Biomedical subjects

B Mikami

Publications and source records attributed to B Mikami.

At least 37 records · Page 2Linked to original sources

PubMed1999

Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.

The crystals of beta-amylase from Bacillus cereus belong to space group P21 with the following cell dimensions: a = 57.70 A, b = 92.87 A, c = 65.93 A, and beta =101.95 degrees. The structures of free and maltose-bound beta-amylases were determined by X-ray crystallography at 2.1 and 2.5 A with R-factors of 0.170 and 0.164, respectively. The final model of the maltose-bound form comprises 516 amino acid residues, four maltose molecules, 275 water molecules, one Ca2+, one acetate, and one sulfate ion. The enzyme consists of a core (beta/alpha)8-barrel domain (residues 5-434) and a C-terminal starch-binding domain (residues 435-613). Besides the active site in the core where two maltose molecules are bound in tandem, two novel maltose-binding sites were found in the core L4 region and in the C-terminal domain. The structure of the core domain is similar to that of soybean beta-amylase except for the L4 maltose-binding site, whereas the C-terminal domain has the same secondary structure as domain E of cyclodextrin glucosyltransferase. These two maltose-binding sites are 32-36 A apart from the active site. These results indicate that the ability of B. cereus beta-amylase to digest raw starch can be attributed to the additional two maltose-binding sites.

Acetates↗

PubMed1999

Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe.

Transferrins bind Fe3+ very tightly in a closed interdomain cleft by the coordination of four protein ligands (Asp60, Tyr92, Tyr191, and His250 in ovotransferrin N-lobe) and of a synergistic anion, physiologically bidentate CO32-. Upon Fe3+ uptake, transferrins undergo a large scale conformational transition: the apo structure with an opening of the interdomain cleft is transformed into the closed holo structure, implying initial Fe3+ binding in the open form. To solve the Fe3+-loaded, domain-opened structure, an ovotransferrin N-lobe crystal that had been grown as the apo form was soaked with Fe3+-nitrilotriacetate, and its structure was solved at 2.1 A resolution. The Fe3+-soaked form showed almost exactly the same overall open structure as the iron-free apo form. The electron density map unequivocally proved the presence of an iron atom with the coordination by the two protein ligands of Tyr92-OH and Tyr191-OH. Other Fe3+ coordination sites are occupied by a nitrilotriacetate anion, which is stabilized through the hydrogen bonds with the peptide NH groups of Ser122, Ala123, and Gly124 and a side chain group of Thr117. There is, however, no clear interaction between the nitrilotriacetate anion and the synergistic anion binding site, Arg121.

Animals↗

PubMed1999

The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution.

The three-dimensional structure of the sevenfold mutant of barley beta-amylase (BBA-7s) with increased thermostability was determined by X-ray crystallography. The enzyme was purified as a single component and crystallized by a hanging drop method in the presence of 14 % PEG 6000. The crystals belong to space group P43212 with cell dimensions a=b=72.11 A, c=250.51 A. The diffraction data up to 2.5 A were collected after soaking the crystal in 100 mM maltose with Rsym of 8.6 %. The structure was determined by a molecular replacement method using soybean beta-amylase (SBA) as a search model and refined to an R-factor of 18.7 %. The final model included 500 amino acid residues, 141 water molecules and three glucose residues, which were located at subsites 1-2 and 4 in the active site. The r.m.s. distance of 485 Calpha atoms between BBA-7s and SBA was 0.62 A. Out of the seven mutated amino acids, four (Ser295Ala, Ile297Val, Ser351Pro and Ala376Ser) were substitutions from the common residues with SBA to the thermostable forms. A comparison of the structures of BBA-7s and SBA indicated that the side-chain of Ser376 makes new hydrogen bonds to the main-chain of an adjacent beta-strand, and that the side-chains of Val297 reduce an unfavorable interaction between the side-chains of Ala314. The mutation of Ser295Ala breaks the hydrogen bond between Ser295 OG and Tyr195 OH, which seems to be the reason for the unoccupied glucose residue at subsite 3. The tandem mutations at 350-352 including substitutions to two Pro residues suggested the reduction of main-chain entropy in the unfolded structure of this solvent-exposed protruded loop.

Amino Acid Sequence↗

PubMed1999

Enzymatic and genetic bases on assimilation, depolymerization, and transport of heteropolysaccharides in bacteria.

When microorganisms utilize macromolecules for their growth, they commonly produce extracellular depolymerization enzymes and then incorporate the depolymerized low-molecular-weight products. Assimilation of heteropolysaccharides (gellan and xanthan) by Bacillus sp. GL1 depends on this generally accepted mechanism. On the other hand, Sphingomonas sp. A1 represents an unexplored specific and interesting system for macromolecule assimilation. In the presence of heteropolysaccharide (alginate), the bacterium forms a mouthlike pit on its cell surface and directly incorporates the macromolecule using a novel ATP-binding cassette transporter (ABC transporter). In this review, we discuss enzymatic and genetic bases on the depolymerization and assimilation routes of heteropolysaccharides in bacteria, with particular emphasis on the novel incorporation system for macromolecules, characteristic post-translational modification processes of polysaccharide lyases and on the mouthlike pit structure on the bacterial cell surface.

Journal Article↗

PubMed1999

Special cell surface structure, and novel macromolecule transport/depolymerization system of Sphingomonas sp A1.

A bacterium isolated from soil as an alginate lyase producer shows characteristic morphological and taxonomical properties consistent with being classified in the genus Sphingomonas. The bacterium utilizes high molecular weight (HMW)-alginate for growth by depolymerization of the polymer with intracellular alginate lyases, which are generated from a common precursor protein through autoregulated post-translational modifications. Electron microscopic observations of the cell surface and of thin sections of cells grown on HMW-alginate revealed dynamic changes in both cell surface and membrane structures. The most remarkable change is recognized in the formation of mouth-like pits which open and close depending on the presence or absence of HMW-alginate. Enzymatic and genetic analyses of HMW-alginate incorporation processes confirmed the presence of a pit-dependent and macromolecule-specific ABC transporter system in cells of Sphingomonas species A1. This is the first description of a bacterium with a pit on the cell surface and a pit-dependent endocytosic uptake system for macromolecules.

Journal Article↗

PubMed1999

Tyrosine 265 of alanine racemase serves as a base abstracting alpha-hydrogen from L-alanine: the counterpart residue to lysine 39 specific to D-alanine.

Alanine racemase of Bacillus stearothermophilus has been proposed to catalyze alanine racemization by means of two catalytic bases: lysine 39 (K39) abstracting specifically the alpha-hydrogen of D-alanine and tyrosine 265 (Y265) playing the corresponding role for the antipode L-alanine. The role of K39 as indicated has already been verified [Watanabe, A., Kurokawa, Y., Yoshimura, T., Kurihara, T., Soda, K., and Esaki, N. (1999) J. Biol. Chem. 274, 4189-4194]. We here present evidence for the functioning of Y265 as the base catalyst specific to L-alanine. The Y265-->Ala mutant enzyme (Y265A), like Y265S and Y265F, was a poor catalyst for alanine racemization. However, Y265A and Y265S catalyzed transamination with D-alanine much more rapidly than the wild-type enzyme, and the bound coenzyme, pyridoxal 5'-phosphate (PLP), was converted to pyridoxamine 5'-phosphate (PMP). The rate of transamination catalyzed by Y265F was about 9% of that by the wild-type enzyme. However, Y265A, Y265S, and Y265F were similar in that L-alanine was inert as a substrate in transamination. The apo-form of the wild-type enzyme catalyzes the abstraction of tritium non-specifically from both (4'S)- and (4'R)-[4'-(3)H]PMP in the presence of pyruvate. In contrast, apo-Y265A abstracts tritium virtually from only the R-isomer. This indicates that the side-chain of Y265 abstracts the alpha-hydrogen of L-alanine and transfers it supra-facially to the pro-S position at C-4' of PMP. Y265 is the counterpart residue to K39 that transfers the alpha-hydrogen of D-alanine to the pro-R position of PMP.

Alanine↗

PubMed1998

Crystal structure of recombinant soybean beta-amylase complexed with beta-cyclodextrin.

In order to study the interaction of soybean beta-amylase with substrate, we solved the crystal structure of beta-cyclodextrin-enzyme complex and compared it with that of alpha-cyclodextrin-enzyme complex. The enzyme was expressed in Escherichia coli at a high level as a soluble and catalytically active protein. The purified recombinant enzyme had properties nearly identical to those of native soybean beta-amylase and formed the same crystals as the native enzyme. The crystal structure of recombinant enzyme complexed with beta-cyclodextrin was refined at 2. 07-A resolution with a final crystallographic R value of 15.8% (Rfree = 21.1%). The root mean square deviation in the position of C-alpha atoms between this recombinant enzyme and the native enzyme was 0.22 A. These results indicate that the expression system established here is suitable for studying structure-function relationships of beta-amylase. The conformation of the bound beta-cyclodextrin takes an ellipsoid shape in contrast to the circular shape of the bound alpha-cyclodextrin. The cyclodextrins shared mainly two glucose binding sites, 3 and 4. The glucose residue 4 was slightly shifted from the maltose binding site. This suggests that the binding site of the cyclodextrins is important for its holding of a cleaved substrate, which enables the multiple attack mechanism of beta-amylase.

Binding Sites↗

PubMed1996

Crystallization and preliminary X-ray diffraction studies of N-acyl-D-glucosamine 2-epimerase from porcine kidney.

N-Acyl-D-glucosamine 2-epimerase from porcine kidney, which was cloned and expressed in Escherichia coli, was crystallized by the vapor-diffusion method, using polyethylene glycol and ammonium acetate as precipitants. The crystals were resistant to X-ray radiation damage and diffracted to more than 2.0 A resolution. The diffraction pattern indicated that the crystals belong to the orthorhombic system, space group P2(1)2(1)2(1), with unit-cell dimensions of a = 78.1, b = 97.2, and c = 100.7 A. It is supposed that the asymmetric unit consists of two N-acyl-D-glucosamine 2-epimerase molecules. Collection of data on the native crystals indicated that they are suitable for X-ray structural analysis.

Animals↗

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↗

PubMed1995

Crystal structure of diferric hen ovotransferrin at 2.4 A resolution.

The three-dimensional structure of diferric hen ovotransferrin has been determined by X-ray crystallography at 2.4 A resolution. The structure was solved by molecular replacement, using the coordinates of diferric human lactoferrin as a search model. Several rounds of simulated annealing and restrained least-squares refinement have resulted in a model structure with an R-factor of 0.171 for the data between 11.0 and 2.4 A resolution. The model comprises 5284 protein atoms (residues 5 to 686), 2 Fe3+, 2 CO3(2)- and 132 water molecules. The overall structure of ovotransferrin is similar to those of human lactoferrin and rabbit serum transferrin, being folded into two homologous lobes, each containing two dissimilar domains with one Fe3+ and one CO3(2)- bound at a specific site in each interdomain cleft. However, the relative orientation of the two lobes, which may be related to the class specificity of transferrins to receptors, is different from either human lactoferrin or rabbit serum transferrin. The angle of the relative orientation in ovotransferrin is increased by 6.8 degrees and 15.7 degrees as compared with to those in rabbit serum transferrin and human lactoferrin, respectively. Interdomain Lys209-Lys301 and Gln541-Lys638 interactions are found near the metal binding site of each lobe. The interlobe interactions and their role in the stabilization of iron binding are discussed.

Animals↗

PubMed1995

Molecular characterization of monodehydroascorbate radical reductase from cucumber highly expressed in Escherichia coli.

Monodehydroascorbate radical (MDA) reductase, an FAD-enzyme, is the first enzyme to be identified whose substrate is an organic radical and catalyzes the reduction of MDA to ascorbate by NAD(P)H. Its cDNA has been cloned from cucumber seedlings (Sano, S., and Asada, K. (1994) Plant Cell Physiol. 35, 425-437), and a plasmid was constructed in the present study that allowed a high level expression in Escherichia coli of the cDNA-encoding MDA reductase using the T7 RNA polymerase expression system. The recombinant MDA reductase was purified to a crystalline state, with a yield of over 20 mg/liter of culture, and it exhibited spectroscopic properties of the FAD similar to those of the enzyme purified from cucumber fruits during redox reactions with NADH and MDA. The red semiquinone of the FAD of MDA reductase was generated by photoreduction. p-Chloromercuribenzoate inhibited the reduction of the enzyme-FAD by NADH, and dicumarol suppressed electron transfer from the reduced enzyme to MDA. The specificity of electron acceptors of the recombinant enzyme appeared to be similar to that of MDA reductase, even though the amino acid sequence encoded by the cDNA was somewhat different from that of the enzyme purified from cucumber fruits. The Km values for NADH and NADPH of the recombinant enzyme indicated a high affinity of the enzyme for NADH. The reaction catalyzed by the enzyme did not exhibit saturation kinetics with MDA up to 3 microM. A second order rate constant for the reduction of the enzyme-FAD with NADH was 1.25 x 10(8) M-1 s-1, as determined by a stopped-flow method, and its value decreased with increases in ionic strength, an indication of the enhanced electrostatic guidance of NADH to the enzyme-FAD.

Cloning, Molecular↗

PubMed1995

The role of SH and S-S groups in Bacillus cereus beta-amylase.

The properties of sulfhydryl (SH) and disulfide (S-S) groups in Bacillus cereus BQ10-S1 Spo III beta-amylase have been investigated to clarify their roles in the enzyme action. Two out of three cysteine residues in B. cereus beta-amylase were found to form an S-S bond, which was found to be located between Cys91 and Cys99 by the analysis of an S-S containing peptide. The replacement of the soybean beta-amylase model around L3 loop 1 revealed that the S-S bond is located at the root of this flexible loop that moves between open and closed forms during catalysis. The analysis of fluorescence labeled peptides revealed that the remaining free SH group was Cys331. Modification of Cys331 with N-ethylmaleimide or p-chloromercuribenzoic acid (PCMB) caused inactivation of the enzyme. The rate constants for the reactions were consistent with those of Cys343 in soybean enzyme. The binding affinity of the PCMB-modified enzyme to maltose was also decreased. These results indicate that the modification of Cys331, which exists as a free SH group in B. cereus beta-amylase caused inactivation by a similar mechanism to that in the case of Cys343 in soybean beta-amylase as assumed from the sequence homology. This cysteine residue has a common role in beta-amylases irrespective their origin.

Bacillus cereus↗

PubMed1994

Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis.

The crystal structures of catalytically competent soybean beta-amylase, unliganded and bathed with small substrates (beta-maltose, maltal), were determined at 1.9-2.2-A resolution. Two molecules of beta-maltose substrate bind to the protein in tandem, with some maltotetraose enzymic condensation product sharing the same binding sites. The beta-amylase soaked with maltal shows a similar arrangement of two bound molecules of 2-deoxymaltose, the enzymic hydration product. In each case the nonreducing ends of the saccharide ligands are oriented toward the base of the protein's active site pocket. The catalytic center, located between the bound disaccharides and found deeper in the pocket than where the inhibitor alpha-cyclodextrin binds, is characterized by the presence of oppositely disposed carboxyl groups of two conserved glutamic acid residues. The OE2 carboxyl of Glu 186 is below the plane of the penultimate glucose residue (Glc 2) of bound maltotetraose, 2.6 A from the oxygen atom of that ligand's penultimate alpha-1,4-glucosidic linkage. The OE2 carboxyl of Glu 380 lies above the plane of Glc 2, 2.8 A from the O-1 atom of the more deeply bound beta-maltose. Saccharide binding does not alter the spatial coordinates of these two carboxyl groups or the overall conformation of the 57-kDa protein. However, the saccharide complexes of the active enzyme are associated with a significant (10 A) local conformational change in a peptide segment of a loop (L3) that borders the active site pocket.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1994

Crystallization and preliminary X-ray analysis of copper amine oxidase from Escherichia coli K-12.

Copper-containing monoamine oxidase (MAO) from Escherichia coli was overproduced in the periplasmic space by expression of the cloned gene. The purified MAO has been crystallized by means of the hanging drop technique using sodium citrate as a precipitant. The crystals belong to the orthorhombic system, space group P2(1)2(1)2(1), with unit cell dimensions of a = 136.1 A, b = 168.4 A and c = 81.6 A. The asymmetric unit contains one molecule of MAO, with a crystal volume per protein mass (Vm) of 2.88 A3/Da and a solvent content of 58% by volume. The crystals diffract X-rays to a resolution limit of at least 2.7 A and are resistant to X-ray radiation damage. They appear to be suitable for X-ray structure analysis.

Amine Oxidase (Copper-Containing)↗

PubMed1994

Crucial role of intralobe peptide-peptide interactions in the uptake and release of iron by ovotransferrin.

The mechanism for reversible iron binding in the N-terminal lobe of ovotransferrin was investigated by a protein fragmentation approach. The iron-saturated N-terminal half-molecule of ovotransferrin was proteolyzed into large 30-kDa (1-279) and small 6-kDa (280-332) fragments by a single cleavage with Achromobacter protease I, producing a stable nicked form. For the separation of the two fragments, denaturing conditions were required. The isolated large fragment contained all four iron-coordinating ligands and the anion-binding ligand, and according to spectroscopic titration analysis, it showed iron binding capacity. The iron-bound large fragment, however, showed a blue-shifted visible absorption spectrum and a much decreased iron stability compared with those of the intact half-molecule. Analyses by ion-exchange chromatography revealed that the large fragment reassociates with the small fragment. In order for reassociation to occur, iron must be bound to the large fragment; upon reassociation, the large fragment regained its stable iron binding capacity as well as a visible absorption spectrum almost indistinguishable from those of the intact half-molecule. These data are consistent with a two-step sequential pathway for reversible iron binding in the N-terminal lobe of ovotransferrin that includes an initial iron binding intermediate having a perturbed metal environment and its transformation into the stable iron-bound holoform by peptide-peptide interactions between the large coordinating and small noncoordinating segments.

Alcaligenes↗

PubMed1994

Two sulfhydryl groups near the active site of soybean beta-amylase.

The less reactive SH groups of soybean beta-amylase, SH4, SH5, and SH6, were modified with p-chloromercuribenzoic acid or N-ethylmaleimide, after the reactive SH groups, SH1, SH2, and SH3, were blocked with 5,5'-dithiobis-(2-nitrobenzoic acid) and cyanide. The enzyme activity decreased, accompanied by the modification of SH4. alpha-Cyclodextrin protected SH4 from the modification more effectively than maltose. The SH4-modified enzyme still bound to glucose, maltose, and alpha-cyclodextrin. SH4 was concerned with neither the catalysis nor substrate binding but its large substituent affected the substrate binding site. The sequencing of the 5-(iodoacetoamidoethyl)-aminoaphthalene-1-sulfonate-labeled peptides showed that SH4, SH5, and SH6 are Cys343, Cys82, and Cys208, respectively. Comparison of the primary structure of beta-amylases also showed that the sequence around SH4 (Cys343), as well as SH2 (Cys95), is strongly conserved between higher plant and bacterial beta-amylases. These results agree with the structure model deduced from X-ray crystallography of soybean beta-amylase.

Amino Acid Sequence↗

PubMed1994

Crystallization and preliminary X-ray analysis of soybean proglycinins modified by protein engineering.

Glycinin is one of the most abundant storage proteins in soybean seeds. We earlier reported the preparation of proglycinins modified by protein engineering to improve food functions. Crystals of the modified proglycinins (delta I, delta V8, IV + 4Met, V + 4Met, Gly12, and Ser88) expressed in Escherichia coli were grown, each under different suitable crystallization conditions. The crystals of delta I, V + 4Met, Gly12, and Ser88 diffracted X-rays sufficiently for crystallographic analysis. delta I, Gly12, and Ser88 crystals were tetragonal, space group P4(1) or P4(3), and with unit cell dimensions a = b = 114.3-115.9 A and c = 145.1-146.1 A. V + 4Met crystals were monoclinic, space group P2, and with unit cell dimensions a = 118.7 A, b = 78.1 A, c = 109.9 A, and beta = 119 degrees. The number of promoters per asymmetric unit of all of the crystals of these four modified proglycinins was about 3. This value is consistent with proglycinins being trimers. These data indicated that most of the modified proglycinin crystals examined here could be studied by X-ray crystallography to elucidate the relationships between the structure and the functional properties of glycinin at molecular level.

Amino Acid Sequence↗

PubMed1993

Structural evidence for a pH-sensitive dilysine trigger in the hen ovotransferrin N-lobe: implications for transferrin iron release.

Members of the transferrin family of proteins are involved in Fe3+ transport (serum transferrins) and are also believed to possess antimicrobial activity (ovotransferrins and lactoferrins). The structure of the monoferric N-terminal half-molecule of hen ovotransferrin, reported here at 2.3-A resolution, reveals an unusual interdomain interaction formed between the side-chain NZ atoms of Lys 209 and Lys 301, which are 2.3 A apart. This strong interaction appears to be an example of a low-barrier hydrogen bond between the two lysine NZ atoms, both of which are also involved in a hydrogen-bonding interaction with the aromatic ring of a tyrosine residue. Crystals of the protein were grown at pH 5.9, which is well below the usual pKa approximately 10 for a lysine side chain. We suggest that the pKa of either one or both of these residues lies below the pH of the structure determination and is, therefore, not positively charged. This finding may serve to explain, on a molecular basis, the pH dependence of transferrin Fe3+ release. We propose that uptake of the Fe(3+)-transferrin complex into an acidic endosome (viz., pH approximately 5.0) via receptor-mediated endocytosis will result in the protonation of both lysine residues. The close proximity of the two resulting positive charges, and their location on opposite domains of the N-lobe, might well be the driving force that opens the two domains of the protein, exposing the Fe3+ ion and facilitating its release.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗