Institute for Protein Research, Osaka University - Tsukihara's Laboratory

Publications

Chimari Okada, Eiki Yamashita, Soo Jae Lee, Satoshi Shibata, Jun Katahira, Atsushi Nakagawa, Yoshihiro Yoneda & Tomitake Tsukihara.
A High-Resolution Structure of the Pre-microRNA Nuclear Export Machinery
Science 326, 1275-1279 (2009). [Abstract in Science]

 

Shoji Maeda, So Nakagawa, Michihiro Suga, Eiki Yamashita, Atsunori Oshima, Yoshinori Fujiyoshi & Tomitake Tsukihara
Structure of the connexin 26 gap junction channel at 3.5 A resolution
Nature 458, 597-602 (2009).[Pub Med] [Full Text in Nature]

Hideaki Tanaka, Koji Kato, Eiki Yamashita, Tomoyuki Sumizawa, Yong Zhou, Min Yao, Kenji Iwasaki, Masato Yoshimura and Tomitake Tsukihara*
The Structure of Rat Liver Vault at 3.5 Angstrom Resolution,
Science, 323, 384-388
(2009). [Pub Med] [Abstract in Science] [Full Text in Science]


Se-Young Son, Jichun Ma, Youhei Kondou, Masato Yoshimura, Eiki Yamashita and Tomitake Tsukihara*
Structure of human monoamine oxidase A at 2.2 A resolution: the control of opening the entry for substrates/inhibitors,
Proc. Natl Acad. Sci. USA, 105(15), 5739-5744.
(2008). [Pub Med]

Kyoko Shinzawa-Itoh, Hiroshi Aoyama, Kazumasa Muramoto, Hirohito Terada, Tsuyoshi Kurauchi, Yoshiki Tadehara, Akiko Yamasaki, Takashi Sugimura, Sadamu Kurono, Kazuo Tsujimoto, Tsunehiro Mizushima, Eiki Yamashita, Tomitake

Structures and physiological roles of all the integral lipids of bovine heart cytochrome c oxidase.

EMBO J. 26, 1713-1725, (2007).[Pub Med]


Kunitoshi Shimokata, Yukie Katayama, Haruka Murayama, Makoto Suematsu, Tomitake Tsukihara, Kazumasa Muramoto, Shinya Yoshikawa and Hideo Shimada
The Proton-Pumping Pathway of Bovine Heart Cytochrome c Oxidase.

Proc. Natl. Acad. USA, 104, 4200-4205 (March 6, 2007) .[Pub Med]



Mallett TC, Wallen JR, Karplus PA, Sakai H, Tsukihara T, Claiborne A.

Structure of coenzyme A-disulfide reductase from Staphylococcus aureus at 1.54 A resolution.

Biochemistry. 45, 11278-11289 (2006).[PubMed]



T.Kohno, H. Hochigai, E. Yamashita, T. Tsukihara & M. Kanaoka.
Crystal structures of the catalytic domain of human stromelysin-1(MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453.
Biochem Biophys Res Commun. 344, 315-22 (2006) [PubMed]

Morimoto K, Yamashita E, Kondou Y, Lee SJ, Arisaka F, Tsukihara T, Nakai M.

The asymmetric IscA homodimer with an exposed [2Fe-2S] cluster suggests the structural basis of the Fe-S cluster biosynthetic scaffold.
J Mol Biol. 360, 117-132 (2006).[PubMed]

Yoshikawa S, Muramoto K, Shinzawa-Itoh K, Aoyama H, Tsukihara T, Shimokata K, Katayama Y, Shimada H.
Proton pumping mechanism of bovine heart cytochrome c oxidase.
Biochim Biophys Acta.  1757,  1110-1116 (2006).[PubMed]

Yoshikawa S, Muramoto K, Shinzawa-Itoh K, Aoyama H, Tsukihara T, Ogura T, Shimokata K, Katayama Y, Shimada H.

Reaction mechanism of bovine heart cytochrome c oxidase.

Biochim Biophys Acta. 1757, 395-400 (2006).[PubMed]


Umena Y, Yorita K, Matsuoka T, Abe M, Kita A, Fukui K, Tsukihara T, Morimoto Y.

Crystallization and preliminary X-ray diffraction study of L-lactate oxidase (LOX), R181M mutant, from Aerococcus viridans.

Acta Crystallogr. F61, 439-441 (2005).[PubMed]



Lee, S. J., Ogasahara, K., Ma, J., Nishio, K., Ishida, M., Yamagata, Y., Tsukihara, T., and Yutani, K. (2005) Conformational changes in the tryptophan synthase from a hyperthermophile.
Biochemistry 44, 11417-11427.[PubMed]

Yamashita, E., Aoyama, H., Yao, M., Muramoto, K., Shinzawa-Itoh, K., Yoshikawa, S., and Tsukihara, T. (2005)
Absolute configuration of the hydroxyfarnesylethyl group of haem A, determined by X-ray structural analysis of bovine
heart cytochrome c oxidase using methods
applicable at 2.8 A resolution.
Acta Cryst. D61, 1373-1377.[PubMed]

Taka, J., Naitow, H., Yoshimura, M., Miyazaki, N., Nakagawa, A., and Tsukihara, T. (2005)
Ab initio crystal structure determination of spherical viruses that exhibit a centrosymmetric location in the unit cell. Acta Cryst. D61, 1099-1106. [PubMed]

Kondou, Y., Kitagawa, D., Takeda, S., Tsuchiya, Y., Yamashita, E., Mizuguchi, M., Kawano, K., and Tsukihara, T. (2005)
Structure of the central Hub of bacteriophage Mu baseplate determined by X-ray crystallography of gp44.
J. Mol. Biol. 352, 976-985. [PubMed] 

Akama, H., Kanemaki, M., Tsukihara, T., Nakagawa, A., and Nakae, T. (2005)
Preliminary crystallographic analysis of the antibiotic discharge outer membrane lipoprotein OprM of Pseudomonas aeruginosa with an exceptionally long unit cell and complex lattice structure.
Acta Cryst. F61, 131-133. [PubMed]

Nishio, K., Morimoto, Y., Ishizuka, M., Ogasahara, K., Tsukihara, T., and Yutani, K. (2005)
Conformational changes in the alpha-subunit coupled to binding of the beta 2-subunit of tryptophan synthase from Escherichia coli: crystal structure of the tryptophan synthase alpha-subunit alone.
Biochemistry 44, 1184-1192. [PubMed]

Miyazaki, N., Hagiwara, K., Naitow, H., Higashi, T., Cheng, R. H., Tsukihara, T., Nakagawa, A., and Omura, T. (2005)
Transcription and the conserved interactions of two major structural proteins of a pair of phytoreoviruses confirm the mechanism of assembly of the outer capsid layer.
J. Mol. Biol. 345, 229-237.[PubMed]

Akama, H., Kanemaki, M., Yoshimura, M., Tsukihara, T., Kashiwagi, S., Yoneyama, H., Narita, S., Nakagawa, A., and Nakae, T. (2004)
Crystal structure of the drug discharge outer membrane protein, OprM, of Pseudomonas aeruginosa.
J. Biol. Chem. 279, 52816-52819[PubMed]

Akama, H., Matsuura, T., Kashiwagi, S., Yoneyama, H., Narita, S., Tsukihara, T., Nakagawa, A., and Nakae, T. (2004)
Crystal structure of the membrane fusion protein, MexA, of the multidrug transporter in Pseudomonas aeruginosa.
J. Biol. Chem. 279, 25939-25942. [PubMed]

Ma, J, Yoshimura, M., Yamashita, E., Nakagawa, A., Ito, A., and Tsukihara, T. (2004)
Structure of rat monoamine oxidase A and its specific recognitions for substrates and inhibitors.
J. Mol. Biol. 338, 103-114.  [PubMed]

Hagiwara, K., Higashi, T., Miyazaki, N., Naitow, H., Cheng, R. H., Nakagawa, A., Mizuno, H., Tsukihara, T., and Omura, T. (2004)

The amino-terminal region of major capsid protein P3 is essential for self-assembly of single-shelled core-like
particles of Rice dwarf virus.

J. Virol. 78, 3145-3148. [PubMed]


Tsunehiro Mizushima, Takeshi Hirao, Yukiko Yoshida, Soo Jae Lee, Tomoki Chiba, Kazuhiro Iwai, Yoshiki Yamaguchi, Tomokate Tsukihara and Keiji Tanaka

Structural basis of sugar-recognizing ubiquitin ligase.

Nature Structural & Molecular Biology, Published online 29 February 2004;doi:10.1038/nsmb732. [Figure] [PubMed]

 

Kunio Hirata, Eiki Yamashita, Hiroshi Aoyama, Kazumasa Muramoto, Kyoko Shinzawa-Itoh, Shinya Yoshikawa and Tomitake Tsukihara

Scaling of one-shot oscillation images with a reference data set.

J. Synchrotron Radiation, (2004). 11, 60-63. [PubMed] [Online Journal]

 

T. Tsukihara, K. Shimokata, Y. Katayama, H. Shimada, K. Muramoto, H. Aoyama, M. Mochizuki, K. Shinzawa-Itoh, E. Yamashita, M. Yao, Y. Ishimura and S. Yoshikawa

The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.

Proc. Natl. Acad. Sci. U.S.A. (2003) 100, 15304-15309. [Figure] [PubMed]

 

S.J. Lee, T. Sekimoto, E. Yamashita, E. Nagoshi, A. Nakagawa, N. Imamoto, M. Yoshimura, H. Sakai, K.T. Chong, T. Tsukihara, & Y. Yoneda

The Structure of Importin- Bound to SREBP-2 : Nuclear Import of a Transcription Factor.

Science, 302, 1571-1575 (2003). [Figure] [PubMed]

 

Atsushi Nakagawa, Naoyuki Miyazaki, Junichiro Taka, Hisashi Naitow, Akira Ogawa, Zui Fujimoto, Hiroshi Mizuno, Takahiko Higashi, Yasuo Watanabe, Toshio Omura, R. Holland Cheng, and Tomitake Tsukihara

The Atomic Structure of Rice Dwarf Virus Reveals the Self-Assembly Mechanism of Component Proteins.

Structure, 11, 1227-1238 (2003). [Figure] [PubMed]

 

A. Ogawa, Y. Takayama, H. Sakai, K T. Chong, S. Takeuchi, A. Nakagawa, S. Nada, M. Okada and T. Tsukihara

Structure of the Carboxyl-terminal Src Kinase, Csk.

J. Biol. Chem. 277, 14351-14354 (2002). [PubMed]

 

M. Unno, T. Mizushima, Y. Morimoto, Y. Tomisugi, K. Tanaka, N. Yasuoka, & T. Tsukihara

The Structure of the Mammalian 20S Proteasome at 2.75 Å Resolution.

Structure 10, 609-618 (2002). [PubMed]

 

M. Odoko, M. Yao, E. Yamashita, R. Nakashima, K. Hirata, H. Aoyama, K. Muramoto, K. Shinzawa-Itoh, S. Yoshikawa and T. Tsukihara

Optimization of the energy constant of the methionine S-C bond for X-PLOR refinement of protein structure.

J. Appl. Cryst., 34, 80-81 (2001). [Online Journal]

 

S. J. Lee, N. Imamoto, H. Sakai, A. Nakagawa, S. Kose, M. Koike, M. Yamamoto, T. Kumasaka, Y. Yoneda and T. Tsukihara

The Adoption of a Twisted Structure of Importin- is Essential for the Protein-protein Interaction Required for Nuclear Transport.

J. Mol. Biol., 302, 251-264 (2000). [PubMed]

 

M. J. Fei, E. Yamashita, N. Inoue, M. Yao, H. Yamaguchi, T. Tsukihara, K. Shinzawa-Itoh, R. Nakashima and S. Yoshikawa,

X-ray structure of azide-bound fully oxidized cytrochrome c oxidase from bovine heart muscle at 2.9 Å resolution.

Acta Cryst. D56, 529-535 (2000). [PubMed]

 

S. Mitsuhashi, T. Mizushima, E. Yamashita, M. Yamamoto, T. Kumasaka, H. Moriyama, T. Ueki, S. Miyachi and T. Tsukihara

X-ray Structure of -Carbonic Anhydrase from the Red Alga, Porphyridium purpureum, Reveals a Novel Catalytic Site for CO2 Hydration.

J. Biol. Chem. 275, 5521-5526 (2000). [PubMed]

 

H. Naitow, Y. Morimoto, H. Mizuno, H. Kano, T. Omura, M. Koizum and T. Tsukihara

A low-resolution structure of rice dwarf virus determined by ab intio phasing.

Acta Cryst. D55, 77-84 (1999). [PubMed] [Online Journal]

 

T. Tomizaki, E. Yamashita, H. Yamaguchi, H. Aoyama, T. Tsukihara, K. Shinzawa-Itoh, R. Nakashima, R. Yaono and S. Yoshikawa

Structure analysis of bovine heart cytochrome c oxidase at 2.8 Å resokution.

Acta Cryst. D55, 31-45 (1999), [PubMed]

 

T. Tsukihara and S. Yoshikawa

Crystal Structural Studies of a Membrane Protein Complex, Cytochrome c Oxidase from Bovine Heart.

Acta Cryst., A54, 895-904 (1998), [PubMed] [Online Journal]

 

S. Yoshikawa, K. Shinzawa-Itoh,, R. Nakashima, R. Yaono, E. Yamashita, N. Inoue, M. Yao, M. Fei, C. Peters Libeu, T. Mizushima, H. Yamaguchi, T. Tomizaki anf T. Tsukihara

Redox-Coupled Crystal Structural Changes in Bovine Herart Cytochrome c Oxidase.

Science, 280, 1723-1729 (1998). [PubMed]

 

T.Tsukihara, H. Aoyama, E.Yamashita, T. Tomizaki, H. Yamaguchi, K.Shinzawa-Itoh, R. Nakashima, R. Yaono and S.Yoshikawa

The Whole Structure of the 13-Subinit Oxidized Cytochrome c Oxidase at 2.8 Å. 

Science, 272, 1136-1144 (1996). [PubMed]

 

T.Tsukihara, H. Aoyama, E.Yamashita, T. Tomizaki, H. Yamaguchi, K.Shinzawa-Itoh, R. Nakashima, R. Yaono and S.Yoshikawa,

Structure of Metal Sites of Oxidized Bovine Heart Cytochrome c Oxidase at 2.8 Å Resolution.

Science, 269, 1069-1074(1995). [PubMed]