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27 citations found for Miyazono,

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Chondroitin sulfate ABC lyases are broad-specificity glycosaminoglycan-degrading enzymes. The crystallization of two isozymes of such a lyase produced by P. vulgaris is described.

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The KaiC-like protein PH0187 from the hyperthermophilic archaeon P. horikoshii OT3 was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. The crystal of PH0187 diffracted X-rays to 2.75 Å resolution.

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NADPH-dependent 5-keto-D-gluconate reductase from G. suboxydans IFO12528 (5KGR) was expressed, purified and crystallized with 5-keto-D-gluconate and NADPH using the sitting-drop vapour-diffusion method. Crystals of the 5KGR-NADPH complex and of the 5KGR-NADPH-5-keto-D-gluconate complex diffracted X-rays to 1.75 and 2.26 Å resolution, respectively.

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NADPH-dependent L-sorbose reductase from G. frateurii (SR) was expressed, purified and crystallized with L-sorbose or NADPH using the sitting-drop vapour-diffusion method. Crystals of the SR-L-sorbose complex and SR-NADPH complex diffracted X-rays to 2.38 and 1.90 Å resolution, respectively.

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Flap endonuclease 1 from D. amylolyticus was expressed, purified and crystallized by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 2.00 Å resolution.

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The crystal structure of flap endonuclease 1 from the hyperthermophilic archaeon D. amylolyticus was determined at 2.00 Å resolution.

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Purification and crystallization of ginkbilobin-2 and its selenomethionine derivative allowed the collection of complete data to 2.38 Å resolution and multiwavelength anomalous diffraction data sets, respectively.

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Acta Cryst. (2014). A70, C213
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Restriction-modification systems consist of genes that encode a restriction enzyme and a cognate modification methyltransferase. It was believed that restriction enzymes are sequence-specific endonucleases that introduce double-strand breaks at specific sites by catalyzing the cleavages of phosphodiester bonds. R.PabI is a type II restriction enzyme from a hyperthermophilic archaea Pyrococcus abyssi that recognizes 5'-GTAC-3' sequence and cleaves DNA duplexes without the addition of a divalent cation. The structural and mutational analyses of R.PabI in our previous work showed that R.PabI forms a homodimer and has a novel DNA-binding fold called a "half-pipe," which consists of a highly curved anti-parallel [beta]-sheet. Because the structure of R.PabI shares no structural similarity to any other protein, the structural basis of the sequence-recognition and DNA-cleavage mechanisms remained unclear. In this study, we report the crystal structure of R.PabI in complex with a DNA duplex containing the R.PabI recognition sequence. The structure of the R.PabI-DNA complex shows that R.PabI unwinds a DNA duplex at a 5'-GTAC-3' site and flips the guanine and adenine bases out of the DNA helix to recognize the sequence. The electron-density map of the R.PabI-DNA complex shows that R.PabI releases adenine bases from the R.PabI recognition sequence. Biochemical assays using HPLC and MALDI-TOF MS spectrometry also support the observation that R.PabI releases adenine bases by hydrolysis. These results show that R.PabI is not an endonuclease but a sequence-specific adenine DNA glycosylase. R.PabI is the first example of a restriction enzyme that shows DNA glycosylase activity. Mutational analysis reveals the active site of the adenine DNA glycosylase activity of R.PabI. The two opposing apurinic/apyrimidinic (AP) sites generated by R.PabI are cleaved by heat promoted [beta] elimination and/or by endogenous AP endonucleases of host cells to introduce a double-strand break.

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Acylphosphatase from a hyperthermophilic archaea, P. horikoshii OT3, has been crystallized and X-ray diffraction data have been collected to 1.72 Å resolution.


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OsAREB8 from rice (O. sativa), a member of the AREB/ABF family of bZIP transcription factors, was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. A crystal of OsAREB8 in complex with its cognate DNA diffracted X-rays to 3.65 Å resolution.

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Glucokinase from S. griseus (SgGlkA) was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. A crystal of SgGlkA in complex with glucose diffracted X-rays to 1.84 Å resolution.

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A single-strand-specific 3'-5' exonuclease, PhoExo I, from the hyperthermophilic archaeon P. horikoshii OT3 was produced as inclusion bodies in E. coli cells, solubilized by the high-pressure refolding method, purified and crystallized. The crystal of PhoExo I diffracted X-rays to 1.52 Å resolution.

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Acta Cryst. (2011). A67, C346-C347
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The first structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase (GGGPS) from a thermoacidophilic archaeon, Thermoplasma acidophilum, with the substrate sn-glycerol 1-phosphate is described. Structural comparisons of this enzyme with other structurally determined archaeal GGGPS proteins are described.

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A Streptomyces homologue of the mycobacterial integration host factor mIHF was heterologously produced, purified and crystallized in the presence of a 16-mer duplex DNA by the sitting-drop vapour-diffusion method. The best crystal diffracted X-rays to 2.22 Å resolution and belonged to space group C2.

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