Aerobic metabolism of l-β-lysine in a Pseudomonas. Coenzyme A-dependent acetylation of l-β-lysine

An unidentified Pseudomonas, strain B4, capable of using l-β-lysine as a sole carbon, nitrogen and energy source was isolated from soil. The enzyme system required for the oxidation of this substrate is induced by l-β-lysine and to a lesser degree by 4-aminobutyrate. Extracts of the bacterium contain an enzyme catalyzing a reaction between acetyl-CoA and l-β-lysine to form 6-N-acetyl-l-β-lysine. Lysine, ornithine and other diamino and monoamino acids are not acetylated by this enzyme. The relatively high activity of the acetylating enzyme and the absence of enzymes catalyzing direct oxidation or deamination of l-β-lysine, indicate that acetylation is the first step in β-lysine metabolism in this organism. Acetyl-β-lysine is readily deaminated by extracts in the presence of an α-keto acid to form a second product that is uncharged in acid solution.     

D2O-alanine exchange reactions catalyzed by alanine racemase and glutamic pyruvic transminase

NMR studies in D₂O (>90%) reveal that Alanine Racemase (5.1.1.1.) from $\text{B. subtilis}$ catalyzes the exchange of the α hydrogen of $\text{D}$- and $\text{L}$-alanine with D₂O. Glutamic Pyruvic Transaminase (2.6.1.2.) and Glutamic Oxaloacetic Transaminase (2.6.1.1.) catalyze the exchange of α and β hydrogens of $\text{L}$-alanine. The rates of exchange of α and β hydrogens appear to be of the same order of magnitude. The transaminase catalyzed exchange is enhanced by catalytic amounts of pyruvate. The side chain of $\text{L}$-alanine is held more rigidly at the active site of transaminase so that the planar conjugated system can be extended to include the α and β carbons. A generalized mechanism is proposed for the action of pyridoxal phosphate dependent transaminases which extends Braunstein and Snell mechanism to include the structures which contribute to the labilization of β hydrogens of amino acids by the transaminases that have been studied.     

Distribution of ω-Amino Acid: Pyruvate Transaminase and Aminobutyrate: α-Ketoglutarate Transaminase in Microorganisms

The distribution of ω-amino acid transaminases in microorganisms was investigated, ω-Amino acid: pyruvate transaminase (ω-APT) was found in bacteria and yeasts, but not in actinomycetes and fungi. On the contrary, aminobutyrate: α-ketoglutarate transaminase (GABA-T) was shown in most of the microorganisms from bacteria to fungi. β-Alanine is a preferred amino donor for the co-APT reaction. Although bacterial and yeast GABA-T are inactive for β-alanine, fungal and actinomycete enzymes react with this compound and γ-aminobutyrate. In comparing these results with those of plant and mammalian enzymes, two different pathways of co-amino acid metabolism are suggested for bacteria, yeast and plants, i.e. one for β-alanine and the other for γ-aminobutyrate, catalyzed by ω-APT and GABA-T, respectively. In actinomycetes, fungi, and mammals GABA-T may be involved in the metabolism of both ω-amino acids. In addition, evolutionary changes of ω-amino acid transaminases are discussed.     

Purification and Characterization of l-Leucine-α-ketoglutarate Transaminase from Acetobader suboxydans

l-Leucine-α-ketoglutarate (α-KGA) transaminase from Acetobacter suboxydans was purified to the state of homogeneity by the criteria of ultracentrifugation and electrophoresis on a cellulose acetate membrane. The molecular weight was about 80,000 and one mole of pyridoxal 5′-phosphate was bound per mole of enzyme as a coenzyme. The enzyme exhibited absorption maxima at 280, 337 and 414 nm.

The branched-chain amino acids and α-KGA were specific as amino donors and an acceptor. l-Leucine-α-KGA transaminase is suggested to correspond to the enzyme so-called Transaminase B.     

Isolation and characterization of acetylornithine delta-transaminase of wild-type Escherichia coli W. Comparison with arginine-inducible acetylornithine delta-transaminase.

The enzyme that catalyzes the reversible conversion of N-acetylglutamic γ-semialdehyde and l-glutamate to α-N-acetyl-l-ornithine and α-ketoglutarate, acetylornithine δ-transaminase, has been isolated in homogeneous form and crystallized from both the wild-type and the arginine-inducible strains of Escherichia coli W. The molecular weight of the wild-type transaminase is 119,000 while the molecular weight of the arginine-inducible enzyme is 61,000. However, the arginine-inducible acetylornithine δ-transaminase is not a breakdown product of the wild-type, arginine-repressible transaminase. Analysis of crude extracts of the wild-type and arginine-inducible strains by varying the acrylamide concentration in polyacrylamide disc gel electrophoresis showed that arginine-inducible and wild-type transaminases differed in ionic charge. Immunochemical analysis of the two transaminases showed that neither enzyme would cross-react with antibodies prepared against its counterpart. Treatment of the two enzymes with sodium dodecyl sulfate, followed by disc gel electrophoresis revealed that both transaminases were composed of 31,000-dalton subunits. Tryptic digestion of the two transaminases showed that nearly identical peptides were present. The overall data suggest that the wild-type and inducible transaminases were products of two different structural genes. The two transaminases have different molecular weights, ionic charges, and antigenic determinants, but both are composed of similar molecular weight subunits and show a high degree of similarity in amino acid content and peptide composition.     

GABA-TRANSAMINASES OF HUMAN BRAIN AND PERIPHERAL TISSUES—KINETIC AND MOLECULAR PROPERTIES

Abstract— Kinetic experiments with 4-aminobutyrate-2-ketoglutarate transaminase (GABA-T), partially purified from human brain tissue, supported a Bi Bi Ping-Pong type of enzyme mechanism in which the enzyme oscillates between forms bound to pyridoxal phosphate and pyridoxamine phosphate. Extrapolated K _m values were 0.31 m m for γ-aminobutyrate, 0.16 m m for α-ketoglutarate, and 3.8 μ m for pyridoxal phosphate. Very similar kinetic parameters were observed with rat brain enzyme. Apparent molecular weight of human GABA-T by gel filtration was 70,000 ± 3000. Electrofucusing experiments indicated a single ionic form with isoelectric pH = 5.7. Enzyme activity was inhibited by Tris, halides, cadmium and cupric ions, and known GABA-T inhibitors.
GABA-transaminating enzymes isolated from human kidney and liver were found to be similar to the brain enzyme with respect to substrate affinities, cofactor requirements, isoelectric pH values, molecular weights, and response to inhibitors.     

Metabolism of l-β-lysine by a Pseudomonas: Purification and properties of 3-keto-6-acetamidohexanoate cleavage enzyme

Extracts of Pseudomonas B4 grown with l-β-lysine (3,6-diaminohexanoate) as the main energy source are shown to contain a 3-keto-6-acetamidohexanoate cleavage enzyme that converts 3-keto-6-acetamidohexanoate and acetyl · CoA reversibly to 4-acetamidobutyryl · CoA and acetoacetate. The enzyme catalyzes the third step in β-lysine degradation. In unfractionated extracts cleavage enzyme activity is generally assayed spectrophotometrically by coupling the forward reaction with excess 4-acetamidobutyryl · CoA thiolesterase, derived from the same organism, and measuring the rate of CoASH formation by reaction with 5,5-dithiobis(2-nitrobenzoic acid). Enzyme freed of thiolesterase is conveniently assayed by using 4-acetamidobutyryl · CoA and acetoacetate as substrates and measuring acetyl · CoA formation by means of citrate synthase reaction in the presence of 5,5-dithiobis(2-nitrobenzoic acid). The cleavage enzyme has been purified 38-fold to a specific activity of 237 mU/mg. The stoichiometry, equilibrium constant, molecular weight, and various kinetic properties of the enzymatic reaction have been determined. The substrate specificity of the Pseudomonas enzyme differs markedly from that of the analogous 3-keto-5-aminohexanoate cleavage enzyme of Clostridium subterminale strain SB4 and is broader. In the forward reaction 3-ketohexanoate can replace 3-keto-6-acetamidohexanoate, and propionyl · CoA can replace acetyl · CoA as a substrate. In the backward reaction, 4-acetamidobutyryl · CoA can be replaced by any of several CoA thiolesters including the butyryl, valeryl, 4-propionamidobutyryl, 3-acetamidopropionyl, and β-alanyl derivatives, and acetoacetate can be replaced by 2-methylacetoacetate. The products of these reactions have been characterized. Unlike the cleavage enzyme of Clostridium subterminale strain SB4, the Pseudomonas enzyme is not stimulated by Co²⁺ or Mn²⁺ and is not inhibited by EDTA, 5,5-dithiobis(2-nitrobenzoic acid), or p-chloromercuribenzoate. Tracer experiments indicate that carbon atoms 1 and 2 of acetoacetate are derived from carbon atoms 1 and 2 of 3-keto-6-acetamidohexanoate, and carbon atoms 3 and 4 of acetoacetate are derived from the acetyl group of acetyl · CoA. The cleavage enzyme is not formed in detectable amounts when Pseudomonas B4 is grown in a peptone-yeast extract medium.     

Studies of regulatory metabolism in Moniezia expansa: Glutamate,and the absence of the γ-aminobutyrate pathway

Moniezia expansa takes up radioactive glutamate from an isotonic medium, and radiocarbon appears primarily in α-ketoglutarate and succinate. Glutamate-oxaloacetate and glutamate-pyruvate transaminase activities were present in subcellular preparations; however, the enzymes of the γ-aminobutyrate pathway were absent. Further attempts to obtain indirect evidence for the operation of this pathway failed, and the metabolism of glutamate appears to take place via a preliminary transamination to α-ketoglutarate, followed by oxidation to succinate.     

Kinetic Studies on the Inhibition of GABA-T by γ-Vinyl GABA and Taurine

γ-Aminobutyric acid transaminase (GABA-T, EC 2.6.1.19) is a pyridoxal phosphate (PLP) dependent enzyme that catalyzes the degradation of γ-aminobutyric acid. The kinetics of this reaction are studied in vitro, both in the absence, and in the presence of two inhibitors: γ-vinyl GABA (4-aminohex-5-enoic acid), and a natural product, taurine (ethylamine-2-sulfonic acid). A kinetic model that describes the transamination process is proposed. GABA-T from Pseudomonas fluorescens is inhibited by γ-vinyl GABA and taurine at concentrations of 51.0 and 78.5?mM. Both inhibitors show competitive inhibition behavior when GABA is the substrate and the inhibition constant (K_i) values for γ-vinyl GABA and taurine were found to be 26±3?mM and 68±7?mM respectively. The transamination process of α-ketoglutarate was not affected by the presence of γ-vinyl GABA, whereas, taurine was a noncompetitive inhibitor of GABA-T when α-ketoglutarate was the substrate. The inhibition dissociation constant (K_ii) for this system was found to be 96±10?mM. The Michaelis-Menten constant (K_m) in the absence of inhibition, was found to be 0.79±0.11?mM, and 0.47±0.10?mM for GABA and α-ketoglutarate respectively.     

Metabolic pathway of 6-aminohexanoate in the nylon oligomer-degrading bacterium Arthrobacter sp. KI72: identification of the enzymes responsible for the conversion of 6-aminohexanoate to adipate

Arthrobacter sp. strain KI72 grows on a 6-aminohexanoate oligomer, which is a by-product of nylon-6 manufacturing, as a sole source of carbon and nitrogen. We cloned the two genes, nylD ₁ and nylE ₁ , responsible for 6-aminohexanoate metabolism on the basis of the draft genomic DNA sequence of strain KI72. We amplified the DNA fragments that encode these genes by polymerase chain reaction using a synthetic primer DNA homologous to the 4-aminobutyrate metabolic enzymes. We inserted the amplified DNA fragments into the expression vector pColdI in Escherichia coli, purified the His-tagged enzymes to homogeneity, and performed biochemical studies. We confirmed that 6-aminohexanoate aminotransferase (NylD₁) catalyzes the reaction of 6-aminohexanoate to adipate semialdehyde using α-ketoglutarate, pyruvate, and glyoxylate as amino acceptors, generating glutamate, alanine, and glycine, respectively. The reaction requires pyridoxal phosphate (PLP) as a cofactor. For further metabolism, adipate semialdehyde dehydrogenase (NylE₁) catalyzes the oxidative reaction of adipate semialdehyde to adipate using NADP⁺ as a cofactor. Phylogenic analysis revealed that NylD₁ should be placed in a branch of the PLP-dependent aminotransferase sub III, while NylE₁ should be in a branch of the aldehyde dehydrogenase superfamily. In addition, we established a NylD₁/NylE₁ coupled system to quantify the aminotransferase activity and to enable the conversion of 6-aminohexaoate to adipate via adipate semialdehyde with a yield of > 90%. In the present study, we demonstrate that 6-aminohexanoate produced from polymeric nylon-6 and nylon oligomers (i.e., a mixture of 6-aminohexaoate oligomers) by nylon hydrolase (NylC) and 6-aminohexanoate dimer hydrolase (NylB) reactions are sequentially converted to adipate by metabolic engineering technology.

     

A continuous automated assay of lipolysis during perifusion of isolated fat cells

Cysteine sulfinate transaminase (E.C. 2.6.1,l-cysteine sulfinate:2 oxoglutarate aminotransferase) catalyzes the conversion of cysteine sulfinate and α-ketoglutarate to 3-sulfonyl pyruvate and glutamate. A simple two-step assay has been developed to measure the enzyme activity in the high speed supernatant of whole brain homogenate. In the first step, the supernatant is incubated in the presence of exogenous substrate, then glutamate dehydrogenase is added to catalyze the conversion of glutamate to α-ketoglutarate, and the concomitant production of NADH is fluorimetrically monitored. The apparent K_m values of cysteine sulfinate transaminase for cysteine sulfinate and α-ketoglutarate are 1.24 and 0.22 mm, respectively. This assay is extremely rapid and has a high sensitivity, samples containing as low as 30 ng of protein may be accurately assayed.     

The ilvEDA operon of Escherichia coli K12 encodes only one valine-alpha-ketoglutarate transaminase activity.

Transaminase B of $\text{E. coli}$ K12 was purified to apparent homogeneity as measured by SDS acrylamide gel electrophoresis, immunoelectrophoresis, and amino terminal sequence analysis. The valine- and isoleucine-α-ketoglutarate dependent transaminase activities of pure enzyme as well as crude extracts were characterized by immunologic and kinetic methods. The data disprove the existence of a separate valine-α-ketoglutarate transaminase within the $\text{ilvEDA}$ operon.     

Ornithine transaminase from Cucurbita maxima cotyledons

During germination a marked increase in both soluble and particulate ornthine transaminase occurs in pumpkin cotyledons. Both enzymes had a pH optimum of 8.3 and a requirement for ornthine and α-ketoglutarate. Other keto acids or amino donors showed little activity. The enzymes required an active sulphydryl group for maximum activity. Exogenous pyridoxal phosphate was not required, but hydroxylamine inhibited the reaction and added pyridoxal phosphate overcame this inhibition. Proline inhibited the reaction and may play a role in the fate of ornithine in pumpkin cotyledons.     

Characterization of the S289A,D mutants of yeast cystathionine β-synthase

Cystathionine β-synthase (CBS) catalyzes the pyridoxal 5′-phosphate (PLP)-dependent condensation of l-serine and l-homocysteine to form l-cystathionine in the first step of the reverse transsulfuration pathway. Residue S289 of yeast CBS, predicted to form a hydrogen bond with the pyridine nitrogen of the PLP cofactor, was mutated to alanine and aspartate. The k_cat/K_m^l-Ser of the S289A mutant is reduced by a factor of ～ 800 and the β-replacement activity of the S289D mutant is undetectable. Fluorescence energy transfer between tryptophan residue(s) of the enzyme and the PLP cofactor, observed in the wild-type enzyme and diminished in the S289A mutant, is absent in S289D. These results demonstrate that residue S289 is essential in maintaining the properties and orientation of the pyridine ring of the PLP cofactor. The reduction in activity of ytCBS-S289A suggests that ytCBS catalyzes the α,β-elimination of l-Ser via an E1cB mechanism.     

Engineering a single-chain Fv antibody to alpha v beta 6 integrin using the specificity-determining loop of a foot-and-mouth disease virus

The αvβ6 integrin is a promising target for cancer therapy. Its expression is up-regulated de novo on many types of carcinoma where it may activate transforming growth factor-β1 and transforming growth factor-β3, interact with the specific extracellular matrix proteins and promote migration and invasion of tumor cells. The viral protein 1 (VP1) coat protein of the O₁ British field strain serotype of foot-and-mouth disease virus is a high-affinity ligand for αvβ6, and we recently reported that a peptide derived from VP1 exhibited αvβ6-specific binding in vitro and in vivo. We hypothesized that this peptide could confer binding specificity of an antibody to αvβ6. A 17-mer peptide of VP1 was inserted into the complementarity-determining region H3 loop of MFE-23, a murine single-chain Fv (scFv) antibody reactive with carcinoembryonic antigen (CEA). The resultant scFv (B6-1) bound to αvβ6 but retained residual reactivity with CEA. This was eliminated by point mutation (Y100bP) in the variable heavy-chain domain to create an scFv (B6-2) that was as structurally stable as MFE-23 and reacted specifically with αvβ6 but not with α5β1, αvβ3, αvβ5, αvβ8 or CEA. B6-2 was internalized into αvβ6-expressing cells and inhibited αvβ6-dependent migration of carcinoma cells. B6-2 was subsequently humanized. The humanized form (B6-3) was obtained as a non-covalent dimer from secretion in Pichia pastoris (115 mg/l) and was a potent inhibitor of αvβ6-mediated cell adhesion. Thus, we have used a rational stepwise approach to create a humanized scFv with therapeutic potential to block αvβ6-mediated cancer cell invasion or to deliver and internalize toxins specifically to αvβ6-expressing tumors.     

The relationship of 4-aminobutyric acid metabolism to ammoniagenesis in renal cortex

Mitochondrial 4-aminobutyrate aminotransferase in rat kidney can utilize pyruvate as the acceptor for the amino group of 4-aminobutyrate. Renal 4-aminobutyrate aminotransferase activity at saturating equimolar concentration of 4-aminobutyrate and 5 mM pyruvate is 42.8 ± 2.5 μmol/g protein per h (mean ± S.E.M.) or 70% of 4-aminobutyrate aminotransferase activity with equimolar α-ketoglutarate. 4-Aminobutyrate aminotransferase in brain does not transaminate with pyruvate. Since pyruvate is an important mitochondrial metabolite in kidney, net disposal of glutamate via the 4-aminobutyrate pathway is possible. The renal 4-aminobutyrate pathway in the rat has other distinctive features when compared with the pathway in rat brain. Most inhibitors of rat neuronal glutamate decarboxylase were ineffective against the renal form of the enzyme, but 20 mM semicarbazide inhibited the latter form by 80% (P < 0.001) in vitro and reduced renal 4-aminobutyrate content by 75% (P < 0.001) in vivo. In the presence of 20 mM semicarbazide, ammoniagenesis by rat renal cortex slices incubated in 1 mM glutamine was inhibited 26% (P < 0.01). Semicarbazide was proportionately less effective (15% inhibition) when ammoniagenesis was stimulated (+243%) in slices prepared from chronically acidotic animals, and was no deterrant to ammoniagenesis when non-acidotic slices were incubated in supraphysiologic concentrations of 10 mM glutamine. We conclude that whereas integrity of the renal 4-aminobutyrate pathway may contribute to glutamate disposal and thus ammoniagenesis under physiologic conditions, the pathway is a passive participant in the overall process of ammoniagenesis.     

Inducible and repressible acetylornithine delta-transaminase in Escherichia coli: different proteins

Two acetylornithine δ-transaminases which have different physical and kinetic properties have been isolated from a mutant of E. coli W. Sephadex gel filtration has shown the molecular weight of one transaminase to be approximately 119,000; the second transaminase has a molecular weight of about 61,000. The two transaminases can be separated by ammonium sulfate fractionation. The K_m values of the smaller and larger molecular-weight species for N^α-acetylornithine are 3.1 mm and 1.3 mm, respectively. The K_m for α-ketoglutarate is 1.1 mm for both enzymes. The presence of arginine in the growth medium represses the synthesis of the 119,000 molecular-weight transaminase and induces the synthesis of the 61,000 molecular-weight species.     

Comparison of the activation energy barrier for succinimide formation from α- and β-aspartic acid residues obtained from density functional theory calculations

The l-α-Asp residues in peptides or proteins are prone to undergo nonenzymatic reactions to form l-β-Asp, d-α-Asp, and d-β-Asp residues via a succinimide five-membered ring intermediate. From these three types of isomerized aspartic acid residues, particularly d-β-Asp has been widely detected in aging tissue. In this study, we computationally investigated the cyclization of α- and β-Asp residues to form succinimide with dihydrogen phosphate ion as a catalyst (H₂PO₄⁻). We performed the study using B3LYP/6-31 + G(d,p) density functional theory calculations. The comparison of the activation barriers of both residues is discussed. All the calculations were performed using model compounds in which an α/β-Asp-Gly sequence is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Moreover, H₂PO₄⁻ catalyzes all the steps of the succinimide formation (cyclization-dehydration) acting as a proton-relay mediator. The calculated activation energy barriers for succinimide formation of α- and β-Asp residues are 26.9 and 26.0 kcal mol^− 1, respectively. Although it was experimentally confirmed that β-Asp has higher stability than α-Asp, there was no clear difference between the activation barriers. Therefore, the higher stability of β-Asp residue than α-Asp residue may be caused by an entropic effect associated with the succinimide formation.     

Holo- and apo-cystalysin from Treponema denticola: two different conformations

Cystalysin, the key virulence factor in the bacterium Treponema denticola responsible for periodontis, is a pyridoxal 5′-phosphate (PLP) enzyme which catalyzes, in addition to α,β-elimination of l-cysteine, racemization and transamination of both enantiomers of alanine. In this paper several indicators have been used as probes of the different conformational status of T. denticola cystalysin in the holo and apo form. Compared to holoenzyme, the apoenzyme displays an altered reactivity of cysteine residues, a significantly different pI, and a differential susceptibility to proteinase K. The site of cleavage that is accessible in apocystalysin and masked in holocystalysin has been identified by mass spectrometry as the peptide bond between Phe 360 and Gly 361. This cleavage results in the loss of the C-terminal fragment corresponding to a molecular mass of 4289.21 ± 0.1 Da. The major fragment of cleaved enzyme retains its dimeric structure, binds the coenzyme with an affinity ∼5000-fold lower than that of uncleaved holoenzyme, and in the reconstituted form is able to form the external aldimine with substrates. Although the break causes the loss of lyase, racemase and transaminase activities of d-alanine, it does not abolish the transaminase activity of l-alanine. Possible mechanistic and physiological implications are proposed.     

Selectivity in vitamin B-6 model reactions: Selective α or β deuteration of amino acids under transamination or racemization conditions

Al(III)-catalyzed reactions of vitamin B-6 (pyridoxal)-amino acid schiff bases have been studied in ²H₂O. By using excess of the amino acid and varying conditions, amino acids selectively deuterated in the α-position, the β-position, or in both α- and β-positions are isolated. Reaction conditions are those of model systems in which amino acids are known to be reversibly transaminated and racemized by pyridoxal and Al(III). The racemization reaction leads to α-deuteration of the amino acid while transamination followed by its reverse leads to both α- and β-deuteration. The two reactions are viewed as passing through a common dihydropyridine intermediate. The Al(III) serves as an interesting model for the enzyme in that it not only catalyzes transamination and racemization but also can be made to select which of these reactions predominates. This selective catalysis of these reactions is attributed to strong and different pH dependence of the reactivity of various sites of the dihydropyridine intermediate for vitamin B-6 catalysis when incorporated in an Al(III) complex. The biochemical importance of this selectivity and the practical extension of the method of deuteration to other amino acids is discussed.