Interactions of Cations with the Cytoplasmic Pores of Inward Rectifier K^+ Channels in the Closed State

This research was originally published in Journal of Biological Chemistry. Atsushi Inanobe, Atsushi Nakagawa, and Yoshihisa Kurachi. Interactions of Cations with the Cytoplasmic Pores of Inward Rectifier K^+ Channels in the Closed State. Journal of Biological Chemistry. 2011; 286, 41801-41811. © the American Society for Biochemistry and Molecular Biology

Conformational changes underlying pore dilation in the cytoplasmic domain of mammalian inward rectifier K^+ channels

Inanobe A, Nakagawa A, Kurachi Y (2013) Conformational Changes Underlying Pore Dilation in the Cytoplasmic Domain of Mammalian Inward Rectifier K^+ Channels. PLOS ONE 8(11): e79844. https://doi.org/10.1371/journal.pone.007984

Structural characteristics of the redox-sensing coiled coil in the voltage-gated H^+ channel

This research was originally published in Journal of Biological Chemistry. Yuichiro Fujiwara, Kohei Takeshita, Atsushi Nakagawa and Yasushi Okamura. Structural characteristics of the redox-sensing coiled coil in the voltage-gated H^+ channel. Journal of Biological Chemistry. 2013; 288, 17968-17975. © the American Society for Biochemistry and Molecular Biology

A structural determinant for the control of PIP_2 sensitivity in G protein-gated inward rectifier K^+ channels

Inward rectifier K^+ (Kir) channels are activated by phosphatidylinositol-( 4,5)-bisphosphate (PIP_2), but G protein-gated Kir (K_G) channels further require either G protein βγ subunits (Gβγ) or intracellular Na^+ for their activation. To reveal the mechanism(s) underlying this regulation, we compared the crystal structures of the cytoplasmic domain of K_G channel subunit Kir3.2 obtained in the presence and the absence of Na^+. The Na^+ -free Kir3.2, but not the Na^+ -plus Kir3.2, possessed an ionic bond connecting the N terminus and the CD loop of the C terminus. Functional analyses revealed that the ionic bond between His-69 on theNterminus and Asp-228 on the CD loop, which are known to be critically involved in Gβγ- and Na^+ -dependent activation, lowered PIP_2 sensitivity. The conservation of these residues within the K_G channel family indicates that the ionic bond is a character that maintains the channels in a closed state by controlling the PIP_2 sensitivity.This research was originally published in Journal of Biological Chemistry. Atsushi Inanobe, Atsushi Nakagawa, Takanori Matsuura and Yoshihisa Kurachi. A structural determinant for the control of PIP2 sensitivity in G protein-gated inward rectifier K^+ channels. Journal of Biological Chemistry. 2010; 285, 38517-38523. © the American Society for Biochemistry and Molecular Biology

Crystal structure of lipoate-protein ligase A from Escherichia coli : Determination of the lipoic acid-binding site

This research was originally published in Journal of Biological Chemistry. Kazuko Fujiwara, Sachiko Toma, Kazuko Okamura-Ikeda, Yutaro Motokawa, Atsushi Nakagawa and Hisaaki Taniguchi. Crystal structure of lipoate-protein ligase A from Escherichia coli : Determination of the lipoic acid-binding site. Journal of Biological Chemistry. 2005; 280, 33645-33651. © the American Society for Biochemistry and Molecular Biology

Structural mechanism and photoprotective function of water-soluble chlorophyll-binding protein

This research was originally published in Journal of Biological Chemistry. Daisuke Horigome, Hiroyuki Satoh, Nobue Itoh, Katsuyoshi Mitsunaga, Isao Oonishi, Atsushi Nakagawa and Akira Uchida. Structural mechanism and photoprotective function of water-soluble chlorophyll-binding protein. Journal of Biological Chemistry. 2007; 282, 6525-6531. © the American Society for Biochemistry and Molecular Biology

The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA

This research was originally published in Journal of Biological Chemistry. Ahmet Can Berkyurek, Isao Suetake, Kyohei Arita, Kohei Takeshita, Atsushi Nakagawa, Masahiro Shirakawa and Shoji Tajima. The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA. Journal of Biological Chemistry. 2014; 289, 379-386. © the American Society for Biochemistry and Molecular Biology

Crystal structure of the membrane fusion protein, MexA, of the multidrug transporter in Pseudomonas aeruginosa

This research was originally published in Journal of Biological Chemistry. Hiroyuki Akama, Takanori Matsuura, Sachiko Kashiwagi, Hiroshi Yoneyama, Shin-ichiro Narita, Tomitake Tsukihara, Atsushi Nakagawa and Taiji Nakae. Crystal structure of the membrane fusion protein, MexA, of the multidrug transporter in Pseudomonas aeruginosa. Journal of Biological Chemistry. 2004; 279, 25939-25942. © the American Society for Biochemistry and Molecular Biology

Structural basis for the membrane association of ankyrinG via palmitoylation

Fujiwara, Y., Kondo, H., Shirota, M. et al. Structural basis for the membrane association of ankyrinG via palmitoylation. Sci Rep 6, 23981 (2016) doi:10.1038/srep2398

Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata : Implications of domain structure for its membrane pore-formation mechanism

CEL-III is a Ca^＋ -dependent and galactose-specific lectin purified from the sea cucumber, Cucumaria echinata, which exhibits hemolytic and hemagglutinating activities. Six molecules of CEL-III are assumed to oligomerize to form an ion-permeable pore in the cell membrane. We have determined the crystal structure of CEL-III by using single isomorphous replacement aided by anomalous scattering in lead at 1.7 Å resolution. CEL-III consists of three distinct domains as follows: the N-terminal two carbohydrate-binding domains (1 and 2), which adopt β-trefoil folds such as the B-chain of ricin and are members of the (QXW)_3 motif family; and domain 3, which is a novel fold composed of two α-helices and one β-sandwich. CEL-III is the first Ca^ -dependent lectin structure with two β-trefoil folds. Despite sharing the structure of the B-chain of ricin, CEL-III binds five Ca^ ions at five of the six subdomains in both domains 1 and 2. Considering the relatively high similarity among the five subdomains, they are putative binding sites for galactose-related carbohydrates, although it remains to be elucidated whether bound Ca^ is directly involved in interaction with carbohydrates. The paucity of hydrophobic interactions in the interfaces between the domains and biochemical data suggest that these domains rearrange upon carbohydrate binding in the erythrocyte membrane. This conformational change may be responsible for oligomerization of CEL-III molecules and hemolysis in the erythrocyte membranes.This research was originally published in Journal of Biological Chemistry. Tatsuya Uchida, Takayuki Yamasaki, Seiichiro Eto, Hajime Sugawara, Genji Kurisu, Atsushi Nakagawa, Masami Kusunoki and Tomomitsu Hatakeyama. Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata : Implications of domain structure for its membrane pore-formation mechanism. Journal of Biological Chemistry. 2004; 279, 37133-37141. © the American Society for Biochemistry and Molecular Biology