Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3 (2009)
Tsuda, Kengo, Kuwasako, Kanako, Takahashi, Mari, Someya, Tatsuhiko, Inoue, Makoto, Terada, Takaho, ...
The CUG-binding protein 1 (CUG-BP1) is a member of the CUG-BP1 and ETR-like factors (CELF) family or the Bruno-like family and is involved in the control of splicing, translation and mRNA...
Nagata, Takashi, Suzuki, Sakura, Endo, Ryuta, Shirouzu, Mikako, Terada, Takaho, Inoue, Makoto, ...
The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3′...
Crystal structure of the human receptor activity-modifying protein 1 extracellular domain (2008)
Kusano, Seisuke, Kukimoto-Niino, Mutsuko, Akasaka, Ryogo, Toyama, Mitsutoshi, Terada, Takaho, Shirouzu, Mikako, ...
Receptor activity-modifying protein (RAMP) 1 forms a heterodimer with calcitonin receptor-like receptor (CRLR) and regulates its transport to the cell surface. The CRLR·RAMP1 heterodimer functions...
Nomura, Takaomi, Nakatsuchi, Masato, Sugita, Daiyu, Nomura, Mamoru, Kaminishi, Tatsuya, Takemoto, Chie, ...
The stalk protein L12 is the only multiple component in 50S ribosomal subunit. In Escherichia coli, two L12 dimers bind to the C-terminal domain of L10 to form a pentameric complex, L10[(L12)2]2,...
Ohnishi, Satoshi, Tochio, Naoya, Tomizawa, Tadashi, Akasaka, Ryogo, Harada, Takushi, Seki, Eiko, ...
The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a β-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW...
Solution structure of the zinc finger HIT domain in protein FON (2007)
He, Fahu, Umehara, Takashi, Tsuda, Kengo, Inoue, Makoto, Kigawa, Takanori, Matsuda, Takayoshi, ...
The zinc finger HIT domain is a sequence motif found in many proteins, including thyroid hormone receptor interacting protein 3 (TRIP-3), which is possibly involved in maturity-onset diabetes of the...
Solution structure of the general transcription factor 2I domain in mouse TFII-I protein (2007)
Doi-Katayama, Yukiko, Hayashi, Fumiaki, Inoue, Makoto, Yabuki, Takashi, Aoki, Masaaki, Seki, Eiko, ...
The general transcription factor TFII-I, with the corresponding gene name GTF2I, is an unusual transcriptional regulator that associates with both basal and signal-induced transcription factors....
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Konno, Takayuki, Hanawa-Suetsugu, Kyoko, Lee, SungGa, ...
Transfer-messenger RNA (tmRNA) plays a dual role as a tRNA and an mRNA in trans-translation, during which the ribosome replaces mRNA with tmRNA encoding the tag-peptide. These processes have been...
Connell, Sean R., Takemoto, Chie, Wilson, Daniel N., Wang, Hongfei, Murayama, Kazutaka, Terada, Takaho, ...
Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S•EF-G ribosomal complex at 7.3 Å resolution and the crystal structure of...
The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli (2007)
Dong, Xuesong, Kato-Murayama, Miyuki, Muramatsu, Tomonari, Mori, Hirotada, Shirouzu, Mikako, Bessho, Yoshitaka, ...
Leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase) is an N-end rule pathway enzyme, which catalyzes the transfer of Leu and Phe from aminoacyl-tRNAs to exposed N-terminal Arg or Lys...
The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli (2007)
Dong, Xuesong, Kato-Murayama, Miyuki, Muramatsu, Tomonari, Mori, Hirotada, Shirouzu, Mikako, Bessho, Yoshitaka, ...
Leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase) is an N-end rule pathway enzyme, which catalyzes the transfer of Leu and Phe from aminoacyl-tRNAs to exposed N-terminal Arg or Lys...
ThermusthermophilustmRNA andtranstranslation (2007)
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Shirouzu, Mikako, Yokoyama, Shigeyuki, Muto, Akira, ...
In transtranslation, ribosome switches the template for protein synthesis from an mRNA to tmRNA. The molecular mechanism of transtranslation remains mysterious. In order to clarify how tmRNA move...
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Konno, Takayuki, Hanawa-Suetsugu, Kyoko, Lee, SungGa, ...
Transfer-messenger RNA (tmRNA) plays a dual role as a tRNA and an mRNA in trans-translation, during which the ribosome replaces mRNA with tmRNA encoding the tag-peptide. These processes have been...
The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli (2007)
Dong, Xuesong, Kato-Murayama, Miyuki, Muramatsu, Tomonari, Mori, Hirotada, Shirouzu, Mikako, Bessho, Yoshitaka, ...
Leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase) is an N-end rule pathway enzyme, which catalyzes the transfer of Leu and Phe from aminoacyl-tRNAs to exposed N-terminal Arg or Lys...
Frank Schluenzen, Chie Takemoto, Daniel N Wilson, Tatsuya Kaminishi, Joerg M Harms, Kyoko Hanawa-Suetsugu, ...
Schluenzen, Frank, Takemoto, Chie, Wilson, Daniel N, Kaminishi, Tatsuya, Harms, Joerg M ., Hanawa-Suetsugu, Kyoko, ...
Kasugamycin (Ksg) specifically inhibits translation initiation of canonical but not of leaderless messenger RNAs. Ksg inhibition is thought to occur by direct competition with initiator transfer RNA....
Solution structure of the antifreeze-like domain of human sialic acid synthase (2006)
Hamada, Toshiyuki, Ito, Yoko, Abe, Takamasa, Hayashi, Fumiaki, Güntert, Peter, Inoue, Makoto, ...
The structure of the C-terminal antifreeze-like (AFL) domain of human sialic acid synthase was determined by NMR spectroscopy. The structure comprises one - and two single-turn 310-helices and two...
Ito, Kaori, Arai, Ryoichi, Fusatomi, Emiko, Kamo-Uchikubo, Tomomi, Kawaguchi, Shin-Ichi, Akasaka, Ryogo, ...
TTHA0727 is a conserved hypothetical protein from Thermus thermophilus HB8, with a molecular mass of 12.6 kDa. TTHA0727 belongs to the carboxymuconolactone decarboxylase (CMD) family (Pfam 02627). A...
Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3 (2006)
Arai, Ryoichi, Kukimoto-Niino, Mutsuko, Kuroishi, Chizu, Bessho, Yoshitaka, Shirouzu, Mikako, Yokoyama, Shigeyuki
PH0459, from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, is a probable haloacid dehalogenase with a molecular mass of 26,725 Da. Here, we report the 2.0 Å crystal structure of PH0459...
Solution structure of the antifreeze-like domain of human sialic acid synthase (2006)
Hamada, Toshiyuki, Ito, Yoko, Abe, Takamasa, Hayashi, Fumiaki, Güntert, Peter, Inoue, Makoto, ...
The structure of the C-terminal antifreeze-like (AFL) domain of human sialic acid synthase was determined by NMR spectroscopy. The structure comprises one α- and two single-turn 310-helices and two...
Ito, Kaori, Arai, Ryoichi, Fusatomi, Emiko, Kamo-Uchikubo, Tomomi, Kawaguchi, Shin-ichi, Akasaka, Ryogo, ...
TTHA0727 is a conserved hypothetical protein from Thermus thermophilus HB8, with a molecular mass of 12.6 kDa. TTHA0727 belongs to the carboxymuconolactone decarboxylase (CMD) family (Pfam 02627). A...
Tochio, Naoya, Koshiba, Seizo, Kobayashi, Naohiro, Inoue, Makoto, Yabuki, Takashi, Aoki, Masaaki, ...
Microtubule-associated protein/microtubule affinity-regulating kinases (MARKs)/PAR-1 are common regulators of cell polarity that are conserved from nematode to human. All of these kinases have a...
Solution structure of the antifreeze-like domain of human sialic acid synthase (2006)
Hamada, Toshiyuki, Ito, Yoko, Abe, Takamasa, Hayashi, Fumiaki, Güntert, Peter, Inoue, Makoto, ...
The structure of the C-terminal antifreeze-like (AFL) domain of human sialic acid synthase was determined by NMR spectroscopy. The structure comprises one - and two single-turn 310-helices and two...
Ito, Kaori, Arai, Ryoichi, Fusatomi, Emiko, Kamo-Uchikubo, Tomomi, Kawaguchi, Shin-Ichi, Akasaka, Ryogo, ...
TTHA0727 is a conserved hypothetical protein from Thermus thermophilus HB8, with a molecular mass of 12.6 kDa. TTHA0727 belongs to the carboxymuconolactone decarboxylase (CMD) family (Pfam 02627). A...
Adaptation of intronic homing endonuclease for successful horizontal transmission (2005)
Kurokawa, Sayuri, Bessho, Yoshitaka, Higashijima, Kyoko, Shirouzu, Mikako, Yokohama, Shigeyuki, Watanabe, Kazuo I., ...
Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8 (2005)
Handa, Noriko, Terada, Takaho, Doi-Katayama, Yukiko, Hirota, Hiroshi, Tame, Jeremy R.H., Park, Sam-Yong, ...
The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the...
Solution structure of the PWWP domain of the hepatoma-derived growth factor family (2005)
Nameki, Nobukazu, Tochio, Naoya, Koshiba, Seizo, Inoue, Makoto, Yabuki, Takashi, Aoki, Masaaki, ...
Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF...
Kukimoto-Niino, Mutsuko, Shibata, Rie, Murayama, Kazutaka, Hamana, Hiroaki, Nishimoto, Madoka, Bessho, Yoshitaka, ...
TT1426, from Thermus thermophilus HB8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (PRTase) domain, as revealed by a Pfam database search. The 2.01 Å crystal...
Functional analysis of factors involved in trans-translation (2005)
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Konno, Takayuki, Matsuta, Noriko, Kurita, Daisuke, ...
trans-translation is a rescue system for stalled ribosomes to terminate the translation for recycling of ribosome and lead the incomplete protein on the stalled ribosome to degradation. In...
Pantoja-Uceda, David, López-Méndez, Blanca, Koshiba, Seizo, Inoue, Makoto, Kigawa, Takanori, Terada, Takaho, ...
The three-dimensional structure of the rhodanese homology domain At4g01050(175–195) from Arabidopsis thaliana has been determined by solution nuclear magnetic resonance methods based on 3043 upper...
Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 A resolution (2005)
Arai, Ryoichi, Kukimoto-Niino, Mutsuko, Uda-Tochio, Hiroko, Morita, Satoshi, Uchikubo-Kamo, Tomomi, Akasaka, Ryogo, ...
The enhancer of rudimentary gene, e(r), of Drosophila melanogaster encodes an enhancer of rudimentary (ER) protein with functions implicated in pyrimidine biosynthesis and the cell cycle. The ER...
Interaction Analysis between tmRNA and SmpB from Thermus thermophilus (2005)
Nameki, Nobukazu, Someya, Tatsuhiko, Okano, Satoshi, Suemasa, Reiko, Kimoto, Michiko, Hanawa-Suetsugu, Kyoko, ...
Small protein B, SmpB, is a tmRNA-specific binding protein essential for trans-translation. We examined the interaction between SmpB and tmRNA from Thermus thermophilus, using biochemical and NMR...
Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8 (2005)
Handa, Noriko, Terada, Takaho, Doi-Katayama, Yukiko, Hirota, Hiroshi, Tame, Jeremy R.H., Park, Sam-Yong, ...
The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the...
Kukimoto-Niino, Mutsuko, Shibata, Rie, Murayama, Kazutaka, Hamana, Hiroaki, Nishimoto, Madoka, Bessho, Yoshitaka, ...
TT1426, from Thermus thermophilus HB8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (PRTase) domain, as revealed by a Pfam database search. The 2.01 Å crystal...
Solution structure of the PWWP domain of the hepatoma-derived growth factor family (2005)
Nameki, Nobukazu, Tochio, Naoya, Koshiba, Seizo, Inoue, Makoto, Yabuki, Takashi, Aoki, Masaaki, ...
Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF...
Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 A resolution (2005)
Arai, Ryoichi, Kukimoto-Niino, Mutsuko, Uda-Tochio, Hiroko, Morita, Satoshi, Uchikubo-Kamo, Tomomi, Akasaka, Ryogo, ...
The enhancer of rudimentary gene, e(r), of Drosophila melanogaster encodes an enhancer of rudimentary protein with functions implicated in pyrimidine biosynthesis and the cell cycle. The ER homolog...
Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3 (2005)
Arai, Ryoichi, Kukimoto-Niino, Mutsuko, Kuroishi, Chizu, Bessho, Yoshitaka, Shirouzu, Mikako, Yokoyama, Shigeyuki
PH0459, from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, is a probable haloacid dehalogenase with a molecular mass of 26,725 Da. Here, we report the 2.0 Å crystal structure of PH0459...
Solution structure of a BolA-like protein from Mus musculus (2004)
Kasai, Takuma, Inoue, Makoto, Koshiba, Seizo, Yabuki, Takashi, Aoki, Masaaki, Nunokawa, Emi, ...
The BolA-like proteins are widely conserved from prokaryotes to eukaryotes. The BolA-like proteins seem to be involved in cell proliferation or cell-cycle regulation, but the molecular function is...
Solution structure of the RWD domain of the mouse GCN2 protein (2004)
Nameki, Nobukazu, Yoneyama, Misao, Koshiba, Seizo, Tochio, Naoya, Inoue, Makoto, Seki, Eiko, ...
GCN2 is the &agr;-subunit of the only translation initiation factor (eIF2&agr;) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus,...
Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8 (2004)
Wang, Hongfei, Takemoto, Chie Hori, Murayama, Kazutaka, Sakai, Hiroaki, Tatsuguchi, Ayako, Terada, Takaho, ...
Ribosomal protein L27 is located near the peptidyltransferase center at the interface of ribosomal subunits, and is important for ribosomal assembly and function. We report the crystal structure of...
Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8 (2004)
Kukimoto-Niino, Mutsuko, Murayama, Kazutaka, Kato-Murayama, Miyuki, Idaka, Miki, Bessho, Yoshitaka, Tatsuguchi, Ayako, ...
TT1887 and TT1465 from Thermus thermophilus HB8 are conserved hypothetical proteins, and are annotated as possible lysine decarboxylases in the Pfam database. Here we report the crystal structures of...
Establishment of Stable hFis1 Knockdown Cells with an siRNA Expression Vector (2004)
Arai, Ryoichi, Ito, Kaori, Wakiyama, Motoaki, Matsumoto, Eiko, Sakamoto, Ayako, Etou, Yuuka, ...
Yeast Fis1p participates in mitochondrial fission, together with Dnm1p and Mdv1p. Recently, human Fis1 (hFis1) was reported to be involved in mitochondrial fission, together with Drp1. We established...
Solution structure of a BolA-like protein from Mus musculus (2004)
KASAI, TAKUMA, INOUE, MAKOTO, KOSHIBA, SEIZO, YABUKI, TAKASHI, AOKI, MASAAKI, NUNOKAWA, EMI, ...
The BolA-like proteins are widely conserved from prokaryotes to eukaryotes. The BolA-like proteins seem to be involved in cell proliferation or cell-cycle regulation, but the molecular function is...
Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8 (2004)
Kukimoto-Niino, Mutsuko, Murayama, Kazutaka, Kato-Murayama, Miyuki, Idaka, Miki, Bessho, Yoshitaka, Tatsuguchi, Ayako, ...
TT1887 and TT1465 from Thermus thermophilus HB8 are conserved hypothetical proteins, and are annotated as possible lysine decarboxylases in the Pfam database. Here we report the crystal structures of...
Pantoja-Uceda, David, López-Méndez, Blanca, Koshiba, Seizo, Inoue, Makoto, Kigawa, Takanori, Terada, Takaho, ...
The three-dimensional structure of the rhodanese homology domain At4g01050(175–195) from Arabidopsis thaliana has been determined by solution nuclear magnetic resonance methods based on 3043 upper...
Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8 (2004)
Wang, Hongfei, Takemoto, Chie Hori, Murayama, Kazutaka, Sakai, Hiroaki, Tatsuguchi, Ayako, Terada, Takaho, ...
Ribosomal protein L27 is located near the peptidyltransferase center at the interface of ribosomal subunits, and is important for ribosomal assembly and function. We report the crystal structure of...
Access the most recent version at doi: 10.1110/ps.g03104003 References (2003)
Motonori Ota, Haruki Nakamura, Seiki Kuramitsu, Mikako Shirouzu, Shigeyuki Yokoyama, Email Alerting
Crystal structure of the conserved protein TT1542 from thermophilus
In vitro analysis of the initial steps of trans-translation (2003)
Takada, Kazuma, Hori-Takemoto, Chie, Kawazoe, Masahito, Lee, SungGa, Shirouzu, Mikako, Yokoyama, Shigeyuki, ...
tmRNA has a dual function both as tRNA and mRNA and facilitates trans-translation. We observed the tagging derived from tmRNA from Bacillus subtilis in vivo and in vitro. Our studies give progressive...
Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8 (2003)
Handa, Noriko, Terada, Takaho, Kamewari, Yuki, Hamana, Hiroaki, Tame, Jeremy R.H., Park, Sam-Yong, ...
The TT1542 protein from Thermus thermophilus HB8 is annotated as a conserved hypothetical protein, and belongs to the DUF158 family in the Pfam database. A BLAST search revealed that homologs of...
Structural basis of replication origin recognition by the DnaA protein (2003)
Fujikawa, Norie, Kurumizaka, Hitoshi, Nureki, Osamu, Terada, Takaho, Shirouzu, Mikako, Katayama, Tsutomu, ...
Escherichia coli DnaA binds to 9 bp sequences (DnaA boxes) in the replication origin, oriC, to form a complex initiating chromosomal DNA replication. In the present study, we determined the crystal...
In vitro analysis of the initial steps of trans-translation (2003)
Takada, Kazuma, Hori-Takemoto, Chie, Kawazoe, Masahito, Lee, SungGa, Shirouzu, Mikako, Yokoyama, Shigeyuki, ...
Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells (2002)
Sakamoto, Kensaku, Hayashi, Akiko, Sakamoto, Ayako, Kiga, Daisuke, Nakayama, Hiroshi, Soma, Akiko, ...
A suppressor tRNATyr and mutant tyrosyl‐tRNA synthetase (TyrRS) pair was developed to incorporate 3‐iodo‐l‐tyrosine into proteins in mammalian cells. First, the Escherichia coli...
Kitanaka, Chifumi, Kato, Keisuke, Ijiri, Rieko, Sakurada, Kaori, Tomiyama, Arata, Noguchi, Kohji, ...
Background: Neuroblastoma undergoes spontaneous regression frequently during its natural course. Although programmed cell death (PCD) has been implicated in this process, accumulating evidence...
Ito, Nobutoshi, Nureki, Osamu, Shirouzu, Mikako, Yokoyama, Shigeyuki, Hanaoka, Fumio
At the initiation of chromosomal DNA replication, DNA primases synthesize short RNA primers, which are subsequently elongated by DNA polymerases. To understand the structural basis for the primer...
Kukimoto, Mutsuko, Nureki, Osamu, Shirouzu, Mikako, Katada, Toshiaki, Hirabayashi, Yoshio, Sugiya, Hiroshi, ...
The cell surface antigen CD38 is a multifunctional ectoenzyme that acts as an NAD+ glycohydrolase, an ADP-ribosyl cyclase, and also a cyclic ADP-ribose hydrolase. The extracellular catalytic...
Kiga, Daisuke, Sakamoto, Kensaku, Kodama, Koichiro, Kigawa, Takanori, Matsuda, Takayoshi, Yabuki, Takashi, ...
Tyrosyl–tRNA synthetase (TyrRS) from Escherichia coli was engineered to preferentially recognize 3-iodo-l-tyrosine rather than l-tyrosine for the site-specific incorporation of 3-iodo-l-tyrosine...
Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells
Sakamoto, Kensaku, Hayashi, Akiko, Sakamoto, Ayako, Kiga, Daisuke, Nakayama, Hiroshi, Soma, Akiko, ...
A suppressor tRNATyr and mutant tyrosyl-tRNA synthetase (TyrRS) pair was developed to incorporate 3-iodo-l-tyrosine into proteins in mammalian cells. First, the Escherichia coli suppressor tRNATyr...
Structural basis of replication origin recognition by the DnaA protein
Fujikawa, Norie, Kurumizaka, Hitoshi, Nureki, Osamu, Terada, Takaho, Shirouzu, Mikako, Katayama, Tsutomu, ...
Escherichia coli DnaA binds to 9 bp sequences (DnaA boxes) in the replication origin, oriC, to form a complex initiating chromosomal DNA replication. In the present study, we determined the crystal...
Crystal structure of elongation factor P from Thermus thermophilus HB8
Hanawa-Suetsugu, Kyoko, Sekine, Shun-ichi, Sakai, Hiroaki, Hori-Takemoto, Chie, Terada, Takaho, Unzai, Satoru, ...
Translation elongation factor P (EF-P) stimulates ribosomal peptidyltransferase activity. EF-P is conserved in bacteria and is essential for cell viability. Eukarya and Archaea have an EF-P...
Yamasaki, Kazuhiko, Kigawa, Takanori, Inoue, Makoto, Tateno, Masaru, Yamasaki, Tomoko, Yabuki, Takashi, ...
The B3 DNA binding domain is shared amongst various plant-specific transcription factors, including factors involved in auxin-regulated and abscisic acid–regulated transcription. Herein, we report...
Solution Structure of an Arabidopsis WRKY DNA Binding DomainW⃞
Yamasaki, Kazuhiko, Kigawa, Takanori, Inoue, Makoto, Tateno, Masaru, Yamasaki, Tomoko, Yabuki, Takashi, ...
The WRKY proteins comprise a major family of transcription factors that are essential in pathogen and salicylic acid responses of higher plants as well as a variety of plant-specific reactions. They...
Hatakeyama, Mariko, Kimura, Shuhei, Naka, Takashi, Kawasaki, Takuji, Yumoto, Noriko, Ichikawa, Mio, ...
ErbB tyrosine kinase receptors mediate mitogenic signal cascade by binding a variety of ligands and recruiting the different cassettes of adaptor proteins. In the present study, we examined heregulin...
Kiga, Daisuke, Sakamoto, Kensaku, Kodama, Koichiro, Kigawa, Takanori, Matsuda, Takayoshi, Yabuki, Takashi, ...
Tyrosyl–tRNA synthetase (TyrRS) from Escherichia coli was engineered to preferentially recognize 3-iodo-l-tyrosine rather than l-tyrosine for the site-specific incorporation of 3-iodo-l-tyrosine...
Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells
Sakamoto, Kensaku, Hayashi, Akiko, Sakamoto, Ayako, Kiga, Daisuke, Nakayama, Hiroshi, Soma, Akiko, ...
A suppressor tRNATyr and mutant tyrosyl-tRNA synthetase (TyrRS) pair was developed to incorporate 3-iodo-l-tyrosine into proteins in mammalian cells. First, the Escherichia coli suppressor tRNATyr...
Structural basis of replication origin recognition by the DnaA protein
Fujikawa, Norie, Kurumizaka, Hitoshi, Nureki, Osamu, Terada, Takaho, Shirouzu, Mikako, Katayama, Tsutomu, ...
Escherichia coli DnaA binds to 9 bp sequences (DnaA boxes) in the replication origin, oriC, to form a complex initiating chromosomal DNA replication. In the present study, we determined the crystal...
Crystal structure of elongation factor P from Thermus thermophilus HB8
Hanawa-Suetsugu, Kyoko, Sekine, Shun-ichi, Sakai, Hiroaki, Hori-Takemoto, Chie, Terada, Takaho, Unzai, Satoru, ...
Translation elongation factor P (EF-P) stimulates ribosomal peptidyltransferase activity. EF-P is conserved in bacteria and is essential for cell viability. Eukarya and Archaea have an EF-P...
Yamasaki, Kazuhiko, Kigawa, Takanori, Inoue, Makoto, Tateno, Masaru, Yamasaki, Tomoko, Yabuki, Takashi, ...
The B3 DNA binding domain is shared amongst various plant-specific transcription factors, including factors involved in auxin-regulated and abscisic acid–regulated transcription. Herein, we report...
Solution Structure of an Arabidopsis WRKY DNA Binding DomainW⃞
Yamasaki, Kazuhiko, Kigawa, Takanori, Inoue, Makoto, Tateno, Masaru, Yamasaki, Tomoko, Yabuki, Takashi, ...
The WRKY proteins comprise a major family of transcription factors that are essential in pathogen and salicylic acid responses of higher plants as well as a variety of plant-specific reactions. They...
Hatakeyama, Mariko, Kimura, Shuhei, Naka, Takashi, Kawasaki, Takuji, Yumoto, Noriko, Ichikawa, Mio, ...
ErbB tyrosine kinase receptors mediate mitogenic signal cascade by binding a variety of ligands and recruiting the different cassettes of adaptor proteins. In the present study, we examined heregulin...
Sasaki, Hiroshi M., Sekine, Shun-ichi, Sengoku, Toru, Fukunaga, Ryuya, Hattori, Motoyuki, Utsunomiya, Yukiko, ...
To achieve accurate aminoacylation of tRNAs with their cognate amino acids, errors in aminoacylation are corrected by the “editing” mechanism in several aminoacyl-tRNA synthetases....
Murayama, Kazutaka, Kato-Murayama, Miyuki, Katsura, Kazushige, Uchikubo-Kamo, Tomomi, Yamaguchi-Hirafuji, Machiko, Kawazoe, Masahito, ...
The three-dimensional structure of the APE2540 protein from A. pernix K1 has been determined by the multiple anomalous dispersion method at 1.7 Å resolution. The structure includes two monomers in...
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Konno, Takayuki, Hanawa-Suetsugu, Kyoko, Lee, SungGa, ...
Transfer-messenger RNA (tmRNA) plays a dual role as a tRNA and an mRNA in trans-translation, during which the ribosome replaces mRNA with tmRNA encoding the tag-peptide. These processes have been...
Pioszak, Augen A., Murayama, Kazutaka, Nakagawa, Noriko, Ebihara, Akio, Kuramitsu, Seiki, Shirouzu, Mikako, ...
Three structures of a putative RNA 5-methyluridine methyltransferase from T. thermophilus, including its complex with S-adenosyl-l-homocysteine, are presented. The structures reveal the mode of...
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA
Bessho, Yoshitaka, Shibata, Rie, Sekine, Shun-ichi, Murayama, Kazutaka, Higashijima, Kyoko, Hori-Takemoto, Chie, ...
tmRNA and small protein B (SmpB) are essential trans-translation system components. In the present study, we determined the crystal structure of SmpB in complex with the entire tRNA domain of the...
Structural Characterization of the Ribosome Maturation Protein, RimM▿
Suzuki, Sakura, Tatsuguchi, Ayako, Matsumoto, Eiko, Kawazoe, Masahito, Kaminishi, Tatsuya, Shirouzu, Mikako, ...
The RimM protein has been implicated in the maturation of the 30S ribosomal subunit. It binds to ribosomal protein S19, located in the head domain of the 30S subunit. Multiple sequence alignments...
Inagaki, Eiji, Sakamoto, Keiko, Obayashi, Naomi, Terada, Takaho, Shirouzu, Mikako, Bessho, Yoshitaka, ...
Galactokinase from P. horikoshii has been crystallized in both the apo form and as a ternary complex with α-d-galactose and an ATP analogue. The crystals were characterized by X-ray diffraction. The...
Inagaki, Eiji, Sakamoto, Keiko, Obayashi, Naomi, Terada, Takaho, Shirouzu, Mikako, Bessho, Yoshitaka, ...
An erratum to the paper by Inagaki et al. [(2006), Acta Cryst. F62, 169–171].
The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli
Dong, Xuesong, Kato-Murayama, Miyuki, Muramatsu, Tomonari, Mori, Hirotada, Shirouzu, Mikako, Bessho, Yoshitaka, ...
Leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase) is an N-end rule pathway enzyme, which catalyzes the transfer of Leu and Phe from aminoacyl-tRNAs to exposed N-terminal Arg or Lys...
Tochio, Naoya, Koshiba, Seizo, Kobayashi, Naohiro, Inoue, Makoto, Yabuki, Takashi, Aoki, Masaaki, ...
Microtubule-associated protein/microtubule affinity-regulating kinases (MARKs)/PAR-1 are common regulators of cell polarity that are conserved from nematode to human. All of these kinases have a...
Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3
Arai, Ryoichi, Kukimoto-Niino, Mutsuko, Kuroishi, Chizu, Bessho, Yoshitaka, Shirouzu, Mikako, Yokoyama, Shigeyuki
PH0459, from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, is a probable haloacid dehalogenase with a molecular mass of 26,725 Da. Here, we report the 2.0 Å crystal structure of PH0459...
Solution structure of the antifreeze-like domain of human sialic acid synthase
Hamada, Toshiyuki, Ito, Yoko, Abe, Takamasa, Hayashi, Fumiaki, Güntert, Peter, Inoue, Makoto, ...
The structure of the C-terminal antifreeze-like (AFL) domain of human sialic acid synthase was determined by NMR spectroscopy. The structure comprises one α- and two single-turn 310-helices and two...
Ito, Kaori, Arai, Ryoichi, Fusatomi, Emiko, Kamo-Uchikubo, Tomomi, Kawaguchi, Shin-ichi, Akasaka, Ryogo, ...
TTHA0727 is a conserved hypothetical protein from Thermus thermophilus HB8, with a molecular mass of 12.6 kDa. TTHA0727 belongs to the carboxymuconolactone decarboxylase (CMD) family (Pfam 02627). A...
Topological Analysis of MAPK Cascade for Kinetic ErbB Signaling
Nakakuki, Takashi, Yumoto, Noriko, Naka, Takashi, Shirouzu, Mikako, Yokoyama, Shigeyuki, Hatakeyama, Mariko
Ligand-induced homo- and hetero-dimer formation of ErbB receptors results in different biological outcomes irrespective of recruitment and activation of similar effector proteins. Earlier...
Shinkai, Akeo, Ohbayashi, Naomi, Terada, Takaho, Shirouzu, Mikako, Kuramitsu, Seiki, Yokoyama, Shigeyuki
Thermus thermophilus σE, an extracytoplasmic function σ factor from the extremely thermophilic bacterium Thermus thermophilus HB8, bound to the RNA polymerase core enzyme and showed transcriptional...
Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7)
Arai, Ryoichi, Yoshikawa, Seiko, Murayama, Kazutaka, Imai, Yuzuru, Takahashi, Ryosuke, Shirouzu, Mikako, ...
The crystal structure of human UBE2G2/UBC7 was solved at 2.56 Å resolution. The superimposition of UBE2G2 on UbcH7 in a c-Cbl–UbcH7–ZAP70 ternary complex suggested that the two loop regions of...
Solution structure of the rhodanese homology domain At4g01050(175–295) from Arabidopsis thaliana
Pantoja-Uceda, David, López-Méndez, Blanca, Koshiba, Seizo, Inoue, Makoto, Kigawa, Takanori, Terada, Takaho, ...
The three-dimensional structure of the rhodanese homology domain At4g01050(175–195) from Arabidopsis thaliana has been determined by solution nuclear magnetic resonance methods based on 3043 upper...
Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Å resolution
Arai, Ryoichi, Kukimoto-Niino, Mutsuko, Uda-Tochio, Hiroko, Morita, Satoshi, Uchikubo-Kamo, Tomomi, Akasaka, Ryogo, ...
The enhancer of rudimentary gene, e(r), of Drosophila melanogaster encodes an enhancer of rudimentary (ER) protein with functions implicated in pyrimidine biosynthesis and the cell cycle. The ER...
Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8
Handa, Noriko, Terada, Takaho, Doi-Katayama, Yukiko, Hirota, Hiroshi, Tame, Jeremy R.H., Park, Sam-Yong, ...
The isoprenoid quinones exist widely among prokaryotes and eukaryotes. They play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. In the...
Solution structure of the PWWP domain of the hepatoma-derived growth factor family
Nameki, Nobukazu, Tochio, Naoya, Koshiba, Seizo, Inoue, Makoto, Yabuki, Takashi, Aoki, Masaaki, ...
Among the many PWWP-containing proteins, the largest group of homologous proteins is related to hepatoma-derived growth factor (HDGF). Within a well-conserved region at the extreme N-terminus, HDGF...
Kukimoto-Niino, Mutsuko, Shibata, Rie, Murayama, Kazutaka, Hamana, Hiroaki, Nishimoto, Madoka, Bessho, Yoshitaka, ...
TT1426, from Thermus thermophilus HB8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (PRTase) domain, as revealed by a Pfam database search. The 2.01 Å crystal...
Solution structure of the RWD domain of the mouse GCN2 protein
Nameki, Nobukazu, Yoneyama, Misao, Koshiba, Seizo, Tochio, Naoya, Inoue, Makoto, Seki, Eiko, ...
GCN2 is the α-subunit of the only translation initiation factor (eIF2α) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which...
Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8
Wang, Hongfei, Takemoto, Chie Hori, Murayama, Kazutaka, Sakai, Hiroaki, Tatsuguchi, Ayako, Terada, Takaho, ...
Ribosomal protein L27 is located near the peptidyltransferase center at the interface of ribosomal subunits, and is important for ribosomal assembly and function. We report the crystal structure of...
Crystal structures of possible lysine decarboxylases from Thermus thermophilus HB8
Kukimoto-Niino, Mutsuko, Murayama, Kazutaka, Kato-Murayama, Miyuki, Idaka, Miki, Bessho, Yoshitaka, Tatsuguchi, Ayako, ...
TT1887 and TT1465 from Thermus thermophilus HB8 are conserved hypothetical proteins, and are annotated as possible lysine decarboxylases in the Pfam database. Here we report the crystal structures of...
Solution structure of a BolA-like protein from Mus musculus
Kasai, Takuma, Inoue, Makoto, Koshiba, Seizo, Yabuki, Takashi, Aoki, Masaaki, Nunokawa, Emi, ...
The BolA-like proteins are widely conserved from prokaryotes to eukaryotes. The BolA-like proteins seem to be involved in cell proliferation or cell-cycle regulation, but the molecular function is...
Dictyostelium IQGAP-related Protein Specifically Involved in the Completion of Cytokinesis
Adachi, Hiroyuki, Takahashi, Yasuhiro, Hasebe, Takeshi, Shirouzu, Mikako, Yokoyama, Shigeyuki, Sutoh, Kazuo
The gapA gene encoding a novel RasGTPase-activating protein (RasGAP)–related protein was found to be disrupted in a cytokinesis mutant of Dictyostelium that grows as giant and multinucleate cells...
Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8
Handa, Noriko, Terada, Takaho, Kamewari, Yuki, Hamana, Hiroaki, Tame, Jeremy R.H., Park, Sam-Yong, ...
The TT1542 protein from Thermus thermophilus HB8 is annotated as a conserved hypothetical protein, and belongs to the DUF158 family in the Pfam database. A BLAST search revealed that homologs of...
Solution structure of the general transcription factor 2I domain in mouse TFII-I protein
Doi-Katayama, Yukiko, Hayashi, Fumiaki, Inoue, Makoto, Yabuki, Takashi, Aoki, Masaaki, Seki, Eiko, ...
The general transcription factor TFII-I, with the corresponding gene name GTF2I, is an unusual transcriptional regulator that associates with both basal and signal-induced transcription factors....
Solution structure of the zinc finger HIT domain in protein FON
He, Fahu, Umehara, Takashi, Tsuda, Kengo, Inoue, Makoto, Kigawa, Takanori, Matsuda, Takayoshi, ...
The zinc finger HIT domain is a sequence motif found in many proteins, including thyroid hormone receptor interacting protein 3 (TRIP-3), which is possibly involved in maturity-onset diabetes of the...
Nagata, Takashi, Suzuki, Sakura, Endo, Ryuta, Shirouzu, Mikako, Terada, Takaho, Inoue, Makoto, ...
The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3′...
Ion binding and selectivity of the rotor ring of the Na+-transporting V-ATPase
Murata, Takeshi, Yamato, Ichiro, Kakinuma, Yoshimi, Shirouzu, Mikako, Walker, John E., Yokoyama, Shigeyuki, ...
The vacuole-type ATPases (V-ATPases) are proton pumps in various intracellular compartments of eukaryotic cells. Prokaryotic V-ATPase of Enterococcus hirae, closely related to the eukaryotic enzymes,...
Tanaka, Hiroaki, Umehara, Takashi, Inaka, Koji, Takahashi, Sachiko, Shibata, Rie, Bessho, Yoshitaka, ...
Crystallization of the transcription termination factor NusA under microgravity conditions significantly reduced the twinning content (1.0%) compared with terrestrially grown crystals (18.3%) and...
Structure of a UPF0150-family protein from Thermus thermophilus HB8
Okazaki, Nobuo, Kumei, Maki, Manzoku, Miho, Kuramitsu, Seiki, Shirouzu, Mikako, Shinkai, Akeo, ...
The crystal structure of the hypothetical protein TTHA0281 from T. thermophilus HB8 has been determined at 1.9 Å resolution. The TTHA0281 protein forms a homotetramer in which each monomer adopts...
Ohnishi, Satoshi, Tochio, Naoya, Tomizawa, Tadashi, Akasaka, Ryogo, Harada, Takushi, Seki, Eiko, ...
The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a β-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW...
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3
Tsuda, Kengo, Kuwasako, Kanako, Takahashi, Mari, Someya, Tatsuhiko, Inoue, Makoto, Terada, Takaho, ...
The CUG-binding protein 1 (CUG-BP1) is a member of the CUG-BP1 and ETR-like factors (CELF) family or the Bruno-like family and is involved in the control of splicing, translation and mRNA...
Kawashima, Toshiyuki, Bao, Ying Chun, Minoshima, Yukinori, Nomura, Yasushi, Hatori, Tomonori, Hori, Tetsuya, ...
In addition to their pleiotropic functions under physiological conditions, transcription factors STAT3 and STAT5 also have oncogenic activities, but how activated STATs are transported to the nucleus...
Nishimura, Mitsuhiro, Kaminishi, Tatsuya, Kawazoe, Masahito, Shirouzu, Mikako, Takemoto, Chie, Yokoyama, Shigeyuki, ...
A truncated variant of human ribosomal protien L10 was prepared and crystallized. Diffraction data were collected to 2.5 Å resolution.
Crystal structure of the human receptor activity-modifying protein 1 extracellular domain
Kusano, Seisuke, Kukimoto-Niino, Mutsuko, Akasaka, Ryogo, Toyama, Mitsutoshi, Terada, Takaho, Shirouzu, Mikako, ...
Receptor activity-modifying protein (RAMP) 1 forms a heterodimer with calcitonin receptor-like receptor (CRLR) and regulates its transport to the cell surface. The CRLR·RAMP1 heterodimer functions...
Structure of the minimized α/β-hydrolase fold protein from Thermus thermophilus HB8
Xie, Yong, Takemoto, Chie, Kishishita, Seiichiro, Uchikubo-Kamo, Tomomi, Murayama, Kazutaka, Chen, Lirong, ...
The crystal structure of the minimized α/β-hydrolase fold protein encoded by the gene TTHA1544 from T. thermophilus HB8 has been determined at 2.0 Å resolution.
Solution structure of the RNA binding domain in the human muscleblind-like protein 2
He, Fahu, Dang, Weirong, Abe, Chikage, Tsuda, Kengo, Inoue, Makoto, Watanabe, Satoru, ...
The muscleblind-like (MBNL) proteins 1, 2, and 3, which contain four CCCH zinc finger motifs (ZF1–4), are involved in the differentiation of muscle inclusion by controlling the splicing patterns of...