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Masayuki Yamasaki

Publications and source records attributed to Masayuki Yamasaki.

At least 19 recordsLinked to original sources
PubMed2006

Crystallization and preliminary X-ray analysis of an exotype alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, a member of polysaccharide lyase family 15.

Almost all alginate lyases depolymerize alginate in an endolytical fashion via a beta-elimination reaction. The alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, consisting of 776 amino-acid residues, is a novel exotype alginate lyase classified into polysaccharide lyase family 15. The enzyme was crystallized at 293 K by sitting-drop vapour diffusion with polyethylene glycol 4000 as a precipitant. Preliminary X-ray analysis showed that the Atu3025 crystal belonged to space group P2(1) and diffracted to 2.8 angstroms resolution, with unit-cell parameters a = 107.7, b = 108.3, c = 149.5 angstroms, beta = 91.5 degrees.

Agrobacterium tumefaciens↗
PubMed2006

Crystallization and preliminary X-ray analysis of the rhamnogalacturonan lyase YesW from Bacillus subtilis strain 168, a member of polysaccharide lyase family 11.

Rhamnogalacturonan lyases degrade rhamnogalacturonan I, a major component of pectin, through a beta-elimination reaction. YesW from Bacillus subtilis strain 168 is a novel rhamnogalacturonan lyase classified into polysaccharide lyase family 11 (PL-11). The enzyme was crystallized at 293 K using the sitting-drop vapour-diffusion method with 2-methyl-2,4-pentanediol (MPD) as a precipitant. Preliminary X-ray analysis revealed that the YesW crystals belong to space group P2(1) and diffract to 2.40 angstroms resolution, with unit-cell parameters a = 56.7, b = 105.6, c = 101.4 A, beta = 94.9 degrees. This is the first report on the crystallization and preliminary X-ray analysis of a family PL-11 rhamnogalacturonan lyase.

Bacillus subtilis↗
PubMed2005

A structural basis for depolymerization of alginate by polysaccharide lyase family-7.

Alginate lyases depolymerize alginate, a heteropolysaccharide consisting of alpha-L-guluronate and beta-D-mannuronate, through a beta-elimination reaction. Their structure/function relationships are expected to provide information valuable to future industrial alginate processing and drug design for Pseudomonas aeruginosa alginate biofilm-dependent infection, but much remains unknown. Here, we present the crystal structure at 1.0 A resolution and the results of mutational analysis of Sphingomonas sp. A1 alginate lyase A1-II', which is grouped into the polysaccharide lyase (PL) family-7. The overall structure of A1-II' uses a beta-sandwich fold, and it has a large active cleft covered by two short flexible loops. Comparison with other family PL-7 structures indicated that loop opening is necessary for substrate binding when the catalytic reaction is initiated. In contrast to the disorder in many side-chains on the protein surface, the three adjacent beta-strands at the center of the active cleft are well ordered. This results from hydrogen bond networks and stacking-like associations identical with those in other family PL-7 structures. Disruption of these interactions by site-directed mutagenesis (R146A, E148A, R150A, Q189A, and K280A) makes the protein insoluble or greatly decreases its activity. The A1-II' structure includes two sulfate ions in the active cleft. Ammonium sulfate was a potent inhibitor with a Ki of 2.5 mM, indicating that our structure represents a model of the inhibitory state. Results of mutational analysis and continuous hydrogen bond networks suggest that Arg146, Gln189, His191, and Tyr284 form an active center. Tyr284OH appears particularly crucial to the catalytic reaction, which is supported by sulfate ion binding and the proximity to the C5 and O4 atoms of subsite +1 in the model obtained by energy minimization calculations using tri-mannuronate. The structural basis shown by this study is similar in many respects to that of the family PL-5 enzymes.

Alginates↗
PubMed2005

Dynamic mechanism for the serpin loop insertion as revealed by quantitative kinetics.

The serpin conformational change by insertion of the reactive center loop into beta-sheet A plays a central role in multiple physiological consequences such as serine proteinase inhibition, latency and serpinopathic polymerization. To study the dynamic mechanism for the loop insertion, a novel kinetic method was established utilizing the ovalbumin mutant R339T/A352R; the loop insertion progressed after the cleavage of P1-P1' (Arg352-Ser353) by trypsin was quenched at pH 8 and 0.5 degrees C, and different conformers were quantified by separation using ion-exchange HPLC. The apparent first-order rate constant k(app) determined for various R339T/A352R derivatives differing in conformational stability was greatly increased by lowering the pH. The pH-dependence of k(app) indicated that the protonation of side-chain(s) with a pK(a) value of around 4.6 is a pre-requisite for the loop insertion. The theoretical rate constant k for the protonated form calculated from k(app) was highly variable, depending on the ovalbumin derivative; structural modifications that give increased mobility to helix F and the sheet-A half (s3A/s2A/s1A) resulted in a striking increase in the loop insertion rate constant k. The k values were determined at different temperatures for all the ovalbumin derivatives, and DeltaH(double dagger) and DeltaS(double dagger) values for the loop insertion reaction were determined according to the transition theory. The formation of the transition state was highly endothermic with minor entropy gain, requiring a DeltaG(double dagger) larger than 18 kcal/mol, which can offset the hydrogen-bond cleavages between s3A and s5A. These results are consistent with the transition state with an opened sheet A and altered orientation of helix F.

Animals↗
PubMed2005

Crystallization and preliminary X-ray analysis of alginate lyases A1-II and A1-II' from Sphingomonas sp. A1.

Alginate lyases depolymerize alginate, a heteropolysaccharide consisting of alpha-L-guluronate and beta-D-mannuronate, through a beta-elimination reaction. The alginate lyases A1-II (25 kDa) and A1-II' (25 kDa) from Sphingomonas sp. A1, which belong to polysaccharide lyase family PL-7, exhibit 68% homology in primary structure but have different substrate specificities. To determine clearly the structural basis for substrate recognition in the depolymerization mechanism by alginate lyases, both proteins were crystallized at 293 K using the vapour-diffusion method. A crystal of A1-II belonged to space group P2(1) and diffracted to 2.2 A resolution, with unit-cell parameters a = 51.3, b = 30.1, c = 101.6 A, beta = 100.2 degrees, while a crystal of A1-II' belonged to space group P2(1)2(1)2(1) and diffracted to 1.0 A resolution, with unit-cell parameters a = 34.6, b = 68.5, c = 80.3 A.

Alginates↗
PubMed2005

NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex.

NAD kinase is a key enzyme in NADP biosynthesis. We solved the crystal structure of polyphosphate/ATP-NAD kinase from Mycobacterium tuberculosis (Ppnk) complexed with NAD (Ppnk-NAD) at 2.6A resolution using apo-Ppnk structure solved in this work, and revealed the details of the structure and NAD-binding site. Superimposition of tertiary structures of apo-Ppnk and Ppnk-NAD demonstrated a substantial conformational difference in a loop (Ppnk-flexible loop). As a quaternary structure, these Ppnk structures exhibited tetramer as in solution condition. Notably, the Ppnk-flexible loop was involved in the intersubunit contact and probably related to the NAD-binding of the other subunit. Furthermore, the two residues (Asp189, His226) substantially contributed to creating NAD-binding site on the other subunit. The two residues and the residues involved in NAD-binding were conserved. However, residues corresponding to the Ppnk-flexible loop were not conserved, making us to speculate that the Ppnk-flexible loop may be Ppnk-specific.

Amino Acid Sequence↗
PubMed2005

Prevalence of the metabolic syndrome using the Third Report of the National Cholesterol Educational Program Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (ATP III) and the modified ATP III definitions for Japanese and Mongolians.

BACKGROUND: A clustering of insulin resistance, hypertension, and dyslipidemia has been labeled as metabolic syndrome. Asians have a lower frequency of obesity than do Caucasians but have an increasing tendency toward metabolic syndrome. METHODS: We conducted a cross-sectional study of individuals aged 30-60 years. We analyzed the health data of 596 Japanese and Mongolians for metabolic syndrome based on the Third Report of the National Cholesterol Educational Program Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (ATP III) definition and the three modified ATP III definitions. RESULTS: The prevalence of metabolic syndrome using ATP III criteria was 6% for the Japanese and 12% for the Mongolians, a remarkable lower prevalence relative to the reported prevalence in the United States. With the exception of visceral obesity, the prevalences of individual metabolic abnormalities within each of the two Asian groups were similar to each other and to reported rates of prevalence in the United States. CONCLUSIONS: A universal metabolic syndrome definition is inappropriate for comparisons of metabolic syndrome among Asian ethnic groups. We believe that the ATP III index for visceral obesity should be adjusted for Asian populations.

Adult↗
PubMed2005

Mulberry (Morus alba L.) leaves and their major flavonol quercetin 3-(6-malonylglucoside) attenuate atherosclerotic lesion development in LDL receptor-deficient mice.

The effects of dietary consumption of mulberry (Morus alba L.) leaves and their major flavonol glycoside, quercetin 3-(6-malonylglucoside) (Q3MG), on the development of atherosclerotic lesions, in relation to the susceptibility of plasma LDL to oxidative modification, was studied in LDL receptor-deficient (LDLR-/-) mice. Male mice aged 8 wk were randomly assigned to 4 groups (control, quercetin, Q3MG, and mulberry). The control group was fed an atherogenic-diet containing 3 g cholesterol and 15 g cocoa butter/100 g. The other experimental groups were fed the same atherogenic diet supplemented with 0.05 g quercetin/100 g for the quercetin group, 0.05 g Q3MG/100 g for the Q3MG group, and 3 g dried mulberry-leaf powder/100 g for the mulberry group. The mice were fed their respective diets for 8 wk. The susceptibility of LDL to oxidative modification was significantly decreased in the Q3MG- and mulberry-treated mice, as evidenced by the 44.3 and 42.2% prolongation of the lag phase for conjugated diene formation compared with that of the control mice. The atherosclerotic lesion area in both the Q3MG- and mulberry-treated mice was significantly reduced by 52% compared with that of the controls. However, in the quercetin group, no protective effects were observed against LDL oxidation or atherosclerotic lesion formation. In conclusion, mulberry leaves attenuated the atherosclerotic lesion development in LDLR-/- mice through enhancement of LDL resistance to oxidative modification, and these antioxidative and antiatherogenic protective effects were attributed mainly to Q3MG, the quantitatively major flavonol glycoside in mulberry leaves.

Administration, Oral↗
PubMed2005

Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.

Generally, when microbes assimilate macromolecules, they incorporate low-molecular-weight products derived from macromolecules through the actions of extracellular degrading enzymes. However, a Gram-negative bacterium, Sphingomonas sp. A1, has a smart biosystem for the import and depolymerization of macromolecules. The bacterial cells directly incorporate a macromolecule, alginate, into the cytoplasm through a "superchannel", as we named it. The superchannel consists of a pit on the cell surface, alginate-binding proteins in the periplasm, and an ATP-binding cassette transporter in the inner membrane. Cytoplasmic polysaccharide lyases depolymerize alginate into the constituent monosaccharides. Other than the proteins characterized so far, novel proteins (e.g., flagellin homologs) have been found to be crucial for the import and depolymerization of alginate through genomics- and proteomics-based identification, thus indicating that the biosystem is precisely constructed and regulated by diverse proteins. In this review, we focus on the structure and function of the bacterial biosystem together with the evolution of related proteins.

Bacterial Proteins↗
PubMed2005

Thermostability of refolded ovalbumin and S-ovalbumin.

Ovalbumin, a member of the serpin superfamily, is transformed into a thermostabilized form, S-ovalbumin, during storage of shell eggs or by an alkaline treatment of the isolated protein (DeltaT(m)=8 degrees C). As structural characteristics of S-ovalbumin, three serine residues (Ser164, Ser236 and Ser320) take the D-amino acid residue configuration, while the conformational change from non-thermostabilized native ovalbumin is very small. To assess the role of the structural characteristics on protein thermostabilization, ovalbumin and S-ovalbumin were denatured to eliminate the conformational modulation effects and then refolded. The denatured ovalbumin and S-ovalbumin were correctly refolded into the original non-denatured forms with the corresponding differential thermostability. There was essentially no difference in the disulfide structures of the native and refolded forms of ovalbumin and S-ovalbumin. These data are consistent with the view that the configuration inversion, which is the only chemical modification directly detected in S-ovalbumin so far, plays a central role in ovalbumin thermostabilization. The rate of refolding of S-ovalbumin was greater than that of ovalbumin, indicating the participation, at least in part, of an increased folding rate for thermodynamic stabilization.

Hot Temperature↗
PubMed2005

Prevalence of the metabolic syndrome using the modified ATP III definitions for workers in Japan, Korea and Mongolia.

A clustering of insulin resistance, hypertension and dyslipidemia has been labeled as the metabolic syndrome. Asians have a lower frequency of obesity than do Caucasians, but have an increasing tendency toward metabolic syndrome. Most data on metabolic syndrome are based on studies from Western countries with only limited information derived from Asian populations. We conducted a cross-sectional study of individuals aged 30-60 yr in workplace settings. We examined and analyzed the health data of 1,384 Japanese, Koreans and Mongolians for metabolic syndrome based on the modified definitions of the working definition proposed by the Third Report of the National Cholesterol Educational Program Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (ATP III definition). The prevalence of metabolic syndrome using the ATP III-BMI30 and ATP III-BMI25 definitions was 7% and 12% for Japanese, 7% and 13% for Koreans, and 12% and 16% for Mongolians, respectively. With the exception of obesity, the prevalences of individual metabolic abnormalities within each of the three Asian groups were similar to each other and to reported rates of prevalence in the U.S.A. Nevertheless, the values of sensitivity and specificity by the metabolic syndrome definitions are remarkably different relative to ethnicity. A universal metabolic syndrome definition is inappropriate for comparisons of metabolic syndrome among Asian ethnic groups. We believe that the ATP III-BMI25 definition is suitable for the determination of metabolic syndrome among Japanese and Koreans, and that the ATP III-BMI30 is more appropriate for Mongolians.

Adult↗
PubMed2004

Predictive values of anthropometric measurements for multiple metabolic disorders in Asian populations.

OBJECTIVE: Asians have a unique feature characterized by a low frequency of obesity, but a high frequency of diabetes and metabolic syndrome. It is important to develop simple and reliable anthropometric measurement tools for multiple metabolic disorders, but the cut-off values of anthropometric measurements for Asians have been less clear than those for Caucasians. RESEARCH DESIGN: Data from 361 Japanese and 252 Mongolians aged 30-60 years were investigated for the relationship between multiple metabolic disorders parameters and anthropometric measurements. Pearson's correlation coefficients and receiver operating characteristic (ROC) analysis were done. RESULTS: Mongolians of both genders had significantly higher values for all anthropometric measurements than did the Japanese. The Japanese anthropometric measurements showed the highest correlation coefficient of the area under the curve (AUC) from an ROC analysis for HDL-C and triglyceride, while the Mongolians showed the highest values for HOMA-IR. BMI and waist circumference (WC) for both ethnic groups showed relatively higher AUCs for the multiple metabolic disorders parameters. Optimal cut-off values predicting multiple metabolic disorders in the Japanese were estimated at 24 BMI and 82 cm WC (men) and 23 BMI and 73 cm WC (women); for the Mongolian, 27 BMI and 92 cm WC (men) and 27 BMI and 84 cm WC (women). CONCLUSIONS: There were great differences in diagnostic accuracy for the anthropometric measurements by ethnicity, and a relatively lower magnitude of differences by kind of anthropometric measurement. The present study suggests that BMI and WC were useful for predicting multiple metabolic disorders in non-diabetic Mongolians and Japanese, while the use of plasma triglyceride and HDL-cholesterol levels in combination with BMI and WC may enhance the ability of predicting metabolic parameters in the Japanese.

Adult↗
PubMed2004

Crystallization and preliminary X-ray analysis of pyridoxal 4-dehydrogenase, the second enzyme in degradation pathway I of pyridoxine.

Pyridoxal 4-dehydrogenase (PLDH; EC 1.1.107) is the second enzyme in the bacterial degradation pathway I of vitamin B(6), which catalyzes the oxidation of pyridoxal to 4-pyridoxolactone using NAD(+). PLDH from Microbacterium luteolum, a dimeric protein with a subunit molecular weight of 38 kDa, was crystallized at 277 K in a drop solution comprising 15%(w/v) polyethylene glycol 4000, 0.15 M sodium acetate, 7.5 mM n-octyl-beta-D-glucoside and 0.075 M Tris-HCl pH 7.5 by the sitting-drop vapour-diffusion method. The crystals were monoclinic and belonged to space group C2, with unit-cell parameters a = 107.0, b = 56.7, c = 130.2 A, beta = 103.6 degrees . Diffraction data were collected from a single crystal to 2.0 A.

Actinomycetales↗
PubMed2004

Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.

Structural and functional analyses of alginate lyases are important in the clarification of the biofilm-dependent ecosystem in Pseudomonas aeruginosa and in the development of therapeutic agents for bacterial disease. Most alginate lyases are classified into polysaccharide lyase (PL) family-5 and -7 based on their primary structures. Family PL-7 enzymes are still poorly characterized especially in structural properties. Among family PL-7, a gene coding for a hypothetical protein (PA1167) homologous to Sphingomonas alginate lyase A1-II was found to be present in the P. aeruginosa genome. PA1167 overexpressed in Escherichia coli cleaved glycosidic bonds in alginate and released unsaturated saccharides, indicating that PA1167 is an alginate lyase catalyzing a beta-elimination reaction. The enzyme acted preferably on heteropolymeric regions endolytically and worked most efficiently at pH 8.5 and 40 degrees C. The specific activity of PA1167, however, was much weaker than that of the known alginate lyase AlgL, suggesting that AlgL plays a main role in alginate depolymerization in P. aeruginosa. In addition to this specific activity, differences were found between PA1167 and AlgL in enzyme properties such as molecular mass, optimum pH, salt effect, and substrate specificity. The first crystal structure of the family PL-7 alginate lyase was determined at 2.0 A resolution. PA1167 was found to form a glove-like beta-sandwich composed of 15 beta-strands and 3 alpha-helices. The structural difference between the beta-sandwich PA1167 of family PL-7 and alpha/alpha-barrel AlgL of family PL-5 may be responsible for the enzyme characteristics. Crystal structures of polysaccharide lyases determined so far indicate that they can be assigned to three folding groups having parallel beta-helix, alpha/alpha-barrel, and alpha/alpha-barrel + antiparallel beta-sheet structures as basic frames. PA1167 is the fourth novel folding structure found among polysaccharide lyases.

Amino Acid Sequence↗
PubMed2004

Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.

Cells of Sphingomonas sp. A1 directly incorporate a macromolecule, alginate, into the cytoplasm through a biosystem, super-channel, consisting of a pit on the cell surface, alginate-binding proteins in the periplasm, and an ATP-binding cassette transporter in the inner membrane. The alginate is finally depolymerized into constituent monosaccharides by polysaccharide lyases present in the cytoplasm. The fundamental frame of the biosystem for alginate transport, and the functions of the pit, binding proteins, and ABC transporter have already been reviewed together with those of alginate-depolymerization processes [Hashimoto et al., J. Biosci. Bioeng., 87, 123-136 (1999)]. In this review, we have attempted to demonstrate the three-dimensional structure and evolution features of the super-channel, and alginate-depolymerization processes by using information obtained mainly through genomics, proteomics, and X-ray crystallography.

Journal Article↗
PubMed2004

Two chimeric chromosomes of Streptomyces coelicolor A3(2) generated by single crossover of the wild-type chromosome and linear plasmid scp1.

Streptomyces coelicolor A3(2) strain 2106 carries a 1.85-Mb linear plasmid, SCP1'-cysD, in addition to a 7.2-Mb linear chromosome. Macrorestriction analysis indicated that both linear DNAs are hybrids of the wild-type chromosome and the linear plasmid SCP1 on each side. Nucleotide sequencing of the fusion junctions revealed no homology between the recombination regions. SCP1'-cysD contains an SCP1 telomere and a chromosomal telomere at each end and therefore does not have terminal inverted repeats. In addition, SCP1'-cysD could not be eliminated from strain 2106 by various mutagenic treatments. Thus, we concluded that both the 7.2-Mb chromosome and SCP1'-cysD are chimeric chromosomes generated by a single crossover of the wild-type chromosome and SCP1. This may be regarded as a model of chromosomal duplication in genome evolution.

Amino Acid Sequence↗