JAEA
  • help
  • PC | SP
  • JP | EN
          
Refine your search：     
Report No.
 - 
Clear All
Search Results: Records 1-20 displayed on this page of 22

Presentation/Publication Type

Initialising ...

Refine

Journal/Book Title

Initialising ...

Meeting title

Initialising ...

First Author

Initialising ...

Keyword

Initialising ...

Language

Initialising ...

Publication Year

Initialising ...

Held year of conference

Initialising ...

Save select records

Journal Articles

Discovery of a selective Cs$$^{+}$$ binding site of a $$beta$$-lactamase from the halophile by anomalous X-ray diffraction

Arai, Shigeki; Shibazaki, Chie; Shimizu, Rumi; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

Kyushu Shinkurotoronko Kenkyu Senta Nempo, 2014, p.17 - 19, 2016/03

https://www.saga-ls.jp/main/1007.html#gsc.tab=0

no abstracts in English

Journal Articles

Nucleoside diphosphate kinase from psychrophilic ${it Pseudoalteromonas}$ sp. AS-131 isolated from Antarctic Ocean

Yonezawa, Yasushi*; Nagayama, Aiko*; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Arai, Shigeki; Kuroki, Ryota; Watanabe, Keiichi*; Arakawa, Tsutomu*; Tokunaga, Masao*

Protein Journal, 34(4), p.275 - 283, 2015/08

https://doi.org/10.1007/s10930-015-9623-0
 Times Cited Count：4 Percentile：10.20(Biochemistry & Molecular Biology)

Nucleoside diphosphate kinase isolated from psychrophilic ${it Pseudoalteromonas}$ sp. AS-131 (ASNDK) was expressed in ${it Escherichia coli}$ and purified to homogeneity. Comparing to mesophilic NDK isolated from ${it Pseudomonas aeruginosa}$, ASNDK exhibited highly elevated thermolability: (1) ${it E. coli}$ expression at 37$$^{circ}$$C as a denatured insoluble form, and (2) 30$$^{circ}$$C lower optimum temperature of enzymatic activity. The subunit structure of ASNDK was suggested to be dimer, as in NDKs isolated from moderate halophiles.

Journal Articles

Structure of a highly acidic $$beta$$-lactamase from the moderate halophile ${it Chromohalobacter}$ sp.560 and the discovery of a Cs$$^{+}$$-selective binding site

Arai, Shigeki; Yonezawa, Yasushi*; Okazaki, Nobuo*; Matsumoto, Fumiko*; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu*; Adachi, Motoyasu; Tamada, Taro; Kawamoto, Masahide*; et al.

Acta Crystallographica Section D, 71(3), p.541 - 554, 2015/03

https://doi.org/10.1107/S1399004714027734
 Times Cited Count：8 Percentile：52.94(Biochemical Research Methods)

The crystal structure of halophilic $$beta$$-lactamase from ${it Chromohalobacter}$ sp.560 (HaBLA) was determined using X-ray crystallography. Moreover, the locations of bound Sr$$^{2+}$$ and Cs$$^{+}$$ ions were identified by anomalous X-ray diffraction. The location of one Cs$$^{+}$$ specific binding site was identified on HaBLA even in the presence of 9-fold molar excess of Na$$^{+}$$ (90 mM Na$$^{+}$$ /10 mM Cs$$^{+}$$). This Cs$$^{+}$$ binding site is formed by two main-chain O atoms and an aromatic ring of a side chain of Trp. An aromatic ring of Trp interacts with Cs$$^{+}$$ by the cation-$$pi$$ interaction. The observation of a selective and high-affinity Cs$$^{+}$$ binding site provides important information that is useful for designing artificial Cs$$^{+}$$ binding sites useful in bioremediation of radioactive isotopes.

Journal Articles

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium ${it Halomonas}$ sp.593

Arai, Shigeki; Yonezawa, Yasushi*; Ishibashi, Matsujiro*; Matsumoto, Fumiko*; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Blaber, M.; Tokunaga, Masao*; Kuroki, Ryota

Acta Crystallographica Section D, 70(3), p.811 - 820, 2014/03

https://doi.org/10.1107/S1399004713033609
 Times Cited Count：13 Percentile：63.81(Biochemical Research Methods)

In order to clarify the structural basis of halophilic characteristics of an alkaline phosphatase derived from the moderate halophile ${it Halomonas}$ sp.593 (HaAP), the tertiary structure of HaAP was determined to 2.1${AA}$ resolution by X-ray crystallography. Structural properties of surface negative charge and core hydrophobicity are shown to be intermediate between halophile and non-halophile characteristics, and may explain the unique functional adaptation to a wide-range of salt concentration.

Journal Articles

Reduction of salt-requirement of halophilic nucleoside diphosphate kinase by engineering S-S bond

Ishibashi, Matsujiro*; Uchino, Manami*; Arai, Shigeki; Kuroki, Ryota; Arakawa, Tsutomu*; Tokunaga, Masao*

Archives of Biochemistry and Biophysics, 525(1), p.47 - 52, 2012/09

https://doi.org/10.1016/j.abb.2012.05.021
 Times Cited Count：7 Percentile：20.11(Biochemistry & Molecular Biology)

Nucleoside diphosphate kinase (HsNDK) from Halobacterium salinarum requires salt at high concentrations for folding. A D148C mutant, in which Asp148 was replaced with Cys, was designed to enhance stability and folding in low salt solution by S-S bond. It showed increased thermal stability by about 10$$^{circ}$$C in 0.2 M NaCl over the wild type HsNDK. It refolded from heat-denaturation even in 0.1 M NaCl, while the wild type required 2 M NaCl to achieve the same level of activity recovery. This enhanced refolding is due to the three S-S bonds between two basic dimeric units in the hexameric HsNDK structure. Moreover, salt concentration dependency of heat-denaturation process and refolding process of the wild type and D148C mutant HsNDKs were investigated by the circular dichroism and native-PAGE analysis.

Journal Articles

A Structural mechanism for dimeric to tetrameric oligomer conversion in ${it Halomonas}$ sp. nucleoside diphosphate kinase

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Blaber, M.; Tokunaga, Masao*; Kuroki, Ryota

Protein Science, 21(4), p.498 - 510, 2012/04

https://doi.org/10.1002/pro.2032
 Times Cited Count：15 Percentile：35.23(Biochemistry & Molecular Biology)

In order to clarify the oligomer state of nucleoside diphosphate kinase (NDK) from moderately halophilic ${it Halomonas}$ sp. 593 (HaNDK), the crystal structure of HaNDK was determined by X-ray crystallography. The crystal structures of the wild-type HaNDK and the mutant HaNDK (E134A) showed a dimer and a tetramer, respectively. The higher ordered association of proteins usually contributes to an increase in thermal stability and substrate affinity. The change in the assembly form by a minimum mutation may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.

Journal Articles

Residue 134 determines the dimer-tetramer assembly of nucleoside diphosphate kinase from moderately halophilic bacteria

Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Arisaka, Fimio*; Arai, Shigeki; Kuroki, Ryota; Arakawa, Tsutomu*; Tokunaga, Masao*

FEBS Letters, 582(7), p.1049 - 1054, 2008/04

https://doi.org/10.1016/j.febslet.2008.02.054
 Times Cited Count：17 Percentile：39.59(Biochemistry & Molecular Biology)

${it Halomonas}$ nucleoside diphosphate kinase (HaNDK) forms a dimeric assembly and ${it Pseudomonas}$ NDK (PaNDK) forms a tetrameric assembly. The mutation of Glu134 to Ala in HaNDK resulted in conversion of the native dimeric structure to the tetramer assembly. Conversely, the mutation of Ala134 to Glu in PaNDK leads to conversion from tetramer to dimer assembly, indicating that a single amino acid substitution at position 134 results in an alteration of the oligomeric structure of NDK. Modeling structure of HaNDK and PaNDK, based on the crystal structure of ${it Myxococcus}$ NDK, suggested sufficient repulsion by Glu134 to disrupt dimer-dimer interaction to form tetramer.

Journal Articles

Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex

Tamada, Taro; Honjo, Eijiro; Maeda, Yoshitake*; Okamoto, Tomoyuki*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

Proceedings of the National Academy of Sciences of the United States of America, 103(9), p.3135 - 3140, 2006/02

https://doi.org/10.1073/pnas.0511264103
 Times Cited Count：99 Percentile：84.59(Multidisciplinary Sciences)

A crystal structure of the signaling complex between human granulocyte colony-stimulating factor (GCSF), and a ligand binding region of GCSF receptor (GCSF-R), has been determined to 2.8${AA}$ resolution. The GCSF:GCSF-R complex formed a 2:2 stoichiometry via a cross-over interaction between the Ig-like domains of GCSF-R and GCSF. The conformation of the complex is quite different to that between human GCSF and the CRH domain of mouse GCSF-R, but similar to that of the interleukin-6 (IL-6)/gp130 signaling complex. The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses.

Journal Articles

Crystallization of a 2:2 complex of Granulocyte-Colony Stimulating Factor (GCSF) with the ligand-binding region of the GCSF receptor

Honjo, Eijiro; Tamada, Taro; Maeda, Yoshitake*; Koshiba, Takumi*; Matsukura, Yasuko*; Okamoto, Tomoyuki*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

Acta Crystallographica Section F, 61(8), p.788 - 790, 2005/08

https://doi.org/10.1107/S1744309105023080
 Times Cited Count：7 Percentile：54.76(Biochemical Research Methods)

Granulocyte colony-stimulating factor (GCSF) receptor receives signals for regulating the proliferation and differentiation of the precursor cells of granulocytes. The complex composed of two GCSFs and two GCSF receptors was crystallized. The crystal of the complex was grown in 1.0 M sodium formate and 0.1 M sodium acetate (pH4.6). It belongs to the space group ${it P}$4$$_{1}$$2$$_{1}$$2 (or its enantiomorph ${it P}$4$$_{3}$$2$$_{1}$$2) with unit cell dimensions of ${it a}$ = ${it b}$ = 110.1 ${AA}$, ${it c}$ = 331.8 ${AA}$. However, the diffraction data from the crystal beyond 5 ${AA}$ resolution could not be collected. Since the heterogeneity of GCSF receptor seems to interrupt growth of good quality crystals, the GCSF receptor was fractionated by achromatography. Crystals of GCSF/fractionated GCSF receptor complex were grown as a new crystal form in 0.2 M ammonium phosphate. The new crystal diffracts beyond 3.0 ${AA}$ resolution and belongs to space group ${it P}$3$$_{1}$$21 (or its enantiomorph ${it P}$3$$_{2}$$21) with unit-cell parameters ${it a}$ = ${it b}$ = 134.8, ${it c}$ = 105.7 ${AA}$.

Oral presentation

X-ray crystallographic analysis of $$beta$$-Lactamase derived from ${it Chromohalobacter}$ sp.560

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

We determined the crystal structure of halophilic $$beta$$-Lactamase obtained from ${it Chromohalobacter}$ sp.560 by X-ray crystallography. Since halophilic enzymes can bind many metal ions on its molecular surface, we are tring to find the Na$$^{+}$$, Mg$$^{2+}$$ and Cs$$^{+}$$ binding sites of halophilic $$beta$$-Lactamase from determined crystal structure.

Oral presentation

Discovery of Cs$$^{+}$$ selective binding site on a halophilic protein

Arai, Shigeki; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

Because various metal ion binding sites exist on halophilic proteins, we proposed that the metal ion binding sites with an affinity to harmful metals and rare metals could be identified using X-ray crystallographic analysis in the presence of those metal ions. In this study, we attempted to identify metal ion binding sites for Sr$$^{2+}$$ and Cs$$^{+}$$ on a halophilic protein HaBLA derived from ${it Chromohalobacter}$ sp.560 (HaBLA) by X-ray crystallographic analysis and anomalous X-ray diffraction analysis. By these analyses, we succeeded in discovering one Cs$$^{+}$$ binding site and three Sr$$^{2+}$$ binding site for one molecule of HaBLA. Moreover, discovered Cs$$^{+}$$ binding site showed high Cs$$^{+}$$ selectivity, which binds Cs$$^{+}$$ even in the presence of 9-fold molar excess of Na$$^{+}$$ (90 mM Na$$^{+}$$ / 10 mM Cs$$^{+}$$).

Oral presentation

Homodimeric crossover structure of the human GCSF-receptor signaling complex

Tamada, Taro; Honjo, Eijiro; Maeda, Yoshitake*; Okamoto, Tomoyuki*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

We have succeeded in crystallization of 2:2 complex between human granulocyte colony-stimulating factor (hGCSF) and the Ig-like and CRH domains of human GCSF-R (hGCSF-R) and determined its tertiary structure by X-ray crystallography at 2.8 ${AA}$ resolution. The signaling 2:2 complex is formed via cross-over interactions between the Ig-like domain of hGCSF-R and the neighboring hGCSF, forming a two-fold axis of crystallographic symmetry. This conformation is quite different from that of the heterogeneous mGCSF-R complex, and more closely resembles the 2:2:2 active assembly of human interleukin-6 (IL-6), human IL-6 $$alpha$$-receptor and human gp130 (which is a shared signal transducing receptor for several cytokines), and the 2:2 assembly of viral IL-6 and human gp130. The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses.

Oral presentation

X-ray crystallographic analysis of $$beta$$-Lactamase derived from ${it Chromohalobacter}$ sp.560

Arai, Shigeki; Tokunaga, Hiroko*; Tamada, Taro; Yonezawa, Yasushi; Adachi, Motoyasu; Yamada, Mitsugu; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

Halophilic proteins can bind various inorganic ions with its negative charges located over the molecular surface. We are investigating the molecular structure of the halophilic proteins because halophilic proteins might be used as a material capturing for the rare metals and/or the radioactive metal ions. Recently, we succeeded in X-ray crystallographic analysis of the halophilic $$beta$$-Lactamase (HaBLA) derived from ${it Chromohalobacter}$ sp.560 at 3.0 ${AA}$ resolution. From this structural analysis, we found that the back bone structure and the positively charged active site feature of HaBLA was similar to those of non-halophilic BLA. The molecular surface of HaBLA were, however, occupied by large number of negative charges. This structural information is very useful to improve the specificity of metals such as Cs or Sr.

Oral presentation

Cs$$^{+}$$ and Sr$$^{2+}$$ recognition mechanism of halophilic $$beta$$-lactamase

Arai, Shigeki; Yonezawa, Yasushi; Adachi, Motoyasu; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

Proteins can distinguish various metal ions. Recently, we succeeded in X-ray crystallographic analysis of the halophilic $$beta$$-Lactamase (HaBLA) derived from ${it Chromohalobacter}$ sp.560 under the existence of Cs+ and Sr2+. Diffraction data at 2.0 ${AA}$ resolution (space group P31, Unit cell a = b =115.9 ${AA}$, c =67.9 ${AA}$, Rmerge 9.6%) was collected. Three Cs$$^{+}$$ and six Sr$$^{2+}$$ metal ion binding sites of HaBLA molecules in the asymmetric unit were identified. This structural information is very useful to create the artificial Cs$$^{+}$$ or Sr$$^{2+}$$ binding site on the protein molecules.

Oral presentation

X-ray crystallographic analysis of Alkaline Phosphatase derived from a moderate halophilic Halomonas sp.593

Arai, Shigeki; Yonezawa, Yasushi*; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

no abstracts in English

Oral presentation

Discovery of Cs selective binding site on a halophilic beta-lactamase by the anomalous X-ray diffraction analysis

Arai, Shigeki; Adachi, Motoyasu; Kawamoto, Masahide*; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

We attempted to discover the Cs$$^{+}$$ and Sr$$^{2+}$$ binding sites on the halophilic $$beta$$-Lactamase (HaBLA) derived from ${it Chromohalobacter}$ sp.560 by the anomalous X-ray diffraction analysis. One Cs$$^{+}$$ ions in the HaBLA crystal were identified by BL7 at SAGA-LS. Three Sr$$^{2+}$$ ions in the HaBLA crystal were identified by BL38B1 at SPring-8 and NW12A at Photon Factory. Discovered Cs$$^{+}$$ binding site can bind Cs$$^{+}$$ selectively from a solution containing Na$$^{+}$$/Cs$$^{+}$$ = 90 mM/10 mM. This Cs$$^{+}$$ binding site is formed by two main-chain O atoms and an aromatic ring of a side chain of Trp. An aromatic ring of Trp interacts with Cs$$^{+}$$ by the cation-$$pi$$ interaction. The observation of metal binding sites with relatively higher Cs$$^{+}$$ selectivity provides important information that is useful for designing artificial Cs$$^{+}$$ binding sites.

Oral presentation

Tertiary structure and low-salt concentration adaptation mechanism of $$beta$$-lactamase from moderate halophile

Arai, Shigeki; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

A high content of acidic residues of halophilic proteins may destabilize the structure of halophilic protein and take away an enzymatic function under low salt concentration. However, periplasmic proteins of moderate halophiles require adapting a wide range of salt concentration (0.5 M - saturated NaCl). In this study, we investigated the structural and functional characteristics of HaBLA derived from periplasm of a moderate halophile ${it Chromohalobacter}$ sp.560. By isothermal titration calorimetry, it was clarified that HaBLA hydrolyses penicillin G under 0 - 4 M NaCl. Moreover, by X-ray crystallographic analysis, we found the positive charges and the hydrophobic cluster near the entrance of the active site of HaBLA. These structural characteristics may attract penicillin G to the active site of HaBLA, which may participate in the low salt concentration adaptation of HaBLA.

Oral presentation

Oligomeric structure of nucleoside diphosphate kinase from Halomonas sp.593 (HaNDK)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

The nucleoside diphosphate kinases (NDKs) are known to have a tetrameric or hexameric oligomer structure formed by association of common dimeric components. We determined the crystal structure of E134A mutant NDK from ${it Halomonas}$ sp. 593 (HaNDK) and found that two kinds of tetrameric assemblies, Type I seen in the ${it Myxococcus}$ NDK tetramer and Type II seen in the ${it E.coli}$ NDK tetramer, appeared in the asymmetric unit. Change in the assembly form may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.

Oral presentation

Ologomeric structure of nucleoside diphosphate kinase from Halomonas sp. 593 (HaNDK)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

The nucleoside diphosphate kinases (NDKs) are known to have a tetrameric or hexameric oligomer structure formed by association of common dimeric components. We determined the crystal structure of E134A mutant NDK from Halomonas sp. 593 (HaNDK) and found that two kinds of tetrameric assemblies, Type I seen in the Myxococcus NDK tetramer and Type II seen in the E.coli NDK tetramer, appeared in the asymmetric unit. Change in the assembly form may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.

Oral presentation

Oligomeric structure of nucleoside diphosphate kinase from ${it Halomonas}$ sp.593 (HaNDK)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Tamada, Taro; Tokunaga, Hiroko*; Ishibashi, Matsujiro*; Tokunaga, Masao*; Kuroki, Ryota

no journal, , 

The nucleoside diphosphate kinases (NDKs) are known to have a tetrameric or hexameric oligomer structure formed by association of common dimeric components. In order to understand the oligomeric structure of NDK, the wild-type NDK from Halomonas sp. 593 (HaNDK) was determined by X-ray crystallography. The wild-type HaNDK only exhibited a dimeric form that is the same as a common dimer unit seen in other NDKs. This is the first evidence of a dimeric structure for HaNDK. To explore the effect of mutation on the assembly form of HaNDK, E134, which is a key interface residue for other tetrameric NDKs, was replaced with Ala, and the structure was determined by X-ray crystallography. Two kinds of tetrameric assemblies, Type I and Type II, appeared in the asymmetric unit of the E134A mutant HaNDK. The change from dimeric to tetrameric assembly is attributed to the removal of negative charge repulsion caused by the E134 in the wild-type HaNDK.

22 (Records 1-20 displayed on this page)