Biomedical subjects

T Kurotsu

Publications and source records attributed to T Kurotsu.

At least 19 recordsLinked to original sources

PubMed1995

Three conserved glycine residues in valine activation of gramicidin S synthetase 2 from Bacillus brevis.

The translated product from the gene fragment containing the second and third domains of gramicidin S synthetase 2 was purified to an essentially homogeneous state. It showed valine- and ornithine-activating activity and the second domain was proved to be the valine-activating domain. Three mutant genes from Bacillus brevis Nagano, BI-3, E-4, and E-5 strains, which encode defective valine-activating domains of gramicidin S synthetase 2, were sequenced. By comparison with the wild-type gene, single point mutations of guanine to adenine were found at the three conserved glycine codons; the 5303rd guanine in BI-3, the 5378th guanine in E-4, and the 4967th guanine in E-5, which corresponded to codon changes of the 1768th glycine to glutamic acid and the 1793rd and the 1656th glycine to aspartic acid. Loss of valine-adenylation activity by mutation at the 1656th glycine proved the direct participation of the TSGT/STGXPKG motif in the adenylation reaction, and suggests that this glycine residue with the conserved lysine residue of the motif forms the phosphate-binding loop for ATP-binding. The 1793rd glycine is a member of the YGXTE motif which was also conserved among adenylate-forming enzymes except acetyl-CoA synthetases. The 1768th glycine residue appears to maintain the conformation of the active site for aminoacyl adenylation since this residue is retained among the adenylate-forming enzymes, though flanking regions are not conserved. These results suggest that these glycine residues are essential for adenylate formation in the antibiotic peptide synthetase family and some other adenylate-forming enzymes.

Amino Acid Isomerases↗

PubMed1995

Purification and properties of branched chain amino acid aminotransferase from gramicidin S-producing Bacillus brevis.

The branched chain amino acid aminotransferase [EC 2.6.1.42] was purified to a homogeneous state from a gramicidin S-producing strain of Bacillus brevis. The enzyme had a molecular weight of about 93,000 and consisted of two identical subunits, each with a molecular weight of about 47,000. One pyridoxal phosphate is bound per subunit. In addition to branched chain amino acids, the enzyme uses L-phenylalanine and L-tryptophan as the amino donor, indicating that B. brevis branched chain amino acid aminotransferase has a broad substrate specificity for the amino donor. The enzyme utilized 2-oxoglutarate as the amino acceptor. The purified enzyme exhibits its absorption maxima at 332 and 427 nm at neutral pH.

Bacillus↗

PubMed1994

Classification of acid denaturation of proteins: intermediates and unfolded states.

A systematic investigation of the effect of acid on the denaturation of some 20 monomeric proteins indicates that several different types of conformational behavior occur, depending on the protein, the acid, the presence of salts or denaturant, and the temperature. Three major types of effects were observed. Type I proteins, when titrated with HCl in the absence of salts, show two transitions, initially unfolding in the vicinity of pH 3-4 and then refolding to a molten globule-like conformation, the A state, at lower pH. Two variations in this behavior were noted: some type I proteins, when titrated with HCl in the absence of salts, show only partial unfolding at pH 2 before the transition to the molten globule state; others of this class form an A state that is a less compact from of the molten globule state. In the presence of salts, these proteins transform directly from the native state to the molten globule conformation. Type II proteins, upon acid titration, do not fully unfold but directly transform to the molten globule state, typically in the vicinity of pH 3. Type III proteins show no significant unfolding to pH as low as 1, but may be caused to behave similarly to type I in the presence of urea. Thus, the exact behavior of a given protein at low pH is a complex interplay between a variety of stabilizing and destabilizing forces, some of which are very sensitive to the environment. In particular, the protein conformation is quite sensitive to salts (anions) that affect the electrostatic interactions, denaturants, and temperature, which cause additional global destabilization.(ABSTRACT TRUNCATED AT 250 WORDS)

Acids↗

PubMed1994

Entire nucleotide sequence for Bacillus brevis Nagano Grs2 gene encoding gramicidin S synthetase 2: a multifunctional peptide synthetase.

Bacillus brevis Nagano grs2 gene, which encodes gramicidin S synthetase 2 (GS2) catalyzing activation and combination of four constituent amino acids of gramicidin S, namely, proline, valine, ornithine, and leucine, has been sequenced. The open reading frame of grs2 gene specifies a 4,450-amino acid protein with a calculated molecular weight of 508,658. There are four domains with a mean of 1,042 amino acid residues containing a repeated sequence of about 600 amino acids, which is highly homologous to the amino-terminal half of gramicidin S synthetase 1 (GS1) (about 40-50% identity). Three domains of grs2 protein, excluding the first one, show homology over the entire sequences of 1,042 amino acids, but the first domain only shows homology in the conserved 600-amino acid sequence. The last 300-amino acid sequence of grs2 protein following the fourt domain has no homology with any of the above sequences. Translation products of subcloned fragments containing the third or the fourth domain catalyzed ornithine- or leucine-dependent ATP-32Pi exchange, respectively. These results, together with a previous report on a proline-activation domain indicated that the repeated and conserved domains are the individual activation sites of the constituent amino acids; the activation sites are arranged in the order of peptide elongation on GS2. Several motifs of grs2 protein are conserved among the multiple domains of peptide synthetases and aminoacyl or acyl adenylate-forming enzymes.

Amino Acid Isomerases↗

PubMed1994

Purification and properties of L-ornithine delta-aminotransferase from gramicidin S-producing Bacillus brevis.

In gramicidin S-producing Bacillus brevis, the addition of L-ornithine to the minimal medium with L-glutamate as the sole carbon and nitrogen source caused an 8-fold induction of L-ornithine delta-aminotransferase [EC 2.6.1.13]. The enzyme was purified to homogeneity. The native enzyme had a molecular weight of about 88,000 after gel filtration and consisted of two subunits with an identical in molecular weight of about 45,000. The enzyme was specific for L-ornithine (Km = 1.05 mM) as an amino donor and for 2-oxoglutarate (Km = 6.25 mM) as an amino acceptor, and catalyzed the conversion of L-ornithine and 2-oxoglutarate, respectively, to glutamic-gamma-semialdehyde, which is spontaneously cyclized to delta 1-pyrroline-5-carboxylate and L-glutamate. The enzyme exhibits an absorption maximum at 425 nm at neutral pH, and 1 mol of pyridoxal phosphate is bound per subunit. The enzyme activity was irreversibly inhibited by gabaculine, and L-ornithine protected the enzyme from the inhibition. The N-terminal amino acid sequence revealed a noteworthy similarity between human and yeast L-ornithine delta-aminotransferases in residues 17-28 of the B. brevis enzyme.

Amino Acid Sequence↗

PubMed1994

Mutant genes of gramicidin S synthetase 1 defective in phenylalanine racemization have the same sequence as the wild gene.

Mutant grs1 genes were cloned and sequenced from the Bacillus brevis Nagano BI-4, C-3, E-1, and E-2 strains, which produce defective gramicidin S synthetase 1 (GS1), lacking racemase activity. Surprisingly, these mutant genes had entirely the same sequence as that of the wild type gene. These mutant strains also produce defective gramicidin S synthetase 2 (GS2), lacking 4'-phosphopantetheine, a prosthetic group of this enzyme. The participation of this group in phenylalanine racemization is suggested.

Amino Acid Isomerases↗

PubMed1993

Effect of single base substitutions at glycine-870 codon of gramicidin S synthetase 2 gene on proline activation.

The mutant gene coding for a proline-activating domain (grs2-pro) was cloned and sequenced from Bacillus brevis Nagano, BII-3 strain, which produces gramicidin S synthetase 2 defective in proline-activation. By comparison of the nucleotide sequence with the wild-type sequence, a single point mutation was found at the 2609th guanine, which was replaced with adenine, resulting in the change of the 870th glycine to glutamic acid. Homology search for the deduced amino acid sequence of grs2-pro gene revealed that the 870th glycine was conserved in adenylate-forming enzymes, and its flanking sequence was highly conserved among the aminoacyl adenylate-forming enzymes, such as antibiotic peptide synthetases: gramicidin S synthetase 1 and 2 (GS1, GS2), tyrocidine synthetase 1 (TS1), and delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS); and other aminoacyl adenylation enzymes: alpha-aminoadipate reductase (LYS2), EntF, and AngR. On the other hand, this flanking sequence was not conserved in the other adenylate-forming enzymes lacking amino acid activation, such as acetyl-CoA synthetase, long-chain acyl-CoA synthetase, luciferase, and 4-coumarate CoA ligase. Single base substitutions at the 870th GGG codon were carried out by oligonucleotide site-directed mutagenesis. Four mutagenized clones were isolated, containing grs2-pro genes which exchange 870-Gly for alanine, valine, arginine, and tryptophan. The translated products from these clones could scarcely catalyze proline-dependent ATP-32PPi exchange reaction. The coil structure of 870-Gly region was lost in the mutants. These results suggest that the 870-Gly residue of grs2-pro protein is essential for aminoacyl-adenylation in the antibiotic peptide synthetase family.

Amino Acid Isomerases↗

PubMed1991

Characterization and location of the L-proline activating fragment from the multifunctional gramicidin S synthetase 2.

Gramicidin S synthetase 2 (GS2) derived from Bacillus brevis is a multifunctional single polypeptide (Mr 280,000) with a 4'-phosphopantetheine residue covalently bound to the enzyme. When GS2 was treated with trypsin or chymotrypsin, fragments with some activity were liberated. The molecular mass of the L-proline activating fragment was 114 kDa on SDS-PAGE. This fragment, when incubated with gramicidin S synthetase 1 (GS1) in the presence of phenylalanine and proline, produced D-Phe-L-Pro dipeptide. The fragment accepted D-phenylalanine from GS1 in the absence of L-proline. The L-proline activating fragment was shown to lack pantothenic acid by microbiological assay. On the other hand, the L-leucine activating fragment, which was partially purified, contained a large amount of pantothenic acid, although it did not form the D-Phe-L-Pro dipeptide. These results indicate that the L-proline activating site is located near an acceptor site for D-phenylalanine on GS2, but that it is not adjacent to a 4'-phosphopantetheine group. The N-terminal sequence (15 amino acid residues) of the L-proline activating fragment obtained by trypsin treatment was identical with that of GS2, indicating that the L-proline activating site is located at the N-terminus of the native synthetase. The N-terminal sequence of GS2 has been matched with the amino acid sequence deduced from the nucleotide sequence 71 bp downstream of the stop codon of the GS1 gene except that the first initiator methionine was not detected.

Amino Acid Isomerases↗

PubMed1991

The nucleotide sequence for a proline-activating domain of gramicidin S synthetase 2 gene from Bacillus brevis.

A fragment encoding proline-activating domain (grs 2-pro) of gramicidin S synthetase 2 (GS 2) was found in an 8.1-kilobase pairs (kb) DNA fragment of Bacillus brevis Nagano, which contained the full length of GS 1 gene (grs 1). The clones designated GS719 and GS708, which expressed gramicidin S synthetase 1, were elucidated to express immunoreactive proteins to GS 2 antibodies with approximate molecular weights of 115,000, 105,000 (GS719), and 110,000 (GS708). The partial purification of the gene products of these clones was carried out using DEAE-Sepharose CL-6B column chromatography. The immunoreactive proteins to GS 2 antibodies were separated from gramicidin S synthetase 1 protein and had specific proline-dependent ATP-32PPi exchange activity. The nucleotide sequence for the proline-activating domain in the 8.1-kb insert was determined. This fragment was 2,879 base pairs long, and encoded 959 amino acids. The calculated molecular weight of 111,671 was consistent with the apparent molecular weight of 115,000 found in SDS-PAGE of the immunoreactive products to GS 2 antibodies. The open reading frame for this protein followed grs 1 gene, though two were separated by a 73-base pair noncoding sequence, and remained open to the end.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Isomerases↗

PubMed1989

Reaction mechanism of gramicidin S synthetase 1, phenylalanine racemase, of Bacillus brevis.

We have demonstrated that gramicidin S synthetase 1 (GS 1), phenylalanine racemase [EC 5.1.1.11], of Bacillus brevis catalyzes the exchange between a proton in the medium and alpha-hydrogen of phenylalanine in the course of the racemase reaction by using tritiated water or L-phenyl[2,3-3H]alanine. GS 1 from some gramicidin S non-producing mutants of B. brevis lacking phenylalanine racemase activity did not catalyze the tritium exchange reaction. The proton exchange between phenylalanine bound as thioester on the GS 1-phenylalanine complex and water in the medium was detected, but 5,5'-dithiobis(2-nitrobenzoic acid)-modified complex lacked both the proton exchange and phenylalanine racemase activity. It is suggested that a base group, probably a sulfhydryl group, on the enzyme functions as proton donor and acceptor during the phenylalanine racemase reaction.

Amino Acid Isomerases↗

PubMed1989

Molecular cloning and nucleotide sequence of the gramicidin S synthetase 1 gene.

The entire gene for gramicidin S synthetase 1 (GS 1) was cloned into the plasmid vector pUC18, and the nucleotide sequences of the GS 1 gene and its flanking region were determined. The full-length clone was 4,539 base pairs long and had an open reading frame of 3,294 nucleotides coding for 1,098 amino acids. The calculated molecular weight of 123,474 agreed with the apparent molecular weight of 120,000 found in SDS-PAGE of GS 1 from B. brevis. The nucleotide sequence of GS 1 gene was highly homologous to that of tyrocidine synthetase 1. The overall similarity between the deduced amino acid sequences of the two genes was 57.5%. The gene product of clone GS309 was easily purified to an essentially homogeneous state by ammonium sulfate fractionation followed by DEAE-Sepharose CL-6B, Ultrogel AcA-34, and second DEAE-Sepharose CL-6B column chromatography. The purified protein catalyzed the D-phenylalanine-dependent ATP-32PPi exchange reaction which is specific for GS 1 activity, and the specific activity of the purified product was nearly the same as the purified GS 1 from B. brevis. The product also showed a weak phenylalanine racemase activity.

Amino Acid Isomerases↗

PubMed1987

Purification and properties of the aromatic amino acid aminotransferase from gramicidin S-producing Bacillus brevis.

The aromatic amino acid aminotransferase was purified to a homogenous state from a gramicidin S-producing strain of Bacillus brevis. The enzyme shows a molecular weight of about 71,000 on gel-filtration. The subunit molecular weight is about 35,000 as determined by sodium dodecyl sulfate gel electrophoresis, indicating that the enzyme is a dimer. The enzyme exhibits absorption maxima near 425 and 330 nm at neutral pH. One mole of pyridoxal phosphate is bound per subunit. The enzyme has amino donor specificity for aromatic amino acids, L-phenylalanine, L-tyrosine, and L-tryptophan, and utilizes 2-oxoglutarate as the amino acceptor. This enzyme activity was separated from both the aspartate aminotransferase activity and the branched chain amino acid aminotransferase activity by chromatography on DEAE-Sephadex.

Amino Acids↗

PubMed1984

A comparative study of sulfhydryl groups required for the catalytic activity of gramicidin S synthetase and isoleucyl tRNA synthetase.

The sulfhydryl groups required for the catalytic activity of gramicidin S synthetase of Bacillus brevis and Escherichia coli isoleucyl tRNA synthetase were compared. In gramicidin S synthetase 2(GS 2), about four sulfhydryl groups react rapidly with 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) or N-ethylmaleimide (NEM), and are essential for gramicidin S formation in the presence of gramicidin S synthetase 1 (GS 1). These sulfhydryl groups are protected against DTNB and NEM reactions by the preincubation of GS 2 with amino acid substrates in the presence of ATP and MgCl2, like the sulfhydryl groups that react rapidly with DTNB or NEM and are required for the catalytic activity of GS 1 and isoleucyl tRNA synthetase. In GS 2, GS 1, and isoleucyl tRNA synthetase, the sulfhydryl group that reacts rapidly with NEM and is required for the catalytic activity is involved in the amino acid binding as a thioester. In isoleucyl tRNA synthetase, it is suggested that isoleucine may be transferred from the isoleucine thioester enzyme complex to tRNA by a mechanism similar to that proposed for gramicidin S synthetase.

Amino Acid Isomerases↗

PubMed1982

Evidence for a single multifunctional polypeptide chain on gramicidin S synthetase 2 obtained from a wild strain and mutant strains of Bacillus brevis.

The structures of the gramicidin S synthetase 2 s (GS 2, heavy enzyme) from a wild strain and mutant strains of Bacillus brevis have been studied by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS). The GS 2s used were obtained from a wild strain and group IV of mutant strains (BII-3, BI-3, BI-9) which lacked one specific amino acid activating activity. SDS polyacrylamide gel electrophoresis of GS 2 bound to a radioactive substrate showed that: first, in the case of the wild enzyme, the radioactivity of the substrate amino acid was detected only in the polypeptide with a molecular weight of about 280,000, regardless of the amino acid species used as substrate; secondly, in the case of the mutant enzyme, the radioactivity of the amino acid which could be activated by the enzyme was also associated with the protein band with a molecular weight of about 280,000. Regardless of the enzyme species tested, a pantothenic acid residue was also present in the protein band with a molecular weight of about 280,000. These results suggest that GS 2 is a multifunctional one polypeptide enzyme and the mutant-type GS 2s from BII-3 (proline-lacking), BI-3 (valine-lacking), and BI-9 (leucine-lacking) are also multifunctional enzymes having molecular weights identical to that of the wild-type enzyme.

Amino Acid Isomerases↗

PubMed1982

Essential arginine residue in gramicidin S synthetase 1 of Bacillus brevis.

Phenylalanine activation of gramicidin S synthetase 1 (GS 1) [EC 5.1.1.11] of Bacillus brevis is inhibited by phenylglyoxal. The inactivation of GS 1 by phenylglyoxal obeys pseudo-first-order kinetics and formation of a reversible enzyme-reagent complex prior to modification is indicated. Both ATP and phenylalanine prevent the inactivation by phenylglyoxal. ATP is competitive with phenylglyoxal, whereas phenylalanine is not. In the presence of ATP, one residue of arginine per mol of protein is protected from the modification as determined by amino acid analysis and incorporation of [7-14C]phenylglyoxal. These results indicate that a single arginine residue of GS 1 is essential for phenylalanine activation in binding the phosphate moiety of ATP.

Adenosine Triphosphate↗

PubMed1982

Characterization of an intracellular serine protease from sporulating cells of Bacillus brevis.

Sporulating cells of Bacillus brevis ATCC 9999 produced a high level of an intracellular serine protease when grown in nutrient medium. The protease activity in the crude extracts of this strain appeared at hour 5 (t5) after the end of exponential growth and increased gradually during sporulation, reaching a maximum at t12 to t13. The enzyme isolated in a partially purified state showed a pH optimum between 7.3 and 9.0 and had an apparent molecular weight of about 60,000. The activity was completely inhibited by phenylmethylsulfonyl fluoride, diisopropyl fluorophosphate, EDTA, and ethylene glycol-bis(beta-aminoethyl ether)-N,N-tetraacetic acid. The protease possessed a high activity for azocoll and low activities for azocasein and 14C-labeled hemoglobin. It cleaved the cyclic decapeptide gramicidin S specifically at the peptide linkage between valine and ornithine and hydrolyzed the oxidized insulin B-chain mainly at peptide bonds 4-5 (Glu-His), 6-7 (Leu-CysSO3H), and 15-16 (Leu-Tyr). No catalysis of bond cleavage by the enzyme on a variety of small peptides or esters was detected. Unlike other Bacillus species, B. brevis ATCC 9999 grown in nutrient medium excreted no extracellular proteases.

Bacillus↗

PubMed1981

Absence of pantothenic acid in gramicidin S synthetase 2 obtained from some mutants of Bacillus brevis.

The pantothenic acid content of gramicidin S synthetase 2(GS 2) was estimated microbiologically with enzymes obtained from the wild strain and gramicidin S-lacking mutant strains of Bacillus brevis. Four mutant enzymes from BI-4, C-3, E-1, and E-2 lacked pantothenic acid. Other mutant enzymes from BII-3, BI-3, BI-9, and BI-2 contained the same amount of pantothenic acid as the wild-type enzyme. Pantothenic acid-lacking GS 2 belonged to group V of mutant enzymes, which could activate all amino acids related to gramicidin S; their complementary enzyme, gramicidin S synthetase 1(GS 1), lacked racemizing activity. To ascertain whether 4'-phosphopantetheine is involved in the formation of D-phenylalanyl-L-prolyl diketopiperazine (DKP) and gramicidin S, combinations were tested of intact GS 1 from the wild strain with various mutant GS 2 either containing or lacking pantothenic acid. Only the combinations of wild-type GS 1 with mutant GS 2 containing pantothenic acid could synthesize DKP. Combinations with pantothenic acid-lacking GS 2 also failed to elongate peptide chains. Pantothenic acid-lacking GS 2 could bind the four amino acids which constitute gramicidin S as acyladenylates and thioesters, but the binding abilities were lower than those of the wild-type enzyme and other mutant enzymes containing the pantothenic group.

Amino Acid Isomerases↗

PubMed1981

Sulfhydryl groups related to the catalytic activity of gramicidin S synthetase 1 of Bacillus brevis.

Gramicidin S synthetase 1 (GS 1) [EC 5.1.1.11] (phenylalanine racemase) of Bacillus brevis contained about six sulfhydryl groups as determined by titration of the enzyme with 5,5'-dithiobis (2-nitrobenzoic acid) (DTNB). Two types of sulfhydryl groups could be detected in the reaction with DTNB. One sulfhydryl group reacted rapidly with DTNB whereas the other five reacted more slowly with it. Phenylalanine racemizing activity was abolished on the rapid sulfhydryl modification with DTNB. When GS 1 of the wild strain was preincubated with phenylalanine at 37 degrees C in the presence of ATP, MgCl(2), and dithiothreitol (DTT), the rapid sulfhydryl modification with DTNB was prevented. When GS 1 was incubated with L-[14C]phenylalanine in the presence of ATP, MgCl(2), and DTT, 1 mol of L-[14C]phenylalanine was incorporated per mol of enzyme protein as an acid-stable phenylalanine thioester-enzyme complex. On the other hand, for GS 1 of a gramicidin S non-producing and phenylalanine racemization-lacking mutant of B. brevis, the substate protection against the rapid sulfhydryl modification was not detected and L-[14C]phenylalanine was not incorporated into the enzyme protein as the thioester complex. These results strongly suggest that one sulfhydryl group of GS 1 which reacts rapidly with DTNB is essential for the racemizing activity.

Adenosine Triphosphate↗