weight (approximately 40,000). The enzyme has a high substrate specificity. In addition to meso-alpha,epsilon-diaminopimelate, lanthionine is deaminated by the enzyme to a far lesser extent. NADP+ is the exclusive cofactor. The pH optima were at about 10.5 for the deamination of meso-alpha,epsilon-diaminopimelate and at 7.5 for its amination. L and D isomers of alpha,epsilon-diaminopimelate and meso-alpha,delta-diaminoadipate competitively inhibit the oxidation of meso-alpha,epsilon-diaminopimelate. Initial velocity and product inhibition studies show that the reductive amination proceeds through a sequential ordered ternary-binary mechanism. NADPH binds first to the enzyme followed by L-alpha-amino-epsilon-ketopimelate and ammonia, and the products are released in the order of meso-alpha,epsilon-diaminopimelate and NADP+. The Michaelis constants are as follows: meso-alpha,epsilon-diaminopimelate (2.5 mM), NADP+ (83 micro M), NADPH (0.2 mM), L-alpha-amino-epsilon-ketopimelate (0.24 mM), and ammonia (12.5 mM). The pro-S hydrogen at C-4 of the dihydronicotinamide ring of NADPH is transferred to the substrate; the enzyme is B-stereospecific. Fluorometric study on binding of NADPH to the enzyme revealed that the enzyme contains two coenzyme binding sites per molecule.

L-Lysine: 2-oxoglutarate 6-aminotransferase. Subunit structure composed of non-identical polypeptides and pyridoxal 5'-phosphate-binding subunit

L-Lysine:2-oxoglutarate 6-aminotransferase from Flavobacterium lutescence (= Achromobacter liquidum) has been shown to be composed of one each of four non-identical subunits, A, B1, B2, and C. The subunits were isolated by gel filtration, and DEAE-cellulose chromatography in the presence of 8 M urea. Their molecular weights were determined by ultracentrifugation, gel electrophoresis and gel filtration: subunit A 24,000; B1 28,000; B2 28,000; C 45,000. These subunits were all different in amino acid composition. Of the two molecules of bound pyridoxal 5'-phosphate, the one which absorbs at 415 nm is bound to subunit B2 and participates in the catalytic action of the enzyme.

A new antitumor enzyme, L-lysine alpha-oxidase from Trichoderma viride. Purification and enzymological properties

L-Lysine alpha-oxidase from Trichoderma viride Y244-2 has been purified to homogeneity. The enzyme shows absorption maxima at 277, 388, and 466 nm and a shoulder around 490 nm and contains 2 mol of FAD/mol of enzyme. The enzyme has a molecular weight of approximately 116,000 and consists of two subunits identical in molecular weight (about 56,000). In addition to L-lysine, L-ornithine, L-phenylalanine, L-tyrosine, L-arginine, and L-histidine are oxidized by the enzyme to a lesser extent. Several lysine analogs such as delta-hydroxylysine are oxidized efficiently. Balance studies showed that 1 mol of L-lysine is converted to an equimolar amount of alpha-keto-epsilon-aminocaproate, ammonia, and hydrogen peroxide with the consumption of 1 mol of oxygen. alpha-Keto-epsilon-aminocaproate spontaneously is dehydrated intramolecularly into delta 1-piperideine-2-carboxylate in the presence of catalase, and is oxidatively decarboxylated into delta-aminovalerate in the absence of catalase. The Michaelis constants are as follows: 0.04 mM for L-lysine, 0.44 mM for L-ornithine, 14 mM for L-phenylalanine, and 1.6 mM for oxygen with L-lysine.

Meso-alpha,epsilon-diaminopimelate D-dehydrogenase: distribution and the reaction product

A high activity of meso-alpha-epsilon-diaminopimelate dehydrogenase was found in extracts of Bacillus sphaericus, Brevibacterium sp., Corynebacterium glutamicum, and Proteus vulgaris among bacteria tested. B. sphaericus IFO 3525, in which the enzyme is most abundant, was chosen to study the enzyme reaction. The enzyme was not induced by the addition of meso-alpha-epsilon-diaminopimelate to the growth medium. The reaction product was isolated and identified as alpha-amino-epsilon-ketopimelate by a comparison of the properties of its 2,4-dinitrophenylhydrazone with those of an authentic sample in silica gel thin-layer chromatography, absorption, infrared and proton nuclear magnetic resonance spectrometry, and elemental analyses. The alpha-amino-epsilon-ketopimelate formed enzymatically was decarboxylated by H2O2 to yield L-alpha-aminoadipate. This suggests that the amino group with D-configuration in the substrate is oxidatively deaminated; the enzyme is a D-amino acid dehydrogenase. L-alpha-Amino-epsilon-ketopimelate undergoes spontaneous dehydration to the cyclic delta1-piperideine-2,6-dicarboxylate. The enzyme reaction is reversible, and meso-alpha-epsilon-diaminopimelate was formed in the reductive amination of L-alpha-epsilon-ketopimelate.

Properties of crystalline leucine dehydrogenase from Bacillus sphaericus

The distribution of bacterial leucine dehydrogenase (L-leucine:NAD+ oxidoreductase, deaminating, EC 1.4.1.9) was investigated, and Bacillus sphaericus (IFO 3525) was found to have the highest activity of the enzyme. Leucine dehydrogenase, which was purified to homogeneity and crystallized from B. sphaericus, has a molecular weight of about 245,000 and consists of six identical subunits (Mr = 41,000). The enzyme catalyzes the oxidative deamination of L-leucine, L-valine, L-isoleucine, L-norvaline, L-alpha-aminobutyrate, and L-norleucine, and the reductive amination of their keto analogues. The enzyme requires NAD+ as a cofactor, which cannot be replaced by NADP+. D-Enantiomers of the substrate amino acids inhibit competitively the oxidation of L-leucine. The enzyme activity is significantly reduced by both sulfhydryl reagents and pyridoxal 5'-phosphate. Purine and pyrimidine bases, nucleosides and nucleotides have no effect on the enzyme activity. Initial velocity and product inhibition studies show that the reductive amination proceeds through a sequential ordered ternary-binary mechanism. NADH binds first to the enzyme followed by alpha-ketoisocaproate and ammonia, and the products are released in the order of L-leucine and NAD+. The Michaelis constants are as follows: L-leucine (1 mM), NAD+ (0.39 mM), NADH (35 micrometer), alpha-ketoisocaproate (0.31 mM), and ammonia (0.2 M). The pro-S hydrogen at C-4 of the dihydronicotinamide ring of NADH is exclusively transferred to the substrate; the enzyme is B-stereospecific.

Properties of taurine: alpha-ketoglutarate aminotransferase of Achromobacter superficialis. Inactivation and reactivation of enzyme

The activity of taurine: alpha-ketoglutarate aminotransferase (taurine: 2-oxoglutarate aminotransferase, EC 2.6.1.55) from Achromobacter superficialis is significantly diminished by treatment of the enzyme with (NH4)2SO4 in the course of purification, and recovered by incubation with pyridoxal phosphate at high temperatures such as 60 degrees C. The inactive form of enzyme absorbing at 280 and 345 nm contains 3 mol of pyridoxal phosphate per mol. The activated enzyme contains additional 1 mol of pyridoxal phosphate with a maximum at 430 nm. This peak is shifted to about 400 nm as a shoulder by dialysis of the enzyme, but the activity is not influenced. The inactive form is regarded as a partially resolved form, i.e. a semiapoenzyme. The enzyme catalyzes transamination of various omega-amino aicds with alpha-ketoglutarate, which is the exclusive amino acceptor. Hypotaurine, DL-beta-aminoisobutyrate, beta-alanine and taurine are the preferred amino donors. The apparent Michaelis constants are as follows; taurine 12 mM, hypotaurine 16 mM, DL-beta-aminoisobutyrate 11 mM, beta-alanine 17 mM, alpha ketoglutarate 11 mM and pyridoxal phosphate 5 micron.

L-Lysine-alpha-ketoglutarate epsilon-aminotransferease. Properties of the bound pyridoxal 5'-phosphate

L-Lysine-alpha-ketoglutarate epsilon-aminotransferase of Flavobacterium lutescens (Achromobacter liquidum) IFO 3084 shows positive circular dichroic bands at 340 and 415 nm where absorption maxima are observed, and fluorescence maxima at 380 and 490 nm on excitation at 340 and 415 nm, respectively. The pyridoxal 5'-phosphate absorbing at 415 nm is bound through an aldimine linkage to an epsilon-amino group of the lysine residue of the protein. Upon aging, the 415 nm pyridoxal 5'-phosphate changes to a less active form (lambda max, 325 nm), which is distinguishable from the 340 nm pyridoxal 5'-phosphate. This 325 nm bound pyridoxal 5'-phosphate is reduced with sodium borohydride and shows no circular dichroism. When the semiapoenzyme is aged under the same conditions, no spectral change is observed. These findings suggest that the pyridoxal 5'-phosphate bound through an aldimine linkage may be converted into a carbinol amine or some other related form by aging.

D-amino acid aminotransferase of Bacillus sphaericus. Enzymologic and spectrometric properties

D-Amino acid aminotransferase, purified to homogeneity and crystallized from Bacillus sphaericus, has a molecular weight of about 60,000 and consists of two subunits identical in molecular weight (30,000). The enzyme exhibits absorption maxima at 280, 330, and 415 nm, which are independent of the pH (5.5 to 10.0), and contains 2 mol of pyridoxal 5'-phosphate per mol of enzyme. One of the pyridoxal-5'-P, absorbing at 415 nm, is bound in an aldimine linkage to the epsilon-amino group of a lysine residue of the protein, and is released by incubation with phenylhydrazine to yield the catalytically inactive form. The inactive form, which is reactivated by addition of pyridoxal 5'phosphate, still has a 330 nm peak and contains 1 mol of pyridoxal 5'-phosphate. Therefore, this form is regarded as a semiapoenzyme. The holoenzyme shows negative circular dichroic bands at 330 and 415 nm. D-Amino acid aminotransferase catalyzes alpha transamination of various D-amino acids and alpha-keto acids. D-Alanine, D-alpha-aminobutyrate and D-glutamate, and alpha-ketoglutarate, pyruvate, and alpha-ketobutyrate are the preferred amino donors and acceptors, respectively. The enzyme activity is significantly affected by both the carbonyl and sulfhydryl reagents. The Michaelis constants are as follows: D-alanine (1.3 and 4.2 mM with alpha-ketobutyrate and alpha-ketoglutarate, respictively), alpha-ketobutyrate (14 mM withD-alanine), alpha-ketoglutarate (3.4 mM with D-alanine), pyridoxal 5'-phosphate (2.3 muM) and pyridoxamine 5'-phosphate (25 muM).

Spectrophotometric determination of pyridoxal and pyridoxal 5'-phosphate with 3-methyl-2-benzothiazolone hydrazone hydrochloride, and their selective assay

A spectrophotometric method with 3-methyl-2-benzothiazolone hydrazone hydrochloride was developed for the determination of pyridoxal and pyridoxal 5'-phosphate, and for the selective determination of each in the presence of the other. Pyridoxal and pyridoxal 5'-phosphate react with the reagent to yield the azine derivatives, which give characteristic absorption spectra. The highest extinction values are obtained when pyridoxal and pyridoxal 5'-phosphate are incubated at pH values of about 3.4 and 8.0 respectively; their maxima are at 430nm. (in 2.74x10(4)) and 380nm. (in 2.24x10(4)) respectively. The azine of pyridoxal is only slightly soluble under the neutral and alkaline conditions, whereas that of pyridoxal 5'-phosphate is substantially insoluble in the acid pH range. This difference in solubility of the azines made possible the selective determination of pyridoxal and pyridoxal 5'-phosphate. alpha-Oxoglutarate and pyruvate are among the substances shown not to interfere with the assay of pyridoxal; their derivatives absorb appreciably only at wavelengths below 420nm. For the assay of pyridoxal 5'-phosphate in the presence of these compounds measurement at 390nm. is necessary.