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At least 631 records · Page 35Linked to original sources
PubMed1990

Purification and complex formation analysis of a cysteine proteinase inhibitor (cystatin) from seeds of Wisteria floribunda.

Seeds of Wisteria floribunda contain several kinds of cysteine proteinase inhibitor (cystatin). We purified and characterized one of these inhibitors, named WCPI-3. The molecular weight of WCPI-3 was estimated to be 17,500 and 15,700 by gel filtration and SDS-PAGE, respectively. The isoelectric point was 5.7. WCPI-3 formed an equimolar complex with native papain and the dissociation constant was estimated to be 6.1 nM. Complex formation between WCPI-3 and Cys25-modified papain, such as S-carboxy-methylated or S-carbamoylmethylated papain, could not be observed by gel filtration or native PAGE analysis. A peptide fragment derived from WCPI-3 digested by Achromobacter proteinase (lysyl endopeptidase) had the amino acid sequence of VVAGVNYRFVLK. The VVAG sequence in this fragment corresponds to the conserved sequence QVVAG which is considered to be one of binding regions to cysteine proteinases. The amino acid sequence of the amino-terminal portion (34 residues) of WCPI-3 was highly homologous to that of oryzacystatin from rice seeds.

Amino Acid Sequence↗
PubMed1990

Cloning and sequence analysis of cDNA for Trimeresurus flavoviridis phospholipase A2, and consequent revision of the amino acid sequence.

A cDNA clone of Trimeresurus flavoviridis phospholipase A2 was isolated from the venom gland cDNA library using DNA amplified by polymerase chain reaction with oligonucleotide primers corresponding to the N- and C-terminal sequences of this enzyme. The amino acid sequence deduced from the cDNA nucleotide sequence determined by the dideoxy termination method was found to be inconsistent in the segment comprising the 69th to 81st positions from that reported previously [Tanaka, S. et al. (1986) J. Biochem. 99, 281-289]. Reinvestigation of the amino acid sequence of the peptide covering the sequence in question showed that the amino acid sequence predicted from the nucleotide sequence is correct. The sequence contains Asn-Asn-Gly (positions 69-71) and it was found that the Asn-Gly bond easily undergoes alpha-beta transpeptidation when digested with Achromobacter protease I at pH 9.0 but not seriously at pH 6.8. It is likely that the transpeptidation reaction caused a failure in the previous sequence determination. The cDNA clone obtained was 597 base pairs long and contained an open reading frame of 414 base pairs coding for 138 amino acid residues. A typical signal peptide sequence (16 amino acid residues long), located at the N-terminal moiety of the deduced sequence, was immediately followed by a polypeptide which corresponds to the mature enzyme. Northern blot analysis showed a single transcript only in the poly(A)+ RNA fraction of the venom gland but not in those of many other organs tested.

Amino Acid Sequence↗
PubMed1991

Amino acid sequence of nuclease S1 from Aspergillus oryzae.

The amino acid sequence of nuclease S1, a nuclease which cleaves both single-stranded DNA and RNA, from Aspergillus oryzae was determined. Reduced and S-carboxymethylated or S-aminoethylated nuclease S1 was digested with Achromobacter protease I, Staphylococcus aureus V8 protease, or endoproteinase Asp-N. Peptides thus obtained were purified by reverse-phase high-performance liquid chromatography and sequenced, and the complete primary structure was established. Nuclease S1 consists of a single peptide chain of 267 amino acid residues bearing N-glycosylated Asns 92 and 228. Five half-cystine residues are present at positions 25, 72, 80, 85, and 216, and the latter four residues are implicated in the formation of disulfide bonds by analogy with those in nuclease P1. Two short stretches of sequences involving His 60 and His 125 are shown to be identical with those involving active site His 119 in bovine ribonuclease A and active-site His 134 in porcine deoxyribonuclease I, respectively.

Amino Acid Sequence↗
PubMed1991

Identification of lysyl residues at the AMP-binding site of biodegradative threonine deaminase from Escherichia coli.

The biodegradative threonine deaminase from Escherichia coli is activated allosterically by AMP. To identify the residues interacting with the phosphate group of AMP at the binding site, we used the affinity labeling reagent, adenosine diphosphopyridoxal (AP2-PL). In the absence of AMP, the enzyme formed the Schiff base with AP2-PL and Scatchard plot analysis showed a biphasic pattern, the respective Kd values for the high- and low-affinity binding phases being 20 and 110 microM. The former value is comparable to the Kd value of the enzyme for AMP. In the presence of AMP, the Schiff base formation was greatly reduced. Although the maximal activating effect of adenosine diphosphopyridoxine, a non-reactive derivative of AP2-PL, was about 13% of that of AMP, the half-saturation concentration was almost the same. These findings suggest that AP2-PL specifically labeled the lysyl residue(s) at the AMP-binding site of the enzyme. To identify the labeled residue(s), we reduced the modified enzyme with sodium borohydride, then cleaved it with cyanogen bromide and Achromobacter lyticus protease I. Reverse-phase HPLC was used to isolate two labeled peptides from the digest. Their amino acid compositions and sequences showed that Lys-111 and Lys-113 were labeled. We conclude that these two lysyl residues are located around the phosphate group of AMP at the allosteric regulation site of the enzyme.

Adenosine Diphosphate↗
PubMed1994

Evidence for conformational change of fatty acid-binding protein accompanying binding of hydrophobic ligands.

Conformational change of rat liver fatty acid-binding protein was investigated by making use of change of protease-susceptibility in the presence or absence of bound oleic acid and clofibrate. Delipidated fatty acid-binding protein was rapidly digested by Achromobacter lysyl endopeptidase, bovine alpha-chymotrypsin, and Staphylococcal V8 protease, while protein recombined with oleic acid was strongly refractory to proteolysis. This observation indicates that a striking change in the conformational state of the protein occurred upon lipid binding, and seems to support the recent hypothesis that the large segment homologous to fatty acid-binding proteins found in a fatty acid-regulated ion channel constitutes a regulatory domain of the channel [Petrou, S., Ordway, R.W., Singer, J.J., and Walsh, J.V., Jr. (1993) Trends Biochem. Sci. 18, 41-42]. Clofibrate, which is a potent peroxisome proliferator and structurally unrelated to oleic acid, also conferred similar protease resistance upon the protein. A possible physiological aspect of the present observation is that the cellular level of free fatty acids, which have metabolic importance and cytotoxicity as well, regulates the turnover rate of fatty acid-binding proteins by modulating the protease susceptibility of the protein.

Animals↗
PubMed1995

Site-specific glycosylation of bovine butyrophilin.

Our previous studies showed that the N-linked sugar chains of most bovine glycoproteins from milk fat globule membranes (MFGM) contain the GalNAc beta 1-->4GlcNAc group [Sato et al. (1993) J. Biochem. 114, 890-900]. Since expression of the disaccharide structure is influenced by peptide sequences near the glycosylation sites [Smith and Baenziger (1992) Proc. Natl. Acad. Sci. USA 89, 329-333], the site-specificity of the N-acetylgalactosaminylated sugar chains was investigated using bovine butyrophilin, a major MFGM glycoprotein with known primary structure. Two glycopeptide fragments which contained the N-linked sugar chains linked to either Asn-55 or Asn-215 residue were obtained by digestion of the protein with Achromobacter protease I. The sugar chains released from each glycopeptide by hydrazinolysis were reduced with NaB3H4. Structural analyses of the oligosaccharides by sequential exoglycosidase digestion and methylation analysis revealed that only complex-type sugar chains with the GalNAc beta 1-->4GlcNAc structure are included in Asn-55-linked oligosaccharides, while only novel hybrid-type sugar chains detected previously in bovine MFGM glycoproteins are included in Asn-215-linked oligosaccharides. The results show that the glycosylation of butyrophilin occurs in a site-specific manner.

Amino Acid Sequence↗
PubMed1995

Dephosphorylation of fetal-tau and paired helical filaments-tau by protein phosphatases 1 and 2A and calcineurin.

We have reported that many sites of tau in fetal brain (fetal-tau) as well as in paired helical filaments (PHF-tau) are phosphorylated. In the present study, we used site-specific antibodies and peptide mapping to examine protein phosphatases involved in dephosphorylation of fetal-tau and PHF-tau. Immunoblot analysis and electrophoretic mobility showed that protein phosphatases 1 and 2A and calcineurin could dephosphorylate fetal-tau and PHF-tau. Phosphoserines 199, 202, 396, and 413 and phosphothreonine 231, numbered according to the longest human tau isoform, were dephosphorylated, as shown by the immunoblot analysis. Phosphoserine 422 was dephosphorylated by protein phosphatase 2A and calcineurin, but not by protein phosphatase 1. Peptide mapping with Achromobacter lyticus protease 1 showed that phosphoserines 199, 202, 235, and 396 and phosphothreonine 231 were dephosphorylated by protein phosphatases. Fetal-tau was more rapidly dephosphorylated by protein phosphatase 2A and calcineurin than PHF-tau. Interestingly, PHF-tau which had not been solubilized with guanidine HCl was little dephosphorylated by protein phosphatases. Thus, PHF-tau in neurofibrillary tangles of Alzheimer's disease brain is likely to be resistant to dephosphorylation by protein phosphatases.

Amino Acid Sequence↗
PubMed1980

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.

Amino Acids↗
PubMed1985

Subtilosin A, a new antibiotic peptide produced by Bacillus subtilis 168: isolation, structural analysis, and biogenesis.

Subtilosin A, a new antibiotic produced by Bacillus subtilis 168, was extracted from culture medium with n-butanol and purified to homogeneity by a combination of gel filtration and thin-layer chromatography. The yield was 5.5 mg from a liter of culture. It had bacteriocidal activity against some gram-positive bacteria. Amino acid analysis and mass spectrometry showed that it was a peptide with a molecular weight of 3398.9, consisting of 32 usual amino acid and some non-amino acid residues. Its amino- and carboxyl-termini were blocked. By analysis of the fragments obtained by partial acid hydrolysis, as well as by chymotryptic and thermolysin digestions of reduced and S-carboxymethylated samples and Achromobacter protease I digestion of performic acid-oxidized samples, the amino acid sequence was determined to be as follows: X-Gly-Leu-Gly-Leu-Trp-Gly-Asn-Lys-Gly-Cys-Ala-Thr-Cys-Ser-(sequence; see text) Ile-Gly-Ala-Ala-Cys-Leu-Val-Asp-Gly-Pro-Ile-Pro-Asp-Glx-Ile-Ala-Gly-Ala. The analyses of cross-linking structures revealed that there were linkages between the amino- and carboxyl-termini and between the Cys-19 and the Glx-28 residues through an unknown residue with a residue weight of 163. Consequently, subtilosin A was deduced to be a cyclic peptide antibiotic with a novel cross-linking structure. The production of subtilosin A begins at the end of vegetative growth and finishes before spore formation. Studies on the correlation between the production of subtilosin A and spore formation with decoyinine in the original strain and in asporogenous mutants of B. subtilis 168 suggested that there was no close correlation between the two phenomena. The production of subtilosin A was repressed by inhibitors of protein and RNA synthesis in contrast to that of many other antibiotic peptides, suggesting that it is synthesized by the mechanism of usual protein synthesis.

Amino Acid Sequence↗
PubMed1985

Exposed tyrosine residues of lambda cro repressor protein evidenced by nitration and photo CIDNP experiments.

The tyrosine residues of lambda cro repressor were partially nitrated with tetranitromethane under mild conditions. After digestion by Achromobacter protease I, the extent of nitration was determined by HPLC and amino acid analysis. Tyr 26 was most easily nitrated and Tyr 51 followed it. Tyr 10 was resistant to nitration. By comparison of the proton magnetic resonance spectrum of the partially nitrated cro protein with the above result, the aromatic proton resonances of the tyrosine side chains could be assigned to individual tyrosine residues. The extent of nitration is parallel to the accessibility to a flavin dye as measured by photo CIDNP (chemically induced dynamic nuclear polarization).

Amino Acids↗
PubMed1986

Complete amino acid sequence of NADH-cytochrome b5 reductase purified from human erythrocytes.

The complete amino acid sequence of soluble NADH-cytochrome b5 reductase purified from human erythrocytes was determined. The enzyme, which contained 8 methionine residues, was cleaved by cyanogen bromide. The resulting nine peptides were separated by gel filtration and purified further by high-performance liquid chromatography. The purified peptides were sequenced by automated Edman degradation. Three large CNBr peptides, residues 1-101, 109-151, and 169-231, were further fragmented with trypsin, Staphylococcus aureus V8 protease or a lysyl endopeptidase of Achromobacter lyticus. The peptides obtained from the tryptic digest of citraconylated FAD-depleted apoprotein completed the alignments of the other peptides. The enzyme was composed of 275 amino acid residues. The 4 functionally important cysteine residues were located in the COOH-terminal portion. The molecular weight of the protein was calculated to be 31,260 without FAD. A prediction of the secondary structure was made by the method of Chou and Fasman. The protein was hydrophilic as a whole (43% polarity), but some regions were rich in hydrophobic residues. From the sequence homology of this enzyme with the pyridine nucleotide-binding sites of other flavoproteins, three candidates for the FAD and NADH-binding domains were suggested.

Amino Acid Sequence↗
PubMed1986

Amino acid sequence of copper,zinc-superoxide dismutase from spinach leaves.

The complete amino acid sequence of Cu,Zn-superoxide dismutase (SOD) from spinach leaves has been determined on the basis of peptides obtained by cyanogen bromide (BrCN) cleavage and by enzymic hydrolyses with Achromobacter lyticus lysylendopeptidase, Staphylococcus aureus V8 protease, trypsin, and thermolysin. The spinach SOD consists of a total of 154 amino acid residues with alanine as the amino(N)-terminus and valine as the carboxy(C-)terminus. The present sequence, which has been established for the enzyme from a plant, is also highly homologous to those of the enzymes from other species. Especially, the residues essential for metal binding and enzyme activity have been extensively conserved among all of the Cu,Zn-SODs hitherto analyzed.

Acetylation↗
PubMed1988

Osteomyelitis secondary to trauma or infected contiguous soft tissue.

Nonhematogenous osteomyelitis (NHO) occurred in 24 pediatric patients (ages 8 months to 18 years; median, 14 years; 23 male) admitted from 1980 to 1985. Predisposing factors included compound fracture (12), deep decubiti (4) and foot puncture (3). Infection involved tibia (7), foot bones (6), proximal femur (3) and ulna (2). Patients presented with drainage (64%), pain or tenderness (44%) and fever (32%) lasting for 1 to 180 days (median, 10 days). In 24% both white blood cell count and erythrocyte sedimentation rate were normal. Initial radiographs were nondiagnostic in 42% after compound fractures. Bone cultures were positive in 15 of 18 (83%) patients for: Staphylococcus aureus (9), Staphylococcus epidermidis (2), Pseudomonas aeruginosa (4), Escherichia coli (2), Enterobacter sp. (2), Streptococcus faecalis, Serratia sp., Klebsiella pneumoniae, Achromobacter xylosoxidans, Aeromonas hydrophila and Pseudomonas fluorescens (1 each). Wound cultures failed to predict bone culture results in 12 of 16 patients (75%). NHO recurred in 8 of 19 patients (42%) despite intravenously administered antibiotics for greater than 28 days and debridement in 7 of 8 patients. The indolent nature of NHO complicates diagnosis, especially in patients with recent compound fractures. Only prompt bone culture can confirm the presence of NHO and reliably guide antimicrobial therapy.

Adolescent↗
PubMed1996

Bordetella trematum sp. nov., isolated from wounds and ear infections in humans, and reassessment of Alcaligenes denitrificans Rüger and Tan 1983.

Ten strains recognized on the basis of a computer-assisted numerical comparison of whole-cell protein patterns as members of a novel species belonging to the family Alcaligenaceae were examined by using an integrated phenotypic and genotypic approach. This species, for which we propose the name Bordetella trematum sp. nov., was more closely related to the type species of the genus Bordetella (Bordetella pertussis) than to the type species of the genus Alcaligenes (Alcaligenes faecalis) and had the general characteristics of members of this family (i.e., a DNA base ratio in the range from 57 to 70 mol%, a fatty acid profile characterized by high percentages of 16:0, 17:0 cyclo, and 14:0 3OH, nonsaccharolytic metabolism, and several classical biochemical characteristics, including aerobic and microaerobic growth, catalase activity, assimilation of citrate, an absence of anaerobic growth, and an absence of acetylmethylcarbinol and indole production, gelatin liquefaction, and esculin hydrolysis). A reevaluation of the criteria used to classify Alcaligenes denitrificans Rüger and Tan 1983 and Achromobacter xylosoxidans Yabuuchi and Ohyama 1971 as subspecies of Alcaligenes xylosoxidans and additional evidence provided in recent studies revealed that, consistent with present standards, it is appropriate to consider these two taxa distinct species of the genus Alcaligenes.

Alcaligenes↗
PubMed2001

Bordetella petrii sp. nov., isolated from an anaerobic bioreactor, and emended description of the genus Bordetella.

A novel Bordetella species was isolated from an anaerobic, dechlorinating bioreactor culture enriched from river sediment. The only strain, Se-1111R(T) (= DSM 12804T = CCUG 43448T), for which the name Bordetella petrii is proposed, is designated the type strain of the novel species. Strain Se-1111R(T) was isolated from the dechlorinating mixed culture due to its ability to anaerobically reduce selenate to elemental selenium. Comparative 16S rDNA sequence analysis showed a close relationship between Se-1111R(T) and members of the genus Bordetella within the beta-Proteobacteria. This close phylogenetic relatedness was also reflected in several metabolic properties of Se-1111R(T), including its incapacity to utilize carbohydrates, by the high G+C content (63.8 mol%) of its DNA and by the presence of Q-8 as the major isoprenoid quinone. DNA-DNA hybridization experiments with type strains of all species of the genus Bordetella and closely related species Achromobacter xylosoxidans subsp. denitrificans provided further evidence for the assignment of strain Se-1111R(T) as a novel species of the genus Bordetella. This genus currently consists of seven aerobic species, all of which are known to occur in close pathogenic, opportunistic or possibly commensal relationships with various host organisms. B. petrii is the first member of this genus isolated from the environment and capable of anaerobic growth. The proposal of the novel species and an emended description of the genus Bordetella is presented.

Anaerobiosis↗
PubMed2002

Brackiella oedipodis gen. nov., sp. nov., gram-negative, oxidase-positive rods that cause endocarditis of cotton-topped tamarin (Saguinus oedipus).

A gram-negative, oxidase-positive, rod-shaped bacterium isolated from the heart of a cotton-topped tamarin was characterized by 16S rDNA sequence analysis, SDS-PAGE of whole-cell proteins, fatty acid analysis and biochemical tests. Outer-membrane proteins, iron-regulated outer-membrane proteins, lipopolysaccharides and siderophore production were studied. On the basis of the results, the organism belongs to the beta-Proteobacteria where it forms a separate line of descent, for which a novel genus and species are proposed, Brackiella oedipodis (LMG 19451T = DSM 13743T = NCIMB 13739T). Nearest phylogenetic neighbours of the new genus are Taylorella, Pelistega, Bordetella, Alcaligenes and Achromobacter.

Animals↗
PubMed1976

Acinetobacter and similar organisms in ear infections.

Fifty-seven strains of acinetobacter-like organisms were isolated over a period of 26 months from the ears of 55 patients with acute or chronic otitis media, or otitis externa, and one strain was isolated in a survey of 50 normal ears. After comparison with eight reference strains, 32 of the isolates were identified as Acinetobacter anitratus, 22 as Acinetobacter Iwoffii, three as Moraxella spp. and one as Achromobacter sp. Analysis of the clinical findings suggests that although most of these organisms played little part in the disease process, a few strains were probably pathogenic in this situation.

Acinetobacter↗
PubMed2003

Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov.

Thirteen Ralstonia pickettii-like isolates from the environment (water, soil and activated sludge) and human clinical samples (including respiratory secretions of cystic fibrosis patients) were investigated in a polyphasic taxonomic study that employed 16S rDNA sequence analysis, DNA-DNA hybridization, determination of DNA base composition, whole-cell protein analysis, biochemical characterization and PCR-based assays. All isolates were classified as a novel Ralstonia species, for which the name Ralstonia insidiosa sp. nov. is proposed. The type strain, LMG 21421T (= CCUG 46789T), was isolated from the sputum of a patient with acute lymphoblastic leukaemia. R. insidiosa can be differentiated from other species of the genus Ralstonia and phenotypically similar species (including the Burkholderia cepacia complex and Achromobacter xylosoxidans) by a variety of biochemical tests, whole-cell protein analysis and several PCR-based assays. Some outstanding issues in the taxonomy of the genus Ralstonia are also discussed.

Base Composition↗