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W Kugimiya

Publications and source records attributed to W Kugimiya.

16 recordsLinked to original sources
PubMed2001

Improvement of the optimum temperature of lipase activity for Rhizopus niveus by random mutagenesis and its structural interpretation.

Random mutagenesis was used to improve the optimum temperature for Rhizopus niveus lipase (RNL) activity. The lipase gene was mutated using the error-prone PCR technique. One desirable mutant was isolated, and three amino acids were substituted in this mutant (P18H, A36T and E218V). The wild-type and this randomly mutated lipase were both purified and characterized. The specific activity of the mutant lipase was 80% that of the wild-type. The optimum temperature of the mutant lipase was higher by 15 degrees C than that of the wild-type. To confirm which substitution contributed to enhancing the optimum temperature for enzymic activity, two chimeric lipases from the wild-type and randomly mutated gene were constructed: chimeric lipase 1 (CL-1; P18H and A36T) and chimeric lipase 2 (CL-2; E218V). Each of the chimeric enzymes was purified, and the optimum temperature for lipase activity was measured. CL-1 had a similar optimum temperature to that of the wild-type, and CL-2 had a higher temperature like the randomly mutated lipase. The mutational effect is interpreted in terms of a three-dimensional structure for the wild-type lipase.

Amino Acid Substitution↗
PubMed2001

Conformational change in a single molecular species, beta3, of beta-conglycinin in acidic ethanol solution.

Several physicochemical experiments were done to obtain further information on the conformational changes occurring in beta-conglycinin in acidic-ethanol solution, using a single molecular species of this protein, beta3. By far-UV circular dichroism (CD), a transition from beta-sheet to alpha-helical structure was observed upon addition of acidic-ethanol, and the alpha-helix content was found to reach 76% in 70% ethanol (pH 2). From analyses of near-UV CD and difference absorption spectra, it was found that the tertiary structure of the beta3 species was significantly altered at ethanol concentrations between 10 and 20%. The profiles of binding of 1-anilinonaphthalene-8-sulfonic acid to the beta3 species during acidic-ethanol denaturation were indicative of the existence of intermediate conformers in the molten globule-like denaturation state. By measuring Fourier transform infrared spectra and estimating the Stokes radius by dynamic light scattering, the beta3 molecules were found to aggregate with an increase in ethanol concentration.

Anilino Naphthalenesulfonates↗
PubMed2001

Novel method using phytase for separating soybean beta-conglycinin and glycinin.

A novel method for separating soybean beta-conglycinin and glycinin from defatted soymilk by a phytase treatment was developed. Phytase was added to defatted soymilk (1000FYT/100 g of protein) at pH 6.0, and the mixture incubated for 1 h at 40 degrees C. This procedure separated beta-conglycinin and glycinin without needing a reducing agent or cooling into the soluble and insoluble fractions, respectively. Simultaneously, most of the phytate in both proteins was removed.

6-Phytase↗
PubMed2000

Thermal stability of Rhizopus niveus lipase expressed in a kex2 mutant yeast.

Lipase from Rhizopus niveus (RNL) has a complex structure, and recombinant RNL, has even more complex structural properties in the yeast, Saccharomyces cerevisiae. These properties are due to the processing and to the size of the glycosylated sugar chain. The processing site was presumed to be that for the proteinase product of the KEX2 gene in yeast. We therefore, constructed an expression system in which the KEX2 gene was disrupted to produce a non-processed type of lipase with high thermal stability. This type of lipase was thermally stable to a temperature 15 degrees C higher than that of each processed type of lipase. This non-processed lipase had 50% residual activity after 2 h at 50 degrees C, while the residual activity of the processed lipases was only 10% after 30-45 min of incubation at 50 degrees C. The CD spectrum of the non-processed type of lipase at 222 nm was almost unchanged by heating, suggesting that this group of lipases had a very rigid structure and that the peptide bond between the A- and B-chain contributed to maintain this rigid structure. On the other hand, the length of the sugar chain bound to the lipase had no effect on the thermal stability.

Enzyme Stability↗
PubMed1999

High-level expression of Rhizopus niveus lipase in the yeast Saccharomyces cerevisiae and structural properties of the expressed enzyme.

Rhizopus niveus lipase (RNL) has a unique structure consisting of two noncovalently bound polypeptides (A-chain and B-chain). To improve this enzyme's properties by protein engineering, we have developed a new expression system for the production of recombinant lipase in the yeast Saccharomyces cerevisiae. For the present study, we developed a more efficient expression system using the strain ND-12B and the multicopy-type plasmid pJDB219. We purified two types of recombinant lipases, each to a single peak by gel-filtration HPLC, although they were found to be heterogeneous by SDS-PAGE. Analysis of reversed-phase HPLC, N-terminal amino acid sequence, and sugar content showed that the difference between the two types of lipases was due mainly to their sugar content (high or low mannose type). Moreover, there were two species within each type of lipase. One kind was processed to the A-chain and B-chain as in the native lipase, while the other remained unprocessed. Although these yeast-purified lipases contained several posttranslational modifications and different glycosylations, their secondary structures were the same as those of the native lipase as measured by circular dichroism spectra and determination of disulfide bonding. This suggests that protein folding of the recombinant lipase occurred correctly in yeast.

Amino Acid Sequence↗
PubMed1998

Cloning of genomic DNA of Rhizopus niveus lipase and expression in the yeast Saccharomyces cerevisiae.

Genomic DNA encoding Lipase I was cloned from Rhizopus niveus strain IFO4759. For expression of this gene in S. cerevisiae, DBY746 was transformed with YEp352PLipS, which had the cloned lipase gene under the control of a PGK promoter. This strain secreted the lipase at a high level (350 U/ml). The strain ND-12B was produced by a mating of DBY746, harboring YEp352PLipS, and NA74-3A, and dissection of asci. This new strain secreted the lipase up to 530 U/ml. Moreover, the lipase was produced most effectively in a medium containing Bacto-yeast extract, soy-peptide, and sucrose.

Blotting, Western↗
PubMed1996

The crystal structure of lipase II from Rhizopus niveus at 2.2 A resolution.

The crystal and molecular structure of Lipase II from Rhizopus niveus was analyzed using X-ray single crystal diffraction data at a resolution of 2.2 A. The structure was refined to an R-factor of 0.19 for all available data. This lipase was purified and crystallized as Lipase I, which contains two polypeptide chains combined through non-covalent interaction. However, during crystal growth, Lipase I was converted to Lipase II, which consists of a single polypeptide chain of 269 amino acid residues, by limited proteolysis. The structure of Lipase II shows a typical alpha/beta hydrolase fold containing the so-called nucleophilic elbow. The catalytic center of this enzyme is analogous to those of other neutral lipases and serine proteases. This catalytic center is sheltered by an alpha-helix lid, which appears in neutral lipases, opening the active site at the oil-water interface.

Amino Acid Sequence↗
PubMed1994

Purification, characterization, and crystallization of two types of lipase from Rhizopus niveus.

The purification and some properties of two types of lipase (Lipase I and Lipase II) from Rhizopus niveus are described. The enzymes were purified to homogeneity by column chromatographies on DEAE-Toyopearl (1 pass) and CM-Toyopearl (2 passes). Lipase I consists of two polypeptide chains [a small peptide with sugar moiety (A-chain) and a large peptide of molecular weight 34,000 (B-chain)]. Lipase II has a molecular weight of 30,000 consisting of a single polypeptide chain. Lipase I appeared to be converted to Lipase II by limited proteolysis by a specific protease a small amount of which is in the culture supernatant from Rh. niveus, because one of the peptides formed has the same N-terminal sequence and C-terminal amino acid as Lipase II, as well as the molecular mass estimated by SDS-PAGE. Lipase I had a pH optimum of 6.0-6.5 and a temperature optimum of 35 degrees C, while, for Lipase II these values were pH 6.0 and 40 degrees C. Both enzymes were obtained in the crystalline state using the hanging drop method of vapor diffusion and PEG as the precipitating agents.

Amino Acid Sequence↗
PubMed1993

Preliminary investigation of crystals of lipase I from Rhizopus niveus.

Lipase I from Rhizopus niveus consists of two polypeptide chains bound non-covalently. Lipase I has been crystallized in a form suitable for X-ray diffraction analysis using the hanging drop method of vapour diffusion at 20 degrees C. The crystals grew at pH 6.0 to 7.0 using 14 to 16% polyethylene glycol 8000 as the precipitant. The crystals are tetragonal with space group P4(1) (or P4(3)) and cell dimensions of a = b = 83.7 A, c = 137.9 A. There are two protein molecules in the asymmetric unit. The diffraction pattern extends to at least 2.5 A resolution.

Lipase↗
PubMed1992

Cloning and sequence analysis of cDNA encoding Rhizopus niveus lipase.

Complementary DNA encoding Rhizopus niveus lipase (RNL) was isolated from the R. niveus IF04759 cDNA library using a synthetic oligonucleotide corresponding to the amino acid sequence of the enzyme. A clone, which had an insert of 1.0 kilobase pairs, was found to contain the coding region of the enzyme. The lipase gene was expressed in Escherichia coli as a lacZ fusion protein. The mature RNL consisted of 297 amino acid residues with a molecular mass of 32 kDa. The RNL sequence showed significant overall homology to Rhizomucor miehei lipase and the putative active site residues were strictly conserved.

Amino Acid Sequence↗
PubMed1986

Molecular cloning and nucleotide sequence of the lipase gene from Pseudomonas fragi.

The gene coding for the lipase of Pseudomonas fragi was cloned into Escherichia coli JM83 by inserting Sau3A-generated DNA fragments into the BamH I site of pUC9. The plasmid isolated, pKKO, was restriction mapped and the position of the lipase gene on the 2.0 kb insert was pinpointed by subcloning. DNA sequencing revealed that the open reading frame comprises 405 nucleotides and gives a preprotein of 135 amino acids with a predicted Mr of 14643. By comparing the putative lipase amino acid sequence with porcine pancreatic, rat lingual and Staphylococcus hyicus lipases the amino acid sequence around the reactive serine was found to be common among the types of lipase which have been reported.

Amino Acid Sequence↗
PubMed1985

Close structural resemblance between putative polymerase of a Drosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus.

We have made a computer-assisted search for homology among polymerases or putative polymerases of various viruses and a transposable element, the Drosophila copia-like element 17.6. The search revealed that the putative polymerase (second open reading frame) of the copia-like element 17.6 bears close resemblance in overall structural organization to the pol gene product of Moloney murine leukaemia virus (M-MuLV): they show significant homology to each other at both the N- and C-terminal portions, suggesting that the 17.6 putative polymerase carries two enzymatic activities, related to reverse transcriptase and DNA endonuclease. The putative polymerase of cauliflower mosaic virus (CaMV) shows striking homology with the putative polymerase of 17.6 over almost its entire length, but it lacks the DNA endonuclease-related sequence. Furthermore, it was shown that the N-terminal ends of the M-MuLV pol product and the CaMV and 17.6 putative polymerases exhibit strong sequence homology with the gag-specific protease (p15) of Rous sarcoma virus (RSV) as well as the amino acid sequence predicted from the gag/pol spacer sequence of human adult T-cell leukaemia virus (HTLV). These p15-related sequences contain a highly conserved stretch of amino acids which show a close similarity with sequences around the active site amino acids Asp-Thr-Gly of the acid protease family, suggesting that they have an activity similar to acid protease. On the basis of the alignment of reverse transcriptase-related sequences, a dendrogram representing phylogenetic relationships among all the viruses compared together with 17.6 was constructed and its evolutionary implication is discussed.

Amino Acid Sequence↗
PubMed1983

Close relationship between the long terminal repeats of avian leukosis-sarcoma virus and copia-like movable genetic elements of Drosophila.

A new species of copia-like movable genetic element termed 17.6 was identified in Drosophila melanogaster, and the nucleotide sequences of its long terminal repeats (LTRs) were determined. The LTRs of 17.6 were not only homologous to those of 297, a sibling movable genetic element of 17.6, but also closely matched those of avian leukosis-sarcoma virus. This made it possible (i) to identify the nucleotide sequences in 17.6 and 297 that correspond to the crucial regulatory sequences for both transcription and reverse transcription in avian leukosis-sarcoma virus and (ii) to divide the LTRs of these two elements into three regions, U3, R, and U5, like those of retrovirus proviruses. Similarity in sequence was also found to a certain extent in other copia-like elements. From these results, we postulate that copia-like movable genetic elements in Drosophila originated from infection of a progenitor Drosophila with a retrovirus from which the present-day avian leukosis-sarcoma virus was derived.

Alpharetrovirus↗
PubMedDate not supplied

Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster.

The largest group of transposable elements in Drosophila melanogaster, copia-like elements, share some important structural features with and are intimately related in evolution to vertebrate retroviruses. To further clarify the relationship between retroviruses and copia-like transposable elements, we set out to determine the complete nucleotide sequence of the genome of 17.6, which has long terminal repeats homologous in nucleotide sequence to those of avian leukaemia-sarcoma virus. We report here that 17.6 contains three long open reading frames comparable with gag, pol and env genes in retrovirus. At the level of amino acid sequence, the longest open reading frame of 17.6 includes a coding sequence similar to that for reverse transcriptase, suggesting a role for this enzyme in the life cycle of some Drosophila copia-like elements, analogous to the situation in retrovirus.

Animals↗