Satoshi Kaneko

Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86

The family 10 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn10A) consists of a GH10 catalytic domain, which is joined by a Gly/Pro-rich linker to a family 13 carbohydrate-binding module (CBM13) that interacts with xylan. To understand how GH10 xylanases and CBM13 recognize decorated xylans, the crystal structure of SoXyn10A was determined in complex with α-l-arabinofuranosyl- and 4-O-methyl-α-d-glucuronosyl-xylooligosaccharides. The bound sugars were observed in the subsites of the catalytic cleft and also in subdomains α and γ of CBM13. The data reveal that the binding mode of the oligosaccharides in the active site of the catalytic domain is entirely consistent with the substrate specificity and, in conjunction with the accompanying paper (Pell, G., Taylor, E. J., Gloster, T. M., Turkenburg, J. P., Fontes, C. M. G. A., Ferreira, L. M. A., Nagy, T., Clark, S. J., Davies, G. J., and Gilbert, H. J. (2004) J. Biol. Chem. 279, 9597-9605), demonstrate that the accommodation of the side chains in decorated xylans is conserved in GH10 xylanases of SoXyn10A against arabinoglucuronoxylan. CBM13 was shown to bind xylose or xylooligosaccharides reversibly by using nonsymmetric sugars as the ligands. The independent multiple sites in CBM13 may increase the probability of substrate binding.

A boron-rhamnogalacturonan-II complex from bamboo shoot cell walls

Abstract A boron-polysaccharide complex was isolated from a Driselase digest of bamboo ( Phyllostachys edulis ) shoot cell walls by successive DEAE Sepharose FF, Bio-Gel P-10 and Mono Q HR 5/5 chromatography. The complex contained 0.15% boron (w/w). The glycosyl residue and linkage composition analyses of the polysaccharide moiety of the complex identified the polysaccharide as a rhamnogalacturonan-II (RG-II), a structurally complex pectic polysaccharide present in the primary cell walls of all higher plants. 11 B NMR spectroscopy showed that boron was present as a tetrahedral borate-diol diester. Removal of boron from the complex decreased the M r by half without any loss of glycosyl residues, suggesting that boron cross-links two RG-II molecules. The boron-RG-II complex from bamboo (a monocot) shoot cell walls has almost the same structure as that of sugar beet (a dicot) cell walls. The results demonstrate that the structure of boron-RG-II complex is very similar in dicots and monocots.

Synthesis of regioisomeric methyl α-L-arabinofuranobiosides

Abstract The three regioisomers of methyl α- l - arabinofuranobioside , namely methyl O-α- l - arabinofuranosyl -(1 → 3)-α- l - arabinofuranoside , methyl O-α- l - arabinofuranosyl -(1 → 3)-α- l - arabinofuranoside , and methyl O-α- l - arabinofuranosyl -(1 → 5)-α- l - arabinofuranoside , were synthesized for use as substrates in studies of the specificity of α- l - arabinofuranosidase . The regiospecifically protected precursors, namely methyl 3,5- di -O- benzoyl -α- l - arabinofuranoside,methyl 2,5-di -O- benzyl -α- l - arabinofuranoside , and methyl 2,3- di -O- benzoyl -α- l - arabinofuranoside , were prepared from 2,3,5- tri -O- benzoyl -α- l - arabinofuranosyl chloride ( 4 ) and methyl 5-O- trityl -α- l - arabinofuranoside , respectively, and glycosylated with 4 in the presence of silver trifluoromethanesulfonate and s -collidine. 1 H and 13 C NMR data for all compounds are presented.

Oligosaccharides generated by partial hydrolysis of the borate-rhamnogalacturonan II complex from sugar beet

The borate-rhamnogalacturonan II complex (B-RG-II), isolated from sugar beet (Beta vulgaris), was partially acid-hydrolyzed. The oligosaccharides generated were characterized by glycosyl-composition and glycosyl-linkage analyses, ES-mass, and NMR spectroscopy. Two disaccharides, alpha-L-Rhap-(1-->5)-D-Kdo and alpha-L-Araf-(1-->5)-Dha, an aceric acid-containing oligosaccharide, and a 2-O-Me-Xyl-containing oligosaccharide, in addition to partially methyl-esterified alpha-(1-->4)-oligogalacturonides were characterized. The data provide additional evidence that B-RG-II isolated from different plant species have identical structures.

Structure and Function of a Family 10 β-Xylanase Chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex

The catalytic domain of xylanases belonging to glycoside hydrolase family 10 (GH10) can be divided into 22 modules (M1 to M22; Sato, Y., Niimura, Y., Yura, K., and Go, M. (1999) Gene (Amst.) 238, 93-101). Inspection of the crystal structure of a GH10 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn10A) revealed that the catalytic domain of GH10 xylanases can be dissected into two parts, an N-terminal larger region and C-terminal smaller region, by the substrate binding cleft, corresponding to the module border between M14 and M15. It has been suggested that the topology of the substrate binding clefts of GH10 xylanases are not conserved (Charnock, S. J., Spurway, T. D., Xie, H., Beylot, M. H., Virden, R., Warren, R. A. J., Hazlewood, G. P., and Gilbert, H. J. (1998) J. Biol. Chem. 273, 32187-32199). To facilitate a greater understanding of the structure-function relationship of the substrate binding cleft of GH10 xylanases, a chimeric xylanase between SoXyn10A and Xyn10A from Cellulomonas fimi (CfXyn10A) was constructed, and the topology of the hybrid substrate binding cleft established. At the three-dimensional level, SoXyn10A and CfXyn10A appear to possess 5 subsites, with the amino acid residues comprising subsites -3 to +1 being well conserved, although the +2 subsites are quite different. Biochemical analyses of the chimeric enzyme along with SoXyn10A and CfXyn10A indicated that differences in the structure of subsite +2 influence bond cleavage frequencies and the catalytic efficiency of xylooligosaccharide hydrolysis. The hybrid enzyme constructed in this study displays fascinating biochemistry, with an interesting combination of properties from the parent enzymes, resulting in a low production of xylose.

Substrate specificity of α-L-arabinofuranosidase from Streptomyces diastatochromogenes 065 toward arabinose-containing oligosaccharides

Abstract α- l -Arabinofuranosidase from Streptomyces diastatochromogenes 065 released only the terminal arabinose of arabinoxylo-oligosaccharides. The enzyme hydrolyzed methyl arabinofuranobiosides to arabinose and methyl arabinofuranoside in the order of (1→2)>(1→3)>(1→5)-linkages. The enzyme preferentially hydrolyzed the (1→3)-linkage over the (1→5)-linkage of methyl arabinofuranotrioside.

Geometric effect and gauge field in nonequilibrium quantum thermostatistics

The concept of work is studied in quantum thermostatistics of a system surrounded by an environment and driven by a slowly varying external force. It is found that there emerges the gauge theoretical structure in a process with a nonequilibrium quasi-stationary state, the field of which is referred to here as the work gauge field. The thermodynamic work as the flux of the work gauge field is considered for a cyclic process in the space of the external-force parameters. As an example, the system of a spin-1/2 interacting with an external magnetic field is analyzed.