Biomedical subjects

Yuko Hidaka

Publications and source records attributed to Yuko Hidaka.

4 recordsLinked to original sources

PubMed2005

alpha-Glucosidase from a strain of deep-sea Geobacillus: a potential enzyme for the biosynthesis of complex carbohydrates.

An alpha-glucosidase from Geobacillus sp. strain HTA-462, one of the deepest sea bacteria isolated from the sediment of the Mariana Trench, was purified to homogeneity and estimated to be a 65-kDa protein by SDS-PAGE. At low ion strength, the enzyme exists in the homodimeric form (130 kDa). It is a thermo- and alkaline-stable enzyme with a half-life of 13.4 h and a maximum hydrolytic activity at 60 degrees C and pH 9.0 in 15 mM glycine-NaOH buffer. The enzyme exclusively hydrolyzed alpha-1,4-glycosidic linkages of oligosaccharides in an exo-type manner. The enzyme had an overwhelming transglycosylation activity and glycosylated various non-sugar molecules when maltose was used as a sugar donor. It converted maltose to isomaltose. The gene encoding the enzyme was cloned and sequenced. The recombinant enzyme could be extracellularly overproduced by Bacillus subtilis harboring its gene and preserved the primary properties of the native enzyme. Site-directed mutagenesis experiments showed that Asp98 is essential for the enzyme activity in addition to Asp199, Asp326, and Glu256.

Amino Acid Sequence↗

PubMed2005

Identification and characterization of coding single-nucleotide polymorphisms within human protocadherin-alpha and -beta gene clusters.

The human protocadherin (Pcdh) gene clusters are located on chromosome 5q31. Single-nucleotide polymorphisms (SNPs) were detected in the Pcdh-alpha and -beta variable exons, and in the Pcdh-alpha constant exon, in samples from 104 individuals. Among coding SNPs (cSNPs), nonsynonymous (amino acid exchange) SNPs were 2.2 times more common than synonymous (silent) changes in the Pcdh-alpha variable exons, but only 1.2 times more common in the Pcdh-beta variable exons. The nonsynonymous SNPs were high in the ectodomain (EC) 1 encoding region of Pcdh-alpha but not of Pcdh-beta. One 48-kb region of extensive linkage disequilibrium (LD) is reported that has two haplotypes extending from the alpha1 to alpha7 genes in the Pcdh-alpha cluster. Here we identified 15 amino acid exchanges in these two major haplotypes; therefore, the two haplotypes encode different sets of Pcdh-alpha proteins in the brain. The distribution of cSNPs was different for each EC region of Pcdh-alpha or -beta. The frequency of cSNPs was negatively correlated with the paralogous sequence diversity. These results suggested that gene conversion events in homologous regions of the Pcdh-alpha and Pcdh-beta clusters generated the cSNPs. Within the cSNPs, gene conversions were found in Pcdh-alpha4 in the major haplotype, and in Pcdh-beta9. These gene conversions were caused by the unequal crossing-over of homologous sequence regions. Thus, nonsynonymous variations in the Pcdh-alpha and -beta genes are possible contributors to the variations in human brain function.

Alleles↗

PubMed2004

Crystallization and preliminary X-ray study of isomaltodextranase from Arthrobacter globiformis.

A recombinant isomaltodextranase (1,6-alpha-D-glucan isomaltohydrolase; EC 3.2.1.94) from an Arthrobacter sp. that hydrolyzes dextrans to generate isomaltose was purified and crystallized using the sitting-drop vapour-diffusion method at 293 K. X-ray diffraction data were collected to 1.8 A. The crystals belong to space group C2, with unit-cell parameters a = 199.1, b = 62.7, c = 57.4, beta = 101.4 degrees. Analysis of the Patterson self-rotation function suggests that the crystal contains one protein molecule in the asymmetric unit.

Arthrobacter↗

PubMed2004

Crystallization and preliminary X-ray study of gamma-type cyclodextrin glycosyltransferase from Bacillus clarkii.

A gamma-cyclodextrin glycosyltransferase (EC 2.4.1.19) from Bacillus clarkii was crystallized using the hanging-drop vapour-diffusion method at 293 K. X-ray diffraction data were collected to 2.2 A. The crystal belongs to space group R3, with unit-cell parameters a = b = 211.6, c = 52.7 A. The asymmetric unit contains one protein molecule, with a corresponding V(M) of 3.03 A(3) Da(-1) and a solvent content of 59.4%. Molecular replacement was successfully carried out using a homology model based on the three-dimensional structure of the CGTase from Thermonanaerobacterium thermosulfurigenes EM1 as a search model.

Bacillus↗