Pyridoxal phosphate-dependent histidine decarboxylases. Cloning, sequencing, and expression of genes from Klebsiella planticola and Enterobacter aerogenes and properties of the overexpressed enzymes.

The hdc genes encoding the inducible pyridoxal-P-dependent histidine decarboxylase (HisDCase) of Klebsiella planticola and Enterobacter aerogenes were isolated, sequenced, and expressed in Escherichia coli under control of the lac promoter, and the overproduced enzymes were purified to homogeneity from the recombinant host. Formation of inclusion bodies during synthesis of the E. aerogenes enzyme was avoided by cooling the culture and inducing at 25 degrees C. The cloned enzymes were produced in amounts three to four times those present in the fully induced native hosts and were identical in properties to those isolated earlier (Guirard, B. M., and Snell, E. E. (1987) J. Bacteriol. 169, 3963-3968). The two enzymes showed 85% sequence identity and also showed 80% sequence identity with the previously sequenced (Vaaler, G. L., Brasch, M. A., and Snell, E. E. (1986) J. Biol. Chem. 261, 11010-11014) HisDCase of Morganella morganii. Nevertheless, antibodies to the M. morganii HisDCase do not cross-react with these enzymes suggesting that the regions of amino acid variations are located on the outer surface of the proteins. All three HisDCases are the same length (377 amino acid residues); encoded N-terminal methionine was completely removed in each case. These closely related pyridoxal-P enzymes show no sequence homology with the pyruvoyl-dependent HisDCases of Gram-positive bacteria.

Site-directed alteration of the active-site residues of histidine decarboxylase from Clostridium perfringens.

To clarify the mechanism of biogenesis and catalysis by the pyruvoyl-dependent histidine decarboxylase (HisDCase) from Clostridium perfringens, 12 mutant genes encoding amino acid substitutions at the active site of this enzyme were constructed and expressed in Escherichia coli. The resulting mutant proteins were purified to homogeneity, characterized, and subjected to kinetic analysis. The results (a) exclude all polar amino acid residues in the active site except Glu-214 as donor of the proton that replaces the carboxyl group of histidine during decarboxylation and, since E214I and E214H are nearly inactive, indicate that Glu-214 is the essential proton donor; (b) demonstrate the importance to substrate binding of hydrophobic interactions between Phe-98, Ile-74, and the imidazole ring of histidine, and of hydrogen bonding between Asp-78 and N2 of the substrate; and (c) demonstrate a significant unidentified role for Glu-81 in the maintenance of the active-site structure. The proposed roles of these amino acid residues are consistent with those assigned on the basis of crystallographic evidence to the corresponding residues at the active site of the related HisDCase from Lactobacillus 30a [Gallagher, T., Snell, E. E., & Hackert, M. L. (1989) J. Biol. Chem. 264, 12737-12743]. Of the residues altered, only Ser-97 was essential for the autocatalytic serinolysis reaction by which this HisDCase, (alpha beta)6, is derived from its inactive, pyruvate-free precursor, proHisDCase, pi 6.(ABSTRACT TRUNCATED AT 250 WORDS)

Pyridoxal 5'-phosphate-dependent histidine decarboxylase. Mechanism of inactivation by alpha-fluoromethylhistidine.

Mechanism-based inactivation of pyridoxal phosphate-dependent histidine decarboxylase by (S)-alpha-(fluoromethyl)histidine was studied. The molar ratio of inactivator to enzyme subunit required for complete inactivation increased from 1.63 at 10 degrees C to 3.00 at 37 degrees C. Two inactivation products were isolated by chromatographic fractionation of the reaction mixture and identified by NMR spectroscopy as 1-(4-imidazolyl)-3(5'-P-pyridoxylidene) acetone (I), the adduct formed between pyridoxal phosphate and inactivator, and 1-(4-imidazolyl) acetone (II), an intermediate compound formed during inactivation. Formation of these two products supports a previously proposed mechanism of inactivation (Hayashi, H., Tanase, S., and Snell, E. E. (1986) J. Biol. Chem. 261, 11003-11009), with minor modifications. A precursor of I was linked covalently to the enzyme by NaBH4 reduction if the reaction was carried out immediately after inactivation, before development of the 403 nm peak of I. A mutant histidine decarboxylase (S322A) in which Ser-322 was changed to Ala was also inactivated by alpha-fluoromethylhistidine demonstrating that Ser-322 is not essential for inactivation even though it is close to the active site and is derivatized by borohydride reduction of the inactivated wild-type enzyme. Following inactivation, both the wild-type and the S322A mutant enzyme could be partially reactivated by prolonged dialysis against buffer.

Cloning, sequencing, expression, and site-directed mutagenesis of the gene from Clostridium perfringens encoding pyruvoyl-dependent histidine decarboxylase.

The DNA encoding pyruvoyl-dependent histidine decarboxylase (HisDCase) of Clostridium perfringens was cloned, sequenced, and overexpressed in Escherichia coli. The gene encodes a single polypeptide of 320 amino acids, Mr 35,526, demonstrating that clostridial HisDCase, which has an (alpha beta)6 structure, is synthesized as a precursor (proHisDCase, pi 6). No pi subunits of proHisDCase were observed in crude or purified preparations of the cloned HisDCase; they appear to undergo rapid cleavage in vivo to the alpha (Mr 24,887) and beta (Mr 10,526) subunits characteristic of this HisDCase. This cleavage occurs between Ser-96 and Ser-97; Ser-97 gives rise to the catalytically essential pyruvoyl group blocking the N-termini of the alpha subunits of the active enzyme. When Ser-97 was converted to an alanyl residue by site-specific mutagenesis, the expressed, inactive protein (pi' 6) contained a single peptide species (pi', Mr 35,510) that was not cleaved either in vivo or in vitro. These results support previous conclusions that activation of the wild-type clostridial proenzyme occurs via nonhydrolytic serinolysis. Although clostridial HisDCase has only a 47% sequence similarity to HisDCase from Lactobacillus 30a, all of the residues known to be important for substrate binding and catalytic action of the Lactobacillus HisDCase are conserved in the C. perfringens enzyme. While the encoded N-terminal Met of clostridial HisDCase is removed by E. coli, the cloned enzyme retains a 10-residue presequence (NKNLEANRNR) not present in the mature enzyme isolated from C. perfringens.

Pyridoxal 5'-phosphate dependent histidine decarboxylase: overproduction, purification, biosynthesis of soluble site-directed mutant proteins, and replacement of conserved residues.

The hdc gene coding for the pyridoxal 5'-phosphate dependent histidine decarboxylase from Morganella morganii has been expressed in Escherichia coli under control of the lac promoter. The enzyme accumulates to 7-8% of total cell protein and is purified to homogeneity by passage through three columns. Fourteen site-directed mutant enzymes were constructed to explore the roles of residues of interest, especially those in the sequence Ser229-X230-His231-N epsilon-(phosphopyridoxylidene)Lys232, since identical sequences also appear in several other decarboxylases. Most of the overproduced mutant proteins were aggregated into inclusion bodies, but when the late log phase cultures were cooled from 37 to 25 degrees C before induction, the mutant proteins were obtained as soluble products. Ala or Cys in place of Ser-229 yielded mutant enzymes about 7% as active as wild-type, indicating that this serine residue is not essential for catalysis but contributes to activity through conformational or other effects. Of the replacements made for His-231 (Asn, Gln, Phe, and Arg), only Gln and Asn gave partially active enzymes (about 12% and 0.2% of wild-type, respectively). The side-chain amide of Gln may act by mimicking the positionally equivalent tau-nitrogen on the imidazole ring of histidine to provide an interaction (e.g., a hydrogen bond) required for efficient catalysis. The Lys-232 residue that interacts with pyridoxal 5'-phosphate appears central to catalytic efficiency since replacing it with Ala yields a mutant protein that is virtually inactive but retains the ability to bind both pyridoxal 5'-phosphate and histidine efficiently.(ABSTRACT TRUNCATED AT 250 WORDS)

Pyruvoyl-dependent histidine decarboxylase. Active site structure and mechanistic analysis.

The structure of the pyruvoyl-dependent histidine decarboxylase has been refined to 2.5 A resolution by the methods of x-ray crystallography from crystals grown at pH 4.8, where the enzyme is optimally active. Models of the active site with and without the bound substrate analog, histidine methyl ester (HisOMe), or the product, histamine, have been produced. Comparison of native and ligand-bound structures reveals no widespread differences in conformation but does reveal motion of a few key residues (Tyr-62', Ile-59', Ser-81) upon binding of HisOMe in the active site. The HisOMe binds with the appropriate alpha-carbon-carbon bond oriented as required to facilitate the formation of the transition state. The binding site contains two pockets, one for the imidazole group, and another for the -COOMe group. In the imidazole pocket, the imidazolium group forms hydrogen bonds with two neighboring carboxylates, Asp-63' and the carboxyl terminus of the beta chain, Ser-81. Hydrophobic contacts are also observed. The carboxylate pocket is predominantly hydrophobic as predicted by Alston and Abeles (Alston, T. A., and Abeles, R. H. (1987) Biochemistry 26,4082-4085), but includes one carboxyl group, that of Glu-197, about 3.5 A from the substrate carboxylate. If Glu-197 is protonated under these conditions, it could serve as the proton donor following decarboxylation; if it is ionized under these conditions, its carboxylate group is appropriately placed to enhance the lability of the substrate carboxylate ion by providing a "push" in promoting the flow of electrons that results in decarboxylation. These and other structural features of the binding complex are discussed as they relate to a proposed mechanism of decarboxylation.

L-Histidinol phosphate aminotransferase from Salmonella typhimurium. Kinetic behavior and sequence at the pyridoxal-P binding site.

A coupled assay with alpha-hydroxyglutarate dehydrogenase was used to analyze the kinetic behavior of histidinol phosphate aminotransferase from Salmonella typhymurium. Data obtained from studies of initial velocity, inhibition by products or substrate analogues, isotope exchange rates, and the determination of the equilibrium constant were consistent only with a Ping-Pong Bi Bi mechanism. Variations in inhibition patterns by different substrate analogues indicate that the microenvironment about the pyridoxal phosphate and the pyridoxamine phosphate forms of histidinol phosphate amino-transferase are different, and favor the presence of one active site with partially overlapping substrate-binding subsites for these 2 forms of the enzyme. Histidinol phosphate aminotransferase also catalyzes decomposition of beta-chloro-L-alanine to pyruvate, NH3 and Cl-; no transamination of this substrate occurs and inactivation of the enzyme accompanies this reaction. After reduction of histidinol-P aminotransferase with [3H]NaBH4, carboxymethylation, and tryptic digestion, one major radioactive peptide absorbing at 325 nm was isolated. Its primary structure was determined to be TLSK*AFALAGLR, where K* is the P-pyridoxyllysine residue. Although this peptide is only 30-40% homologous with the corresponding segment reported for other transaminases, all of these peptides are similar in placement of an hydroxyamino acid residue three residues upstream from the lysine residue, and in the cluster of hydrophobic amino acid residues immediately following the lysine residue.

Nutrition research with lactic acid bacteria: a retrospective view.

From the above discussion, it is apparent that one or another of the lactic acid bacteria requires each of the B vitamins required by animals and that assay methods developed during study of nutrition of bacteria and yeasts have played a large role in the initial or independent discovery, isolation, and characterization of vitamins, vitamin derivatives, and functionally similar substances. Clear examples include biotin, biocytin, lipoic acid, nicotinic acid, pantothenic acid, pantetheine, folic acid and tetrahydrofolic acid (and their derivatives), pyridoxal, pyridoxamine, and pyridoxamine phosphate. Improved assay methods that use these organisms also have provided much of the currently available information concerning distribution and stability of the vitamins in natural products, while quantitative inconsistencies between assays, when traced to their origin, have frequently revealed previously unknown metabolic precursors, products, or functions of the vitamins and have provided explanations of the mechanisms by which certain peptide growth factors act. Extension of such studies to organisms that cannot yet be grown in media of known composition should provide additional insights into currently obscure areas of nutrition.

Amine cations promote concurrent conversion of prohistidine decarboxylase from Lactobacillus 30a to active enzyme and a modified proenzyme.

Activation of prohistidine decarboxylase (pi 6) from Lactobacillus 30a proceeds by an intramolecular, pH- and monovalent cation-dependent reaction in which its constituent pi chains are cleaved nonhydrolytically between Ser-81 and Ser-82 with loss of NH3 and conversion of Ser-82 to the pyruvoyl residue of active histidine decarboxylase (alpha beta)6. Amines with pKa values more than 7.0 substitute for K+ or NH4+ in the activation of prohistidine decarboxylase, but they also catalyze its inactivation in a competing reaction, pi 6----pi'6. Sequence analysis of the appropriate tryptic peptide from amine-inactivated prohistidine decarboxylase established that inactivation results from conversion of Ser-82 of the pi chain to an aminoacrylate residue. The inactivated proenzyme (pi'6) does not form histidine decarboxylase; this fact eliminates one of two postulated mechanisms of activation and, thus, favors activation by beta-elimination of the acyl group of an intermediate ester formed between Ser-81 and Ser-82. L-Histidine is bound by the proenzyme (Kd = 1.7 x 10(-4) M) and is an effective activator; one binding site is present per pi subunit. K+, NH4+, and Na+ competitively inhibit (Ki values = 2.8-4.4 x 10(-3) M) activation by histidine. The data suggest the presence of two classes of monovalent cation binding sites on prohistidine decarboxylase: one (near Ser-82) is readily saturable and one is unsaturable even by 2.4 M K+.

Physical and kinetic properties of a pyridoxal reductase purified from bakers' yeast.

Pyridoxine dehydrogenase (1.1.1.65) (pyridoxal reductase), purified to homogeneity from baker's yeast, is a monomer of Mr approximately 33,000. It catalyzes the reversible oxidation of pyridoxine by NADP to yield pyridoxal and NADPH; equilibrium lies far in the direction of pyridoxine formation (Keq approximately 1.4 X 10(11) l/mol at 25 degrees C). Reduction of pyridoxal occurs most rapidly at pH 6.0-7.0; oxidation of pyridoxine is optimal at pH 8.6. NAD and NADH do not replace NADP and NADPH as substrates; pyridoxine, pyridoxal and pyridoxal 5'-phosphate are the only naturally occurring cosubstrates found. Several other aromatic aldehydes also are reduced, but substrate specificity and other properties of the enzyme distinguish it clearly from other alcohol dehydrogenases or aldehyde reductases. Between pH 6.3 and 7.1 (the intracellular pH of yeast), V/Km with pyridoxal and NADPH as substrates is greater than 600 times that observed with pyridoxine and NADPH as substrates is greater than 600 times that observed with pyridoxine and NADP as substrates. These and other considerations strongly indicate that the dehydrogenase functions in vivo to reduce pyridoxal to pyridoxine, which is the preferred substrate for pyridoxal (pyridoxine) kinase in yeast.

Purification and properties of pyridoxal-5'-phosphate-dependent histidine decarboxylases from Klebsiella planticola and Enterobacter aerogenes.

Histidine decarboxylases from Klebsiella planticola and Enterobacter aerogenes were purified to homogeneity and compared with the histidine decarboxylase from Morganella morganii. All three enzymes required pyridoxal 5'-phosphate as a coenzyme, showed optimal activity at pH 6.5, decarboxylated only histidine among the amino acids derived from protein, and were tetramers or dimers of identical subunits. Amino-terminal sequences of the three enzymes showed up to 81% homology through residue 33, but the enzymes differed sufficiently in amino acid composition and sequence so that no cross-reaction occurred between the K. planticola or E. aerogenes enzymes and antibodies to the decarboxylase from M. morganii. All three enzymes were inhibited by carbonyl reagents; by amino-, carboxyl-, and some methyl-substituted histidines; and by alpha-fluoromethylhistidine. These decarboxylases, all from gram-negative organisms, differed greatly in subunit structure, biogenesis, and other properties from the pyruvoyl-dependent histidine decarboxylases from gram-positive organisms described previously.

Use of p-aminobenzoic acid and tritiated cyanoborohydride for the detection of pyruvoyl residues in proteins.

A procedure for the detection of covalently bound pyruvic acid in purified proteins or in crude extracts is described. The dialyzed sample is first treated with sodium cyanoborohydride to reduce any Schiff bases present and then incubated with p-aminobenzoic acid and sodium [3H]cyanoborohydride. Derivatized proteins are visualized by fluorography following sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Gel slices containing the labeled proteins are hydrolyzed, and, after removal of polyacrylic acid, the hydrolysate is subjected to ion-exchange high-performance liquid chromatography. The presence of pyruvic acid is established by the detection of a tritiated, 280-nm absorbing compound with a retention time corresponding to that of synthetic N-(p-carboxyphenyl)alanine. The procedure is capable of detecting protein-bound pyruvic acid in the picomolar range and is easily modified to screen for other covalently bound keto acids.

Enzymes of vitamin B6 degradation. Purification and properties of pyridoxine 5'-dehydrogenase (oxidase).

Isolation and identification of a soil bacterium, Arthrobacter Cr-7, that grows with pyridoxine as a sole source of carbon and nitrogen are described. An inducible pyridoxine 5'-dehydrogenase (oxidase) (EC 1.1.99.9) that catalyzes conversion of pyridoxine to isopyridoxal, Pyridoxine + X----isopyridoxal + XH2, the first step in utilization of pyridoxine as a growth substrate by this organism, was purified about 520-fold to homogeneity. The enzyme (Mr = 112,000) is a dimer of probably identical subunits and requires FAD (KD(app) = 0.24 microM) as coenzyme. It oxidizes only pyridoxine (Km = 0.18 mM) and a few related compounds (4-deoxypyridoxine, pyridoxamine, pyridoxal) that contain a free 5-CH2OH group and utilizes oxygen (Km = 0.28 mM), 2,6-dichloroindophenol, or quinones, but not NAD+ or NADP+, as hydrogen acceptors (X in reaction above). With pyridoxine and oxygen as substrates, the enzyme has a broad pH optimum (from pH 7.0 to 8.3), a Vmax of 11.9 mumol X min-1 X mg-1, and a turnover number of 22 s-1 at 25 degrees C. The enzyme is strongly inhibited by sulfhydryl reagents. Except for its substrate specificity, these properties do not differ greatly from those of other flavin-dependent oxidases.

Enzymes of vitamin B6 degradation. Purification and properties of isopyridoxal dehydrogenase and 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylic-acid dehydrogenase.

Two NAD+-dependent, highly specific pyridine-5-aldehyde dehydrogenases, 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylic-acid (Compound 1) dehydrogenase and isopyridoxal dehydrogenase, were purified to homogeneity from Pseudomonas MA-1 and Arthrobacter Cr-7, respectively. Both enzymes are induced in response to growth of the organisms on pyridoxine and catalyze steps in the degradation of this compound by these organisms. Compound 1 dehydrogenase (Mr = 65,000) contains two subunits of equal size with methionine as the NH2-terminal amino acid and acts optimally at pH 7.8-8.5. It catalyzes with equal facility (turnover number = 400-670 s-1 molecule-1) both the oxidation of Compound 1 (Km = 65 microM) by NAD+ (Km = 25 microM) to 3-hydroxy-2-methylpyridine-4,5-dicarboxylic acid and the reduction of Compound 1 by NADH (Km = 20 microM) to 4-pyridoxic acid and appears to act as a true dismutase. The possible advantage to the organism of its ability to act as a dismutase is discussed briefly. No oxidation of 4-pyridoxic acid by this enzyme was observed. Isopyridoxal dehydrogenase (Mr = 242,000) contains four subunits of equal size, again with methionine at the NH2 terminus. At its optimal pH of 8.0-8.6, it catalyzes the oxidation of isopyridoxal (Km = 40 microM, turnover number = 10 s-1 molecule-1) by NAD+ (Km = 40 microM) to a mixture of 5-pyridoxic acid and 5-pyridoxolactone, which are produced in constant ratio throughout the course of the reaction. Formation of the two products, although unusual, is readily understandable in terms of the structure of isopyridoxal in solution or the structure of a possible acyl-enzyme intermediate in the oxidative reaction.

Enzymes of vitamin B6 degradation. Purification and properties of 4- and 5-pyridoxolactonases.

4-Pyridoxolactone and 5-pyridoxolactone, formed by dehydrogenation of pyridoxal or isopyridoxal during the bacterial degradation of vitamin B6 by Pseudomonas MA-1 and Arthrobacter Cr-7, respectively, are hydrolyzed to the corresponding acids by distinct inducible lactonases which were purified to homogeneity. 4-Pyridoxolactonase from Pseudomonas MA-1 has an Mr of 54,000 and contains two probably identical subunits of Mr = 28,600. It has a pH optimum of 7.0, a Km of 5.9 microM, and a Vmax at 25 degrees C of 35.2 mumol X min-1 X mg-1. 5-Pyridoxolactonase from Arthrobacter Cr-7 has an Mr of 65,200 and also contains two probably identical subunits of Mr = 32,800. It has a pH optimum of 7.1-7.7, a Km of 300 microM, and a Vmax at 25 degrees C of 21.5 mumol-1 X min-1 X mg-1. The two lactonases require no added cofactors or metal ions; their activities are inhibited by sulfhydryl reagents but are not affected by metal-chelating reagents. Although the two lactonases are entirely specific for their respective substrates, 4-pyridoxolactone is a competitive inhibitor (KI = 52 microM) for 5-pyridoxolactonase, and 5-pyridoxolactone is a competitive inhibitor (KI = 48 microM) for 4-pyridoxolactonase.