Crystal structures of the catalytic domain of a novel glycohydrolase family 23 chitinase from sp. A-471 reveals a unique arrangement of the catalytic residues for inverting chitin hydrolysis

Arimori, Takao*; Kawamoto, Noriko*; Shinya, Shoko*; Okazaki, Nobuo*; Nakazawa, Masami*; Miyatake, Kazutaka*; Fukamizo, Tamo*; Ueda, Mitsuhiro*; Tamada, Taro

Journal of Biological Chemistry, 288(26), p.18696 - 18706, 2013/07

https://doi.org/10.1074/jbc.M113.462135

Chitinase C from sp. A-471 (Ra-ChiC) has a catalytic domain sequence similar to goose type (G-type) lysozymes and, unlike other chitinases, belongs to glycohydrolase (GH) family 23. Using NMR spectroscopy, however, Ra-ChiC was found to interact only with the chitin dimer but not with the peptideglycan fragment. Here we report the crystal structures of wild-type, E141Q, and E162Q of the catalytic domain of Ra-ChiC with or without chitin oligosaccharides. Ra-ChiC has a substrate-binding site including a tunnel-shaped cavity, which determines the substrate specificity. Mutation analyses based on this structural information indicated that a highly conserved Glu141 acts as a catalytic acid, and that Asp226 located at the roof of the tunnel activates a water molecule as a catalytic base. The unique arrangement of the catalytic residues makes a clear contrast to the other GH23 members and also to inverting GH19 chitinases.

Development of next-generation superconducting cyclotron

Ishiyama, Atsushi*; Ueda, Hiroshi*; Fukuda, Mitsuhiro*; Hatanaka, Kichiji*; Miyahara, Nobuyuki*; Yokota, Wataru; Kashima, Naoji*; Nagaya, Shigeo*

Denki Gakkai Kenkyukai Shiryo, Chodendo Oyo Denryoku Kiki Kenkyukai (ASC-10-33), p.83 - 88, 2010/06

Therapy of tumor using radiation, especially heavy particle, is one of the effective treatment for an aged person and a malignant solid tumor. In order to spread the radiation therapy, downsizing of accelerator is necessary for reduction of its vast costs of construction and running. The quality of high temperature superconductors is improving rapidly in recent years, which may lead to realization of the downsizing. This presentation describes a conceptual design of the superconducting cyclotron and its advantage comparing to other type of accelerators.

Development of the main probe for measuring a beam phase width in the JAEA AVF cyclotron

Miyawaki, Nobumasa; Okumura, Susumu; Kurashima, Satoshi; Kashiwagi, Hirotsugu; Yoshida, Kenichi; Yuri, Yosuke; Yuyama, Takahiro; Ishibori, Ikuo; Agematsu, Takashi; Ishizaka, Tomohisa; et al.

Proceedings of 4th Annual Meeting of Particle Accelerator Society of Japan and 32nd Linear Accelerator Meeting in Japan (CD-ROM), p.604 - 606, 2007/00

The main probe of the JAEA AVF cyclotron has been modified to measure a beam phase width in the accelerating region without extracting the beam from the cyclotron, which could cause the beam loss at the extraction device. The main probe consists of a carbon block for a beam current measurement and a plastic scintillator for a beam phase measurement. A correlation between the beam phase width and the position of phase slits was confirmed.

Crystal structure of a novel chitinase, a member of GH family 23, from the moderately thermophilic bacterium sp. A-471

Ueda, Mitsuhiro*; Nakazawa, Masami*; Miyatake, Kazutaka*; Okazaki, Nobuo; Kuroki, Ryota; Tamada, Taro

no journal, , 

Crystal structure of a novel chitinase (Ra-ChiC), a member of GH family 23, from the moderately thermophilic bacterium sp. A-471 has been solved in the active site to 1.9 resolution. Crystal structure of Ra-ChiC was resemble to that of g-type lysozyme. It is well known that the residues involved in catalysis of the g-type lysozymes are Glu73, Asp90, and Asp101. The Glu73 (proton donor) in g-type lysozymes was conserved as Glu141 in the catalytic domain of Ra-ChiC.

Crystal structure of Ra-ChiC belonging to GH family 23

Arimori, Takao; Kawamoto, Noriko*; Okazaki, Nobuo; Nakazawa, Masami*; Miyatake, Kazutaka*; Ueda, Mitsuhiro*; Tamada, Taro

no journal, , 

no abstracts in English

Study on release and transport of aerial radioactive materials in reprocessing plant, 1; Background and event of study

Ueda, Yoshinori*; Takanashi, Mitsuhiro*; Uchiyama, Gunzo; Yoshida, Kazuo; Yamane, Yuichi; Sekine, Keiji*; Fujita, Kunio*

no journal, , 

A study on the release and transport of aerial radioactive materials in reprocessing plants was stared to develop risk assessment methods. The background and event of study will be presented.

Crystal structure of endo-1,4--glucanase from Eisenia foetida

Arimori, Takao*; Ito, Akihiro*; Nakazawa, Masami*; Ueda, Mitsuhiro*; Tamada, Taro

no journal, , 

Crystal structures of the catalytic domain of a novel chitinase belonging to GH family 23

Arimori, Takao*; Kawamoto, Noriko*; Okazaki, Nobuo*; Nakazawa, Masami*; Miyatake, Kazutaka*; Fukamizo, Tamo*; Ueda, Mitsuhiro*; Tamada, Taro

no journal, , 

Chitin, linear -1,4-linked polymer of -acetyl-D-glucosamine (NAG), is the second abundant biopolymer in nature next to cellulose. Hydrolysis of chitin provides useful products, -acetyl-chitooligosaccharides [(NAG)] and chitooligosaccharides, which have a variety of biological functions including antibacterial activity and antitumor activity. We have previously cloned a novel chitinase gene from a moderate thermophilic strain sp. A-471 (Ra-ChiC). Ra-ChiC comprises a signal peptide, a chitin-binding domain, an interdomain linker, and a catalytic domain. The catalytic domain shares amino acid sequence homology with goose type (G-type) lysozymes and, unlike other chitinases, Ra-ChiC belongs to glycohydrolase (GH) family 23. However, Ra-ChiC does not exhibit lysozyme activity, but only chitinase activity. In this study, we aim to reveal how Ra-ChiC catalyzes the hydrolysis of chitin and why Ra-ChiC exhibits chitinase activity instead of lysozyme activity. We determined the crystal structures of the catalytic domain of Ra-ChiC (Ra-ChiC), Ra-ChiC complexed with (NAG), E141Q mutant of Ra-ChiC complexed with (NAG), E162Q mutant of Ra-ChiC, and E162Q mutant of Ra-ChiC complexed with (NAG). These structures provided us structural basis of substrate recognition mechanism and revealed that Ra-ChiC has a unique substrate-binding site including a tunnel-shaped cavity, which determines the substrate specificity. In addition, we also carried out a mutation analysis of acidic amino acid residues located at the active site. As a result, we found that not only a highly conserved Glu141 but also Asp226 located at the roof of the tunnel have quite important roles in catalysis.

Development of new reduced activation HEAs by additive manufacturing method

Hashimoto, Naoyuki*; Isobe, Shigehito*; Oka, Hiroshi*; Hayashi, Shigenari*; Ueda, Mikito*; Yamashita, Shinichiro; Itakura, Mitsuhiro; Tsuru, Tomohito

no journal, , 

Owing to the reduced defects, low cost, and high efficiency, the additive manufacturing (AM) technique has attracted increasingly attention and has been applied in high-entropy alloys (HEAs) in recent years. For the purpose of creating new materials which show no radiation damage or prompt recovery of radiation damage, we launched a new program in which additive-manufactured HEAs are target materials and their fundamental properties are under investigation. In this presentation, we reported the some of new test results which are conducted in the program.

Temporal change of Oligocene to Miocene magmatism in the Toyama basin of the SW Japan arc during back-arc spreading in the Japan Sea

Yamada, Raiki*; Takahashi, Toshiro*; Nagata, Mitsuhiro; Ueda, Hayato*

no journal, , 

Oligocene-Miocene volcanic rocks distributed in the Toyama Sedimentary Basin of the SW Japan Arc are important for clarifying the temporal evolution of subduction zone volcanic activity during back-arc expansion. In this study, we report zircon U-Pb dates, zircon chemical compositions (trace elements and Hf isotopes), and whole rock compositions (major and trace elements, Sr-Nd isotopes). As a result of each analysis, the ca.23 Ma alkali-series rhyolite shows an isotopic composition that supports its high fertility, and is interpreted as magma that has dissolved the continental crust. The 18-17 Ma igneous activity varied from andesite to rhyolite. This magma diversity is thought to involve melting of the mantle saturated with slab fluids and partial melting of the mantle contaminated with slab melt.