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M Kakudo

Publications and source records attributed to M Kakudo.

At least 19 recordsLinked to original sources
PubMed1987

Single crystals of hydrogenase from Desulfovibrio vulgaris Miyazaki F.

The hydrogenase solubilized from the particulate fraction from Desulfovibrio vulgaris Miyazaki F (IAM 12604) has been crystallized. Although the solubilized hydrogenase purified by the previous method (Yagi, T., Kimura, K., Daidoji, H., Sakai, F., Tamura, S., and Inokuchi, H. (1976) J. Biochem. (Tokyo) 79,661-671) revealed a single band upon disc electrophoresis, it could not be crystallized. The apparently homogeneous hydrogenase has been separated into three components of similar molecular weights by high performance liquid chromatography on DEAE-Toyopearl. Each hydrogenase component was successfully crystallized by means of the vapor diffusion method with polyethylene glycol or 2-methyl-2,4-pentanediol as a precipitating agent. Seeding procedure is necessary to grow an x-ray grade crystal. Preliminary x-ray experiments reveal that crystals grown from one component are in space group of P2(1)2(1)2(1) with a = 102.1(1), b = 126.8 (3), and c = 66.9(1) A. The unit cell volume of 8.66 X 10(5) A3 suggests that it contains one molecule/asymmetric unit (Vm = 2.43). The crystals grown from another component are in the same space group with a = 99.6(1), b = 126.8(3), c = 66.9(1) A, and the unit cell volume is 8.45 X 10(5) A3 (Vm = 2.37). The crystals diffract more than 2.5 A and are suitable for complete crystal analysis. Up to 4 A resolution native data have been collected on a diffractometer.

Chromatography, High Pressure Liquid↗
PubMed1984

Refined structure of cytochrome c3 at 1.8 A resolution.

The structure of cytochrome c3 from the sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki has been successfully refined at 1.8 A resolution. The crystallographic R factor is 0.176 for 9907 significant reflections. The isotropic temperature factors of individual atoms were refined and a total of 47 water molecules located on the difference map were incorporated in the refinement. The four heme groups are closely packed, with adjacent pairs of heme planes being nearly perpendicular to each other. The fifth and the sixth ligands of the heme iron atoms are histidine residues with N epsilon 2-Fe distances ranging from 1.88 A to 2.12 A. The histidine co-ordination to the heme iron is different for each heme group. The heme groups are all highly exposed to solvent, although the actual regions exposed differ among the hemes. The four heme groups are located in different environments, and the heme planes are deformed from planarity. The differences in the heme structures and their environments indicate that the four heme groups are non-equivalent. The chemical as well as the physical properties of cytochrome c3 should be interpreted in terms of the structural non-equivalence of the heme groups. The characteristic secondary structural non-equivalence of the heme groups. The characteristic secondary structures of the polypeptide chain of this molecule are three short alpha-helices, two short beta-strands and ten reverse turns.

Binding Sites↗
PubMed1984

Structure and possible catalytic residues of Taka-amylase A.

A complete molecular model of Taka-amylase A consisting of 478 amino acid residues was built with the aid of amino acid sequence data. Some typical structural features of the molecule are described. A model fitting of an amylose chain in the catalytic site of the enzyme showed a possible productive binding mode between substrate and enzyme. On the basis of the difference Fourier analysis and the model fitting study, glutamic acid (Glu230) and aspartic acid (Asp297), which are located at the bottom of the cleft, were concluded to be the catalytic residues, serving as the general acid and base, respectively.

Binding Sites↗
PubMed1983

Structure of rice ferricytochrome c at 2.0 A resolution.

The crystal structure of ferricytochrome c from rice embryos has been solved by X-ray diffraction to a resolution of 2.0 A, applying a single isomorphous replacement method with anomalous scattering effects. The initial molecular model was built on a graphics display system and was refined by the Hendrickson and Konnert method. The R factor was reduced to 0.25. Rice cytochrome c consists of III amino acid residues. In comparison with animal cytochromes c, the peptide chain extends for eight residues at the N-terminal end, which is characteristic for plant cytochromes c. These additional residues display a collagen-like conformation and an irregular reverse turn, and are located around the C-terminal alpha-helix on the surface or the rear side of the molecule. Two hydrogen bonds between the carbonyl oxygen of the N-terminal acetyl group and O eta of Tyr65, and between the peptide carbonyl oxygen of Pro-1 and O epsilon 1 of Gln89, are involved in holding these eight residues on the molecular surface, where Tyr65 and Gln89 are invariant in plant cytochromes c. Except for the extra eight residues, the main-chain conformations of both rice and tuna cytochromes c are essentially identical, though small local conformational differences are found at residues 24, 25, 56 and 57.

Cytochrome c Group↗
PubMed1981

The structure of cytochrome c3 from Desulfovibrio vulgaris Miyazaki at 2.5 A resolution.

The structure of tetraheme cytochrome c3 isolated from Desulfovibrio vulgaris Miyazaki has been determined at 2.5 A resolution by an X-ray diffraction method. Protein phases were computed by the multiple isomorphous replacement method using the native and four heavy atom derivatives, anomalous scattering measurements of the latter being considered. The mean figure of merit was 0.77. Four heme groups are exposed on the surface of the molecule. There are some short helical segments in the polypeptide chain, and hair-pin turns are often observed at glycine and alanine residues.

Amino Acid Sequence↗
PubMed1981

On cytochrome c3 folding.

The structure of cytochrome c3 from Desulfovibrio vulgaris Miyazaki (DvM) is considered in detail by scrutinizing main chain folding together with the structure of the protein from D. desulfuricans Norway (DdN). The relative arrangement of the four heme groups in this molecule is similar to that of DdN and the disposition of alpha-carbon atoms of cysteine and histidine residues binding to heme groups is also similar. Structural differences between the two proteins occur in the shape of some specific loops of the chain on the molecular surface. As a result of a careful comparison of structures and sequences in both cytochromes c3, the reported sequence alignment of the cytochrome c3 family has been revised. Our new proposal of a sequence alignment based on the three-dimensional structures contains 24 evolutionarily conservative residues. All these conservative residues may play an important role in the folding pattern of cytochromes c3.

Amino Acid Sequence↗
PubMed1981

X-ray analysis of a [2Fe-2S] ferrodoxin from Spirulina platensis. Main chain fold and location of side chains at 2.5 A resolution.

A [2Fe-2S] ferrodoxin from Spirulina platensis crystallized in space group C2221 with cell dimensions of a = 62.32, b = 28.51, c = 108.08 A, and alpha = beta = gamma = 90.0 degrees. X-ray structure analysis of the protein was carried out at 2.5 A resolution by the single isomorphous replacement method coupled with the derivative and the native anomalous dispersion methods. Phase angles of 2182 independent reflections were determined and their average figure of merit was 0.58. Each of 98 residues was superposed on the electron density sections enlarged to 2 cm/l A with a half-mirror device (Richards box). About 25% of the total residues form beta-structure and 10% fold in a tow-turn alpha-helix. A beta-barrel-like structure was found in the main chain fold. A polypeptide segment from residues 41 to 49 forms a loop structure outside the barrel. Two iron atoms of the [2Fe-2S] cluster are coordinated by three cysteines in the loop and by Cys-79. Hydrogen bonds of NH....S and OH....S stabilize the loop conformation. Most side chains are reasonably oriented in the molecule. The internal volume of the barrel is occupied by aliphatic nonpolar residues. All the charged groups are accessible to solvent molecules.

Binding Sites↗
PubMed1980

Molecular structure of taka-amylase A. I. Backbone chain folding at 3 A resolution.

The crystal structure of Taka-amylase A was studied by an X-ray diffraction method at 3 A resolution. A total of 452 amino acid residues were found from the electron density map at the present stage. The four disulfide bonds and the branched carbohydrate were also located on the map. The difference electron density map of the maltotriose-soaked crystal showed that a maltose unit was bound in the active center left. The binding of iodine atoms to the enzyme was also studied.

Amylases↗
PubMed1979

Structure of Streptomyces erythraeus lysozyme at 6 A resolution.

A 6 A resolution electron density map has been calculated for a bacterial lysozyme produced by Streptomyces erythraeus. This lysozyme differs from the vertebrate lysozyme in its size, amino acid composition, and specificity. The structure was determined by the method of isomorphous replacement. Three heavy atom derivatives were obtained by soaking crystals of the lysozyme in HgCl2, K2PtCl4, and UO2(NO3)26H2O. The resulting electron density map clearly shows the molecular boundary. The molecule is ellipsoidal in shape with average dimensions 50 A X 35 A X 35 A. High resolution analysis and sequence analysis of the molecule are in progress.

Mercury↗
PubMed1979

Low resolution crystal structures of Taka-amylase A and its complexes with inhibitors.

The molecular structure of Taka-amylase A, an alpha-amylase from Aspergillus oryzae, has been studied at 6 A resolution by X-ray diffraction analysis. The electron density map showed a non-crystallographic three-fold screw arrangement of the molecules in the crystal. The molecule is an ellipsoid with approximate dimensions of 80 x 45 x 35 A and contains a hollow which may correspond to the active center. The inhibitor molecules bind to Taka-amylase A at four different sites, one of which is located in the hollow of the enzyme. The probable position of a thiol group is discussed in connection with heavy atom binding.

Amylases↗
PubMed1979

Low resolution crystal structure of lipase from Geotrichum candidum (ATCC34614).

Lipase from Geotrichum candidum (ATCC34614) is a glycerol ester hydrolase which has a molecular weight of 55,000 with about 7% carbohydrate, displaying a high affinity for triolein. The enzyme was crystallized from more than 2% protein solution without using any salt or organic solvent. The crystals were cross-linked by soaking in 0.37% glutaraldehyde solution (0.1 M acetate buffer solution, pH 5.6). The structure was determined by X-ray diffraction using the isomorphous replacement technique. Two heavy-atom derivatives [K2PtCl4 and UO2(CH3COO)2] were obtained by the soaking method. The electron density map calculated at 5 A resolution clearly showed the molecular boundary. A balsa wood model was made on the basis of the 6 A electron density map. The molecular has an ellipsoidal shape with dimensions of 70 A X 50 A X 50 A. Several columns of density corresponding to alpha-helix and a few clefts were found in the molecule. The active site is presumably located in the vicinity of one of the Pt sites in the Pt-derivative crystal, judging from the inactivation of the enzyme by K2PtCl4.

Cross-Linking Reagents↗
PubMed1979

Structure of bonito heart ferricytochrome c and some remarks on molecular interaction in its crystalline state.

The structure analysis of bonito heart ferricytochrome c was carried out at 2.8 A resolution by X-ray diffraction. The overall features of the molecule are virtually identical with those of bonito ferrocytochromes c and other cytochromes c. In the present work, the modes of molecular packing among cytochromes c were also compared by means of intermolecular distance maps. Some differences in the structures of ferro- and ferricytochrome c may exist on the surface of the molecules.

Amino Acids↗
PubMed1979

Crystallographic data for cytochrome c3 from two strains of Desulfovibrio vulgaris, Miyazaki.

Two crystalline forms of cytochrome c3 isolated from two strains of Desulfovibrio vulgaris, Miyazaki, tentatively designated as D. vulgaris, Miyazki F and D. vulgaris, Miyazaki K, have been found. Both belong to the orthorhombic system, space group P2(1)2(1)2(1), but have different cell dimensions; a=54.1, b=68.9 and c=35.0 A for D. vulgaris, Miyazaki F, and a=43.5, b=41.2, and c=62.9 A for D. vulgaris, Miyazaki K. The asymmetric unit of each crystal contains one molecule of cytochrome c3.

Cytochromes↗
PubMed1978

Crystallization and a 5 A X-ray diffraction study of Aphanothece sacrum ferredoxin.

A chloroplast-type ferredoxin containing two non-heme iron and two labile sulfur atoms per molecule was prepared from Aphanothece sacrum. Crystals were obtained by dialysis against 75% saturated a-monium sulfate solution, and belong to the tetragonal system with cell dimensions a = b = 92.2 A and c = 47.6 A, containing four molecules in an asymmetric unit. The electron density map at 5 A resolution was calculated by using the best phase angles determined by the single isomorphous replacement method coupled with the anomalous dispersion effect. An anomalous dispersion difference Fourier map for the native crystal clearly showed four humps corresponding to the iron atoms in an asymmetric unit. The electron densis surface.

Binding Sites↗
PubMed1978

X-ray analysis of ferredoxin from Spirulina platensis. II. Chelate structure of active center.

A chloroplast-type ferredoxin from Spirulina platenis crystallized in an orthorhombic system, space group C2221, with cell dimensions a=62.32, b=28.51, and c=108.08 A. The electron density map at 2.8 A resolution was prepared by using the best phase angles determined by the single isomorphous replacement method coupled with the anomalous dispersion method. The chelating structure of the acitve center was revealed as follows. Of the six cysteinyl residues in the molecule, Cys 41, Cys 4k, Cys 49, and Cys 79 are involved in the active center. Cys 41 and Cys 46 are coordinated to one iron atom, and Cys 49 and Cys 79 to the other iron atom. Only one of these cysteinyl residues, Cys 79, is comparatively apart from the other three in the amino acids sequence of the molecule, as found in the case of bacterial ferredoxin. It appears that the NH....S hydrogen bonds are around the active center, as in other non-heme iron sulfur proteins.

Binding Sites↗