Jeyaraman Jeyakanthan, Katsumi Takada, Masahide Sawano, Kyoko Ogasahara, Hisashi Mizutani, Naoki Kunishima, ...
The crystal structure of a putative dipeptidase (Phdpd) from Pyrococcus horikoshii OT3 was solved using X-ray data at 2.4 Å resolution. The protein is folded into two distinct entities....
Kanai, Akio, Sato, Asako, Fukuda, Yoko, Okada, Kiyoshi, Matsuda, Takashi, Sakamoto, Taiichi, ...
Using an expression protein library of a hyperthermophilic archaeon, Pyrococcus furiosus, we identified a gene (PF0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase...
Takimoto, Koji, Wakiyama, Motoaki, Yokoyama, Shigeyuki
In mammalian cells, microRNAs (miRNAs) are incorporated into miRNA-induced silencing complexes (miRISCs), which regulate protein expression post-transcriptionally through binding to 3′-untranslated...
Jeyaraman Jeyakanthan, Katsumi Takada, Masahide Sawano, Kyoko Ogasahara, Hisashi Mizutani, Naoki Kunishima, ...
The crystal structure of a putative dipeptidase (Phdpd) from Pyrococcus horikoshii OT3 was solved using X-ray data at 2.4 Å resolution. The protein is folded into two distinct entities. The...
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...
Kumarevel, Thirumananseri, Tanaka, Tomoyuki, Umehara, Takashi, Yokoyama, Shigeyuki
ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global...
Kimoto, Michiko, Kawai, Rie, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
Toward the expansion of the genetic alphabet, we present an unnatural base pair system for efficient PCR amplification, enabling the site-specific incorporation of extra functional components into...
Kimoto, Michiko, Sato, Akira, Kawai, Rie, Yokoyama, Shigeyuki, Hirao, Ichiro
The creation of an extra, unnatural base pair that functions in replication, transcription, and translation, would provide a new system for the expansion of the genetic alphabet. In transcription, an...
Furukawa, Ayako, Nagata, Takashi, Matsugami, Akimasa, Habu, Yuichirou, Sugiyama, Ryuichi, Hayashi, Fumiaki, ...
Human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) is known to play a role in intrinsic cellular immunity against human immunodeficiency virus type 1 (HIV-1). The...
Haraguchi, Yuki, Kuwasako, Kanako, Muto, Yutaka, Bessho, Yoshitaka, Nishimoto, Madoka, Yokoyama, Shigeyuki, ...
SELEX is a conventional method to obtain high affinity nucleic acids to target molecules. In this study, high affinity RNA molecules against SRP19 protein were selected by using a randomized library....
Crystal structure of human selenocysteine tRNA (2009)
Itoh, Yuzuru, Chiba, Shiho, Sekine, Shun-ichi, Yokoyama, Shigeyuki
Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNASec) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNASec. tRNASec has a 9-bp...
Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, ...
Motivation: To resolve the high-dimensionality of the genetic network inference problem in the S-system model, a problem decomposition strategy has been proposed. While this strategy certainly shows...
Rangarajan, Sarani, Jeyakanthan, Jeyaraman, Palappetty, Mridula, Sakamoto, Keiko, Kitamura, Yoshiaki, Agari, Yoshihiro, ...
In view of the biological significance of understanding the ribosomal machinery of both prokaryotes and eukaryotes, the L30e ribosomal protein from Methanocaldococcus jannaschii was cloned,...
Rangarajan, Sarani, Jeyakanthan, Jeyaraman, Palappetty, Mridula, Sakamoto, Keiko, Kitamura, Yoshiaki, Agari, Yoshihiro, ...
In view of the biological significance of understanding the ribosomal machinery of both prokaryotes and eukaryotes, the L30e ribosomal protein from Methanocaldococcus jannaschii was cloned,...
l-Alanine hydrochloride monohydrate (2008)
Kazuhiko Yamada, Akira Sato, Tadashi Shimizu, Toshio Yamazaki, Shigeyuki Yokoyama
Colorless crystals of l-alanine hydrochloride monohydrate, C3H8NO2+·Cl−·H2O, were obtained from a powder sample that had been left standing in a refrigerator for a few years. The...
Hatayama, Minoru, Tomizawa, Tadashi, Sakai-Kato, Kumiko, Bouvagnet, Patrice, Kose, Shingo, Imamoto, Naoko, ...
Disruptions in ZIC3 cause heterotaxy, a congenital anomaly of the left–right axis. ZIC3 encodes a nuclear protein with a zinc finger (ZF) domain that contains five tandem C2H2 ZF motifs. Missense...
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′...
Kumarevel, Thirumananseri, Nakano, Noboru, Ponnuraj, Karthe, Gopinath, Subash C. B., Sakamoto, Keiko, Shinkai, Akeo, ...
Genome analyses have revealed that members of the Lrp/AsnC family of transcriptional regulators are widely distributed among prokaryotes, including both bacteria and archaea. These regulatory...
Hikiba, Juri, Hirota, Kouji, Kagawa, Wataru, Ikawa, Shukuko, Kinebuchi, Takashi, Sakane, Isao, ...
The M200V polymorphism of the human DMC1 protein, which is an essential, meiosis-specific DNA recombinase, was found in an infertile patient, raising the question of whether this homozygous human...
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 extraterminal domain of the bromodomain-containing protein BRD4 (2008)
Lin, Yi-Jan, Umehara, Takashi, Inoue, Makoto, Saito, Kohei, Kigawa, Takanori, Jang, Moon-Kyoo, ...
BRD4, which is a member of the BET (bromodomains and extraterminal) protein family, interacts preferentially with acetylated chromatin and possesses multiple cellular functions in meiosis, embryonic...
Furukawa, Ayako, Nagata, Takashi, Habu, Yuichirou, Sugiyama, Ryuichi, Hayashi, Fumiaki, Yokoyama, Shigeyuki, ...
APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G) is known to have a role in intrinsic cellular immunity against human immunodeficiency virus type1 (HIV-1). The...
Sequences around the unnatural base pair in DNA templates for efficient replication (2008)
Kimoto, Michiko, Kawai, Rie, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
Unnatural base pairs, compatible with PCR amplification, could potentially increase the versatility of nucleic acids. We recently reported an unnatural base pair, between...
Efficient PCR amplification by an unnatural base pair system (2008)
Kimoto, Michiko, Kawai, Rie, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
Expansion of the genetic alphabet by an unnatural base pair system enables the site-specific incorporation of extra functional components into nucleic acids and proteins. In this system, PCR...
Biochemical analysis of the N-terminal domain of human RAD54B (2008)
Sarai, Naoyuki, Kagawa, Wataru, Fujikawa, Norie, Saito, Kengo, Hikiba, Juri, Tanaka, Kozo, ...
The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less...
Fluorescent probing for RNA molecules by an unnatural base-pair system (2007)
Kimoto, Michiko, Mitsui, Tsuneo, Harada, Yoko, Sato, Akira, Yokoyama, Shigeyuki, Hirao, Ichiro
Fluorescent labeling of nucleic acids is widely used in basic research and medical applications. We describe the efficient site-specific incorporation of a fluorescent base analog,...
Keyamura, Kenji, Fujikawa, Norie, Ishida, Takuma, Ozaki, Shogo, Suetsugu, Masayuki, Fujimitsu, Kazuyuki, ...
Escherichia coli DiaA is a DnaA-binding protein that is required for the timely initiation of chromosomal replication during the cell cycle. In this study, we determined the crystal structure of DiaA...
Wakiyama, Motoaki, Takimoto, Koji, Ohara, Osamu, Yokoyama, Shigeyuki
MicroRNAs (miRNAs) are incorporated into miRNP complexes and regulate protein expression post-transcriptionally through binding to 3′-untranslated regions of target mRNAs. Here we describe a...
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....
Analysis of the role of Aurora B on the chromosomal targeting of condensin I (2007)
Takemoto, Ai, Murayama, Akiko, Katano, Miyuki, Urano, Takeshi, Furukawa, Koichi, Yokoyama, Shigeyuki, ...
During mitosis, chromosome condensation takes place, which entails the conversion of interphase chromatin into compacted mitotic chromosomes. Condensin I is a five-subunit protein complex that plays...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Nishida, Masami, Kitamura, Yoshiaki, Baba, Seiki, ...
Thermus thermophilus is an aerobic chemoorganotroph that has been found to grow anaerobically in the presence of nitrate. Crystals of glucose dehydrogenase (GDH) from T. thermophilus HB8 belong to...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Ohmori, Miwa, Agari, Kazuko, Kitamura, Yoshiaki, ...
Thermus thermophilus is a Gram-negative aerobic thermophilic eubacterium which can grow at temperatures ranging from 323 to 355 K. In addition to their importance in thermostability or adaptation...
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...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Baba, Seiki, Kuroishi, Chizu, Ebihara, Akio, ...
The aerobic Gram-positive bacterium Geobacillus kaustophilus is a bacillus species that was isolated from deep-sea sediment from the Mariana Trench. 1,4-Dihydroxy-2-naphthoate (DHNA) synthetase plays...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Baba, Seiki, Chen, Lirong, Liu, Zhi-Jie, ...
The Gram-negative aerobic eubacterium Thermus thermophilus is an extremely important thermophilic microorganism that was originally isolated from a thermal vent environment in Japan. The molybdenum...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Baba, Seiki, Chen, Lirong, Liu, Zhi-Jie, ...
The Gram-negative aerobic eubacterium Thermus thermophilus is an extremely important thermophilic microorganism that was originally isolated from a thermal vent environment in Japan. The molybdenum...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Baba, Seiki, Kuroishi, Chizu, Ebihara, Akio, ...
The aerobic Gram-positive bacterium Geobacillus kaustophilus is a bacillus species that was isolated from deep-sea sediment from the Mariana Trench. 1,4-Dihydroxy-2-naphthoate (DHNA) synthetase plays...
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...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Nishida, Masami, Kitamura, Yoshiaki, Baba, Seiki, ...
Thermus thermophilus is an aerobic chemoorganotroph that has been found to grow anaerobically in the presence of nitrate. Crystals of glucose dehydrogenase (GDH) from T. thermophilus HB8 belong to...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Ohmori, Miwa, Agari, Kazuko, Kitamura, Yoshiaki, ...
Thermus thermophilus is a Gram-negative aerobic thermophilic eubacterium which can grow at temperatures ranging from 323 to 355 K. In addition to their importance in thermostability or adaptation...
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...
Development of an unnatural base pair for efficient PCR amplification (2007)
Hirao, Ichiro, Mitsui, Tsuneo, Kimoto, Michiko, Yokoyama, Shigeyuki
An unnatural base pair system could expand the genetic alphabet, enabling the site-specific incorporation of extra, functional components into nucleic acids and proteins. We developed an unnatural...
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...
An unnatural base pair system for in vitro replication and transcription (2006)
Hirao, Ichiro, Kimoto, Michiko, Mitsui, Tsuneo, Fujiwara, Tsuyoshi, Kawai, Rie, Sato, Akira, ...
The development of unnatural base pairs that function in replication, transcription, and translation could expand the genetic alphabet and enable the site-specific incorporation of functional...
Miyazaki, Satoshi, Kuroda, Yutaka, Yokoyama, Shigeyuki
Background The reliable dissection of large proteins into structural domains represents an important issue for structural genomics/proteomics projects. To provide a practical approach to this issue,...
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....
Access the most recent version at doi: 10.1110/ps.062131106 References (2006)
Akio Ebihara, Min Yao, Ryoji Masui, Isao Tanaka, Shigeyuki Yokoyama, Seiki Kuramitsu, ...
Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain
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...
Computer-aided NMR assay for detecting natively folded structural domains (2006)
Hondoh, Takayuki, Kato, Atsushi, Yokoyama, Shigeyuki, Kuroda, Yutaka
Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of...
Ebihara, Akio, Yao, Min, Masui, Ryoji, Tanaka, Isao, Yokoyama, Shigeyuki, Kuramitsu, Seiki
We have determined the crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 at 1.9 Å resolution. This protein is a member of the Escherichia coli ygcH sequence family,...
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...
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein (2006)
Sarai, Naoyuki, Kagawa, Wataru, Kinebuchi, Takashi, Kagawa, Ako, Tanaka, Kozo, Miyagawa, Kiyoshi, ...
The process of homologous recombination is indispensable for both meiotic and mitotic cell division, and is one of the major pathways for double-strand break (DSB) repair. The human Rad54B protein,...
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein (2006)
Sarai, Naoyuki, Kagawa, Wataru, Kinebuchi, Takashi, Kagawa, Ako, Tanaka, Kozo, Miyagawa, Kiyoshi, ...
The process of homologous recombination is indispensable for both meiotic and mitotic cell division, and is one of the major pathways for double-strand break (DSB) repair. The human Rad54B protein,...
Computer-aided NMR assay for detecting natively folded structural domains (2006)
Hondoh, Takayuki, Kato, Atsushi, Yokoyama, Shigeyuki, Kuroda, Yutaka
Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of...
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...
Ebihara, Akio, Yao, Min, Masui, Ryoji, Tanaka, Isao, Yokoyama, Shigeyuki, Kuramitsu, Seiki
We have determined the crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 at 1.9 Å resolution. This protein is a member of the Escherichia coli ygcH sequence family,...
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...
Computer-aided NMR assay for detecting natively folded structural domains (2006)
Hondoh, Takayuki, Kato, Atsushi, Yokoyama, Shigeyuki, Kuroda, Yutaka
Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of...
Ebihara, Akio, Yao, Min, Masui, Ryoji, Tanaka, Isao, Yokoyama, Shigeyuki, Kuramitsu, Seiki
We have determined the crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 at 1.9 Å resolution. This protein is a member of the Escherichia coli ygcH sequence family,...
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...
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein (2006)
Sarai, Naoyuki, Kagawa, Wataru, Kinebuchi, Takashi, Kagawa, Ako, Tanaka, Kozo, Miyagawa, Kiyoshi, ...
The process of homologous recombination is indispensable for both meiotic and mitotic cell division, and is one of the major pathways for double-strand break (DSB) repair. The human Rad54B protein,...
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...
Tanaka, Yoko, Nakagawa, Noriko, Kuramitsu, Seiki, Yokoyama, Shigeyuki, Masui, Ryoji
GTP cyclohydrolase I (GTPCH1) catalyzes the conversion of GTP to dihydroneopterin 3′-triphosphate. We found that an 8-oxoguanine derivative of GTP (8-oxo-GTP) strongly bound to GTPCH1 from Thermus...
Taka, Junichiro, Ogasahara, Kyoko, Jeyakanthan, Jeyaraman, Kunishima, Naoki, Kuroishi, Chizu, Sugahara, Mitsuaki, ...
The crystal structure of phosphoribosyl anthranilate isomerase (PRAI) from Thermus thermophilus HB8 (TtPRAI) was solved at 2.0 Å resolution. The overall structure of TtPRAI with a dimeric structure...
Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs (2005)
Moriyama, Kei, Kimoto, Michiko, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
Direct site-specific biotinylation of RNA molecules was achieved by specific transcription mediated by unnatural base pairs. Unnatural base pairs between 2-amino-6-(2-thienyl)purine (denoted by s)...
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...
Mitsui, Tsuneo, Kimoto, Michiko, Yokoyama, Shigeyuki, Hirao, Ichiro
Nucleoside derivatives of 2-amino-6-(2-thienyl)purine (s) are fluorescent and can be site-specifically incorporated into RNA by transcription mediated by unnatural base pairs between s and its...
Kimoto, Michiko, Kawai, Rie, Mitsui, Tsuneo, Harada, Yoko, Sato, Akira, Yokoyama, Shigeyuki, ...
To analyze the local conformational changes of RNA molecules, we developed a site-specific fluorescent labeling method for RNA fragments by T7 transcription, using unnatural base pairs between...
Non-hydrogen-bonded base pairs for specific transcription (2005)
Hirao, Ichiro, Mitsui, Tsuneo, Kimoto, Michiko, Kawai, Rie, Sato, Akira, Yokoyama, Shigeyuki
Specific transcription mediated by unnatural base pairs could create novel RNA molecules with increased functionality and expand the genetic code. Here, we report an unnatural base pair between...
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...
Padmanabhan, Balasundaram, Kataoka, Kazuhiro, Umehara, Takashi, Adachi, Naruhiko, Yokoyama, Shigeyuki, Horikoshi, Masami
The structural relationships between histone-binding proteins and DNA-binding proteins are important, since nucleosome-interacting factors possess histone-binding and/or DNA-binding components....
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm (2005)
Kimura, Shuhei, Ide, Kaori, Kashihara, Aiko, Kano, Makoto, Hatakeyama, Mariko, Masui, Ryoji, ...
Motivation: To resolve the high-dimensionality of the genetic network inference problem in the S-system model, a problem decomposition strategy has been proposed. While this strategy certainly shows...
Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein (2004)
Fujikawa, Norie, Kurumizaka, Hitoshi, Nureki, Osamu, Tanaka, Yoshinori, Yamazoe, Mitsuyoshi, Hiraga, Sota, ...
The Escherichia coli SeqA protein recognizes the 11 hemimethylated G‐mA‐T‐C sites in the oriC region of the chromosome, and prevents replication over‐initiation within one cell...
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...
Chikayama, Eisuke, Kurotani, Atsushi, Kuroda, Yutaka, Yokoyama, Shigeyuki
Summary: ProteoMix is a suite of JAVA programs for identifying, annotating, and predicting regions of interest in large sets of amino acid sequences, according to systematic and consistent criteria....
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm (2004)
Kimura, Shuhei, Ide, Kaori, Kashihara, Aiko, Kano, Makoto, Hatakeyama, Mariko, Masui, Ryoji, ...
Motivation: To resolve the high-dimensionality of the genetic network inference problem in the S-system model, a problem decomposition strategy has been proposed. While this strategy certainly shows...
Chikayama, Eisuke, Kurotani, Atsushi, Kuroda, Yutaka, Yokoyama, Shigeyuki
Summary: ProteoMix is a suite of JAVA programs for identifying, annotating and predicting regions of interest in large sets of amino acid sequences, according to systematic and consistent criteria....
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,...
Site-specific fluorescent labeling of RNA by a base-pair expanded transcription system (2004)
Kawai, Rie, Kimoto, Michiko, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
Ribonucleoside 5′-triphosphates of fluorescently-labeled 2-oxo(1H)pyridines, in which carboxyfluorescein (FAM) or carboxytetramethylrhodamine (TAMRA) was attached at position 5, were chemically...
Yokoyama, Hiroshi, Sarai, Naoyuki, Kagawa, Wataru, Enomoto, Rima, Shibata, Takehiko, Kurumizaka, Hitoshi, ...
The Rad51B, Rad51C, Rad51D and Xrcc2 proteins are Rad51 paralogs, and form a complex (BCDX2 complex) in mammalian cells. Mutant cells defective in any one of the Rad51‐paralog genes exhibit...
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...
A Novel Metal-Activated L-Serine O-Acetyltransferase from Thermus thermophilus HB8 (2004)
Kobayashi, Shin-ichiro, Masui, Ryoji, Yokoyama, Shigeyuki, Kuramitsu, Seiki, Takagi, Hiroshi
l-Cysteine is an important amino acid in terms of its industrial applications. The biosynthesis of l-cysteine in enteric bacteria is regulated through the feedback inhibition by l-cysteine 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...
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...
Chikayama, Eisuke, Kurotani, Atsushi, Kuroda, Yutaka, Yokoyama, Shigeyuki
Summary: ProteoMix is a suite of JAVA programs for identifying, annotating, and predicting regions of interest in large sets of amino acid sequences, according to systematic and consistent criteria....
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm (2004)
Kimura, Shuhei, Ide, Kaori, Kashihara, Aiko, Kano, Makoto, Hatakeyama, Mariko, Masui, Ryoji, ...
Motivation: To resolve the high-dimensionality of the genetic network inference problem in the S-system model, a problem decomposition strategy has been proposed. While this strategy certainly shows...
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
An unnatural base pair for efficient incorporation of nucleotide analogs into RNAs (2003)
Hirao, Ichiro, Mitsui, Tsuneo, Kimoto, Michiko, Harada, Yoko, Yokoyama, Shigeyuki
An unnatural base, 2-amino-6-(2-thiazolyl)purine (denoted as v), was developed as an efficient complementary base of another unnatural base, 2-oxo(1H)pyridine (denoted as y). The nucleoside...
Simple preparation of biotinylated RNA by transcription via an unnatural base pair (2003)
Moriyama, Kei, Kimoto, Michiko, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
To develop a convenient method for RNA fragment biotinylation at a specific position, we synthesized ribonucleoside 5′-triphosphates of biotinylated unnatural bases. These unnatural bases were...
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...
Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons (2003)
Takai, Kazuyuki, Yokoyama, Shigeyuki
Many tRNA molecules that recognize the purine‐ending codons but not the pyrimidine‐ending codons have a modified uridine at the wobble position, in which a methylene carbon is attached...
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...
Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein (2003)
Kurumizaka, Hitoshi, Enomoto, Rima, Nakada, Maki, Eda, Keiko, Yokoyama, Shigeyuki, Shibata, Takehiko
The Xrcc3 protein, which is required for the homologous recombinational repair of damaged DNA, forms a complex with the Rad51C protein in human cells. Mutations in either the Xrcc3 or Rad51C gene...
An unnatural base pair for efficient incorporation of nucleotide analogs into RNAs (2003)
Hirao, Ichiro, Mitsui, Tsuneo, Kimoto, Michiko, Harada, Yoko, Yokoyama, Shigeyuki
Simple preparation of biotinylated RNA by transcription via an unnatural base pair (2003)
Moriyama, Kei, Kimoto, Michiko, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
In vitro analysis of the initial steps of trans-translation (2003)
Takada, Kazuma, Hori-Takemoto, Chie, Kawazoe, Masahito, Lee, SungGa, Shirouzu, Mikako, Yokoyama, Shigeyuki, ...
Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase (2003)
FUKAI, SHUYA, NUREKI, OSAMU, SEKINE, SHUN-ICHI, SHIMADA, ATSUSHI, VASSYLYEV, DMITRY G., YOKOYAMA, SHIGEYUKI
The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNAVal, with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based...
An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes (2003)
Yoshimasu, Masatoshi, Aihara, Hideki, Ito, Yutaka, Rajesh, Sundaresan, Ishibe, Satoko, Mikawa, Tsutomu, ...
The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage‐induced replication arrest, and is positively regulated by the...
An NMR study on the interaction of Escherichia coli DinI with RecA±ssDNA complexes (2002)
Masatoshi Yoshimasu, Hideki Aihara, Yutaka Ito, Sundaresan Rajesh, Satoko Ishibe, Tsutomu Mikawa, ...
The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the coprotease...
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...
Mitsui, Tsuneo, Kimoto, Michiko, Harada, Yoko, Sato, Akira, Kitamura, Aya, To, Taiko, ...
A hydrophobic unnatural nucleoside of 4-propynyl-pyrrole-2-carbaldehyde (designated as Pa′) was synthesized to improve its affinity with a pairing partner, 9-methyl-imidazo[(4,5)-b]pyridine (Q), in...
Hirao, Ichiro, Kimoto, Michiko, Mitsui, Tsuneo, Harada, Yoko, Fujiwara, Tsuyoshi, Sato, Akira, ...
Nucleosides of imidazolin-2-one (designated by z) were designed and synthesized as pairing partners of 2-amino-6-(2-thienyl)purine (designated by s). Previously, we developed an unnatural base pair...
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...
Efforts toward creating unnatural base pairs for an expanded genetic code (2001)
Hirao, Ichiro, Mitsui, Tsuneo, Fujiwara, Tsuyoshi, Kimoto, Michiko, To, Taiko, Okuni, Taeko, ...
Photo-regulation of RNA polymerase reaction by use of modified DNA carrying an azobenzene (2001)
Asanuma, Hiroyuki, Tamaru, Daisuke, Yoshida, Takayuki, Yamazawa, Akira, Mitsui, Tsuneo, Okuni, Taeko, ...
Efforts toward creating unnatural base pairs for an expanded genetic code (2001)
Hirao, Ichiro, Mitsui, Tsuneo, Fujiwara, Tsuyoshi, Kimoto, Michiko, To, Taiko, Okuni, Taeko, ...
A series of unnatural base pairs was designed and examined for the expansion of the genetic alphabet and for a better understanding of the mechanism of nucleic acid biosyntheses. To improve the shape...
Photo-regulation of RNA polymerase reaction by use of modified DNA carrying an azobenzene (2001)
Asanuma, Hiroyuki, Tamaru, Daisuke, Yoshida, Takayuki, Yamazawa, Akira, Mitsui, Tsuneo, Okuni, Taeko, ...
Transcription reaction by T7-RNA polymerase was photo-regulated on the basis of two strategies as depicted in Scheme 1. It was found that incorporation reaction of azobenzene-tethered uridine...
Unnatural base pairs between 2-amino-6-(2-thienyl)purine and the complementary bases (2000)
Hirao, Ichiro, Fujiwara, Tsuyoshi, Kimoto, Michiko, Mitsui, Tsuneo, Okuni, Taeko, Ohtsuki, Takashi, ...
The unnatural base, 2-amino-6-(2-thienyl)purine (designated as s), instead of 2-amino-6-(N,N-dimethylamino)purine (designated as x), was designed in order to improve the specificity and efficiency of...
Fujiwara, Tsuyoshi, Sugiyama, Hiroshi, Hirao, Ichiro, Yokoyama, Shigeyuki
Unnatural bases specifically pairing with pyridin-2-one, 2-amino-6-(2-thienyl)purine and 2-amino-6-(2-furanyl)purine, were newly designed to replace 2-amino-6-(N,N-dimethylamino)purine. It was...
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...
Kunda, Takayuki, Takai, Kazuyuki, Yokoyama, Shigeyuki, Takaku, Hiroshi
The protein-synthesizing S30 extract of Escherichia coli contains tRNA, which limits its applications in cell-free protein synthesis. Here, we show that at least Arg- and Ser-acceptor activities can...
Sato, Chiaki, Kim, Jae-Hoon, Abe, Yoshito, Saito, Kazuki, Yokoyama, Shigeyuki, Kohda, Daisuke
The extracellular domain of human EGF receptor (sEGFR) produced by CHO cells has been used in various biophysical studies to elucidate the molecular mechanism of EGF-induced receptor activation. We...
NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C (2000)
Inoue, Makoto, Muto, Yutaka, Sakamoto, Hiroshi, Yokoyama, Shigeyuki
Hu antigen C (HuC) has three RNA-binding domains (RBDs). The N-terminal two, RBD1 and RBD2, are linked in tandem and bind to the AU-rich elements (AREs) in the 3′-untranslated region of particular...
Chemical synthesis of novel base pairs and their enzymatic incorporation into DNA (1999)
Ishikawa, Masahide, Hirao, Ichiro, Yokoyama, Shigeyuki
A novel base pair, 2-amino-6-(N,N-dimethylamino)purine (denoted x) and the counter part, pyridin-2-one (denoted y) were designed. The bulky 6-dimethylamino group of x is expected to eliminate base...
The guanosine binding mechanism of the Tetrahymena group I intron (1999)
Kitamura, Aya, Muto, Yutaka, Watanabe, Satoru, Kim, Insil, Ito, Takuhiro, Nishiya, Yoichi, ...
The Tetrahymena group I intron catalyzes self-splicing through two consecutive transesterification reactions, using a single guanosine-binding site (GBS). In this study, we constructed a model RNA...
Kim, Insil, Muto, Yutaka, Hosono, Kazumi, Kitamura, Aya, Watanabe, Satoru, Ohtsuki, Takashi, ...
Using [5-2H]uridine phosphoramidite, we synthesized a series of 2H-labeled Drosophila Sex-lethal (Sxl) target RNAs, in which all the uridine residues except one were specifically replaced by...
State Transitions by Molecules (1998)
Kensaku Sakamoto, Daisuke Kiga, Ken Komiya, Hidetaka Gouzu, Shigeyuki Yokoyama, Shuji Ikeda, ...
In our previous paper, we described a method by which a state machine is implemented by a single-stranded DNA molecule whose 3 0 -end sequence encodes the current state of the machine. Successive...
State Transitions by Molecules (1998)
Kensaku Sakamoto, Daisuke Kiga, Ken Komiya, Hidetaka Gouzu, Shigeyuki Yokoyama, Shuji Ikeda, ...
In our previous paper, we described a method by which a state machine is implemented by a single-stranded DNA molecule whose 3 0 -end sequence encodes the current state of the machine. Successive...
Towards parallel evaluation and learning of boolean µ-formulas with molecules (1997)
Masami Hagiya, Masanori Arita, Daisuke Kiga, Kensaku Sakamoto, Shigeyuki Yokoyama
Abstract. A--formula is a Boolean formula in which each variable occurs at most once. The paper treats its molecular representation including its queries using techniques in molecular biology. The...
Towards Parallel Evaluation and Learning of Boolean ...-Formulas with Molecules (1997)
Masami Hagiya, Masanori Arita, Daisuke Kiga, Kensaku Sakamoto, Shigeyuki Yokoyama
A ¯--formula is a Boolean formula in which each variable occurs at most once. The paper treats its molecular representation including its queries using techniques in molecular biology. The novelty...
Sakamoto, Taiichi, Kawai, Gota, Katahira, Masato, Kim, Mi Hee, Tanaka, Yoichiro, Kurihara, Yasuyuki, ...
An RNA 28-mer (Rz28) was obtained as a major product by in vitro transcription with T7 RNA polymerase of a promoter-template DNA, which contains a sequence for the enzyme component, RNA 24-mer...
Taguchi, Tomohiko, Muto, Yutaka, Kitajima, Ken, Yokoyama, Shigeyuki, Inoue, Sadako, Inoue, Yasuo
The chemical shifts of ring protons of the β-Man residue in a triantennary complex type N-linked glycan chain having a GlcNAcβ1→6(GlcNAcβ1→2)Manα1β6Manβ sequence were unambiguously...
Nishii, Wataru, Muramatsu, Tomonari, Kuchino, Yoshiyuki, Yokoyama, Shigeyuki, Takahashi, Kenji
Proteolytic trimming of isoprenylated proteins, including Ras, at the C-terminal CAAX motifs is a key event in their activation. However, the protease responsible for the proteolysis has not been...
A Continuous Cell-Free Protein Synthesis System for Coupled Transcription-Translation (1991)
Kigawa, Takanori, Yokoyama, Shigeyuki
A continuous cell-free protein synthesis system [Spirin et al. (1988) Science 242, 1162–1164] was modified so as to be suitable for coupled transcription-translation, a process useful for obtaining...
Kanou, Masayasu, Ohomori, Hisanori, Takaku, Hiroshi, Yokoyama, Shigeyuki, Kawai, Gota, Suhadolnik, Robert.J., ...
The synthesis of sequence-specific 2'–5' oligonucleotides and analogues of 2'-5' linked oligoadenylates containing 8-substituted adenosine derivatives [8-hydroxypropyladenosine (AHPr) and...
TAIJI, Mutsuo, YOKOYAMA, Shigeyuki, MIYAZAWA, Tatsuo
2′ and 3′-O-(N-acetyl-L-phenylalanyl)adenosine (Ac-Phe-Ado) were chemically synthesized. These two isomers were clearly separated from each other by high-performance liquid chromatography (HPLC)....
YAMAMOTO, Nobuko, YAMAIZUMI, Ziro, YOKOYAMA, Shigeyuki, MIYAZAWA, Tatsuo, NISHIMURA, Susumu
A novel modified nucleoside located in the first position of the anticodon of yeast tRNA2aVal was isolated and its chemical structure was characterized as 5-carbamoyl-methyluridine by means of...
Rate of Transacylation between 2' and 3'-O-L-PhenyIalanyIadenosine (1981)
TAIJI, Mutsuo, YOKOYAMA, Shigeyuki, HIGUCHI, Shigesada, MIYAZAWA, Tatsuo
The 270-MHz proton NMR spectra of 2′-O-L-phenylalanyladenosine and 3′-O-L-phenylalanyladenosine in deuterated phosphate buffer were analyzed. The transacylation between these two isomers was...
Yokoyama, Shigeyuki, Yamaizumi, Ziro, Nishimura, Susumu, Miyazawa, Tatsuo
The molecular conformations of naturally occurring 2-thio-pyrimidine nucleosides (5-methylaminomethyl-2-thiouridine, 5-methoxycarbonylmethyl-2-thiouridine and 2-thiocytidine) and 5′-mononucleotides...
The conformational properties of Q nucleotide in aqueous solution (1978)
Yokoyama, Shigeyuki, Miyazawa, Tatsuo, Yamaizumi, Ziro, Nishimura, Susumu
The conformational properties of Q-nucleoside-5′-monophosphate (pQ) in aqueous solution was investigated by 1H-NMR. By the analyses of spin-coupling constants, NOE and spin-lattice relaxation...
An extended DNA structure through deoxyribose-base stacking induced by RecA protein
Nishinaka, Taro, Ito, Yutaka, Yokoyama, Shigeyuki, Shibata, Takehiko
The family of proteins that are homologous to RecA protein of Escherichia coli is essential to homologous genetic recombination in various organisms including viruses, bacteria, lower eukaryotes, and...
Nishinaka, Taro, Shinohara, Akira, Ito, Yutaka, Yokoyama, Shigeyuki, Shibata, Takehiko
Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions...
Unnatural base pairs for specific transcription
Ohtsuki, Takashi, Kimoto, Michiko, Ishikawa, Masahide, Mitsui, Tsuneo, Hirao, Ichiro, Yokoyama, Shigeyuki
An unnatural base pair of 2-amino-6-(N,N-dimethylamino)purine (designated as x) and pyridin-2-one (designated as y) has been developed for specific transcription. The ribonucleoside triphosphates of...
Homologous-pairing activity of the human DNA-repair proteins Xrcc3⋅Rad51C
Kurumizaka, Hitoshi, Ikawa, Shukuko, Nakada, Maki, Eda, Keiko, Kagawa, Wataru, Takata, Minoru, ...
The human Xrcc3 protein is involved in the repair of damaged DNA through homologous recombination, in which homologous pairing is a key step. The Rad51 protein is believed to be the only protein...
Shibata, Takehiko, Nishinaka, Taro, Mikawa, Tsutomu, Aihara, Hideki, Kurumizaka, Hitoshi, Yokoyama, Shigeyuki, ...
Heteroduplex joints are general intermediates of homologous genetic recombination in DNA genomes. A heteroduplex joint is formed between a single-stranded region (or tail), derived from a cleaved...
Shimada, Atsushi, Nureki, Osamu, Goto, Mie, Takahashi, Seizo, Yokoyama, Shigeyuki
Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNAArg: A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few...
Crystal structure of thermostable DNA photolyase: Pyrimidine-dimer recognition mechanism
Komori, Hirofumi, Masui, Ryoji, Kuramitsu, Seiki, Yokoyama, Shigeyuki, Shibata, Takehiko, Inoue, Yorinao, ...
DNA photolyase is a pyrimidine-dimer repair enzyme that uses visible light. Photolyase generally contains two chromophore cofactors. One is a catalytic cofactor directly contributing to the repair of...
NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C
Inoue, Makoto, Muto, Yutaka, Sakamoto, Hiroshi, Yokoyama, Shigeyuki
Hu antigen C (HuC) has three RNA-binding domains (RBDs). The N-terminal two, RBD1 and RBD2, are linked in tandem and bind to the AU-rich elements (AREs) in the 3′-untranslated region of particular...
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...
Tanaka, Yoshinori, Nureki, Osamu, Kurumizaka, Hitoshi, Fukai, Shuya, Kawaguchi, Shinichi, Ikuta, Mari, ...
The human centromere protein B (CENP-B), one of the centromere components, specifically binds a 17 bp sequence (the CENP-B box), which appears in every other α-satellite repeat. In the present...
Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set
Akanuma, Satoshi, Kigawa, Takanori, Yokoyama, Shigeyuki
We developed an effective strategy to restrict the amino acid usage in a relatively large protein to a reduced set with conservation of its in vivo function. The 213-residue Escherichia coli orotate...
The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus
Kawaguchi, Shin-ichi, Müller, Jörg, Linde, Dirk, Kuramitsu, Seiki, Shibata, Takehiko, Inoue, Yorinao, ...
The CsaA protein was first characterized in Bacillus subtilis as a molecular chaperone with export-related activities. Here we report the 2.0 Å-resolution crystal structure of the Thermus...
Renault, Louis, Kerjan, Pierre, Pasqualato, Sebastiano, Ménétrey, Julie, Robinson, Jean-Charles, Kawaguchi, Shin-ichi, ...
The EMAPII (endothelial monocyte-activating polypeptide II) domain is a tRNA-binding domain associated with several aminoacyl-tRNA synthetases, which becomes an independent domain with inflammatory...
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...
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding
Sekine, Shun-ichi, Nureki, Osamu, Dubois, Daniel Y., Bernier, Stéphane, Chênevert, Robert, Lapointe, Jacques, ...
Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including...
An NMR study on the interaction of Escherichia coli DinI with RecA–ssDNA complexes
Yoshimasu, Masatoshi, Aihara, Hideki, Ito, Yutaka, Rajesh, Sundaresan, Ishibe, Satoko, Mikawa, Tsutomu, ...
The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co-...
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...
Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein
Kurumizaka, Hitoshi, Enomoto, Rima, Nakada, Maki, Eda, Keiko, Yokoyama, Shigeyuki, Shibata, Takehiko
The Xrcc3 protein, which is required for the homologous recombinational repair of damaged DNA, forms a complex with the Rad51C protein in human cells. Mutations in either the Xrcc3 or Rad51C gene...
Okabe, Mayuko, Tomita, Kozo, Ishitani, Ryuichiro, Ishii, Ryohei, Takeuchi, Nono, Arisaka, Fumio, ...
CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase], a template-independent RNA polymerase, adds the defined ‘cytidine–cytidine–adenosine’ sequence onto the 3′ end of tRNA. The...
Takai, Kazuyuki, Yokoyama, Shigeyuki
Many tRNA molecules that recognize the purine-ending codons but not the pyrimidine-ending codons have a modified uridine at the wobble position, in which a methylene carbon is attached directly to...
Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein
Fujikawa, Norie, Kurumizaka, Hitoshi, Nureki, Osamu, Tanaka, Yoshinori, Yamazoe, Mitsuyoshi, Hiraga, Sota, ...
The Escherichia coli SeqA protein recognizes the 11 hemimethylated G-mA-T-C sites in the oriC region of the chromosome, and prevents replication over-initiation within one cell cycle. The crystal...
Yokoyama, Hiroshi, Sarai, Naoyuki, Kagawa, Wataru, Enomoto, Rima, Shibata, Takehiko, Kurumizaka, Hitoshi, ...
The Rad51B, Rad51C, Rad51D and Xrcc2 proteins are Rad51 paralogs, and form a complex (BCDX2 complex) in mammalian cells. Mutant cells defective in any one of the Rad51-paralog genes exhibit...
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...
Sakamoto, Kensaku, Ishimaru, Satoshi, Kobayashi, Takatsugu, Walker, James R., Yokoyama, Shigeyuki
The Escherichia coli argU10(Ts) mutation in the argU gene, encoding the minor tRNAArg species for the rare codons AGA and AGG, causes pleiotropic defects, including growth inhibition at high...
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...
Kobayashi, Takatsugu, Sakamoto, Kensaku, Takimura, Tetsuo, Sekine, Ryo, Vincent, Kelly, Kamata, Kenji, ...
The genetic code in a eukaryotic system has been expanded by the engineering of Escherichia coli tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically...
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...
Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs
Moriyama, Kei, Kimoto, Michiko, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
Direct site-specific biotinylation of RNA molecules was achieved by specific transcription mediated by unnatural base pairs. Unnatural base pairs between 2-amino-6-(2-thienyl)purine (denoted by s)...
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...
Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain
Sakata, Eri, Yamaguchi, Yoshiki, Kurimoto, Eiji, Kikuchi, Jun, Yokoyama, Shigeyuki, Yamada, Shingo, ...
Parkin, a product of the causative gene of autosomal-recessive juvenile parkinsonism (AR-JP), is a RING-type E3 ubiquitin ligase and has an amino-terminal ubiquitin-like (Ubl) domain. Although a...
Kitamura, Aya, Muto, Yutaka, Watanabe, Satoru, Kim, Insil, Ito, Takuhiro, Nishiya, Yoichi, ...
In the second step of the two consecutive transesterifications of the self-splicing reaction of the group I intron, the conserved guanosine at the 3' terminus of the intron (omegaG) binds to the...
Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase
FUKAI, SHUYA, NUREKI, OSAMU, SEKINE, SHUN-ICHI, SHIMADA, ATSUSHI, VASSYLYEV, DMITRY G., YOKOYAMA, SHIGEYUKI
The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNAVal, with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based...
Minagawa, Asako, Takaku, Hiroaki, Ishii, Ryohei, Takagi, Masamichi, Yokoyama, Shigeyuki, Nashimoto, Masayuki
Thermotoga maritima tRNase Z cleaves pre-tRNAs containing the 74CCA76 sequence precisely after the A76 residue to create the mature 3′ termini. Its crystal structure has revealed a four-layer...
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein
Sarai, Naoyuki, Kagawa, Wataru, Kinebuchi, Takashi, Kagawa, Ako, Tanaka, Kozo, Miyagawa, Kiyoshi, ...
The process of homologous recombination is indispensable for both meiotic and mitotic cell division, and is one of the major pathways for double-strand break (DSB) repair. The human Rad54B protein,...
An extended DNA structure through deoxyribose-base stacking induced by RecA protein
Nishinaka, Taro, Ito, Yutaka, Yokoyama, Shigeyuki, Shibata, Takehiko
The family of proteins that are homologous to RecA protein of Escherichia coli is essential to homologous genetic recombination in various organisms including viruses, bacteria, lower eukaryotes, and...
Nishinaka, Taro, Shinohara, Akira, Ito, Yutaka, Yokoyama, Shigeyuki, Shibata, Takehiko
Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions...
Unnatural base pairs for specific transcription
Ohtsuki, Takashi, Kimoto, Michiko, Ishikawa, Masahide, Mitsui, Tsuneo, Hirao, Ichiro, Yokoyama, Shigeyuki
An unnatural base pair of 2-amino-6-(N,N-dimethylamino)purine (designated as x) and pyridin-2-one (designated as y) has been developed for specific transcription. The ribonucleoside triphosphates of...
Homologous-pairing activity of the human DNA-repair proteins Xrcc3⋅Rad51C
Kurumizaka, Hitoshi, Ikawa, Shukuko, Nakada, Maki, Eda, Keiko, Kagawa, Wataru, Takata, Minoru, ...
The human Xrcc3 protein is involved in the repair of damaged DNA through homologous recombination, in which homologous pairing is a key step. The Rad51 protein is believed to be the only protein...
Shibata, Takehiko, Nishinaka, Taro, Mikawa, Tsutomu, Aihara, Hideki, Kurumizaka, Hitoshi, Yokoyama, Shigeyuki, ...
Heteroduplex joints are general intermediates of homologous genetic recombination in DNA genomes. A heteroduplex joint is formed between a single-stranded region (or tail), derived from a cleaved...
Shimada, Atsushi, Nureki, Osamu, Goto, Mie, Takahashi, Seizo, Yokoyama, Shigeyuki
Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNAArg: A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few...
Crystal structure of thermostable DNA photolyase: Pyrimidine-dimer recognition mechanism
Komori, Hirofumi, Masui, Ryoji, Kuramitsu, Seiki, Yokoyama, Shigeyuki, Shibata, Takehiko, Inoue, Yorinao, ...
DNA photolyase is a pyrimidine-dimer repair enzyme that uses visible light. Photolyase generally contains two chromophore cofactors. One is a catalytic cofactor directly contributing to the repair of...
NMR studies on functional structures of the AU-rich element-binding domains of Hu antigen C
Inoue, Makoto, Muto, Yutaka, Sakamoto, Hiroshi, Yokoyama, Shigeyuki
Hu antigen C (HuC) has three RNA-binding domains (RBDs). The N-terminal two, RBD1 and RBD2, are linked in tandem and bind to the AU-rich elements (AREs) in the 3′-untranslated region of particular...
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...
Tanaka, Yoshinori, Nureki, Osamu, Kurumizaka, Hitoshi, Fukai, Shuya, Kawaguchi, Shinichi, Ikuta, Mari, ...
The human centromere protein B (CENP-B), one of the centromere components, specifically binds a 17 bp sequence (the CENP-B box), which appears in every other α-satellite repeat. In the present...
Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set
Akanuma, Satoshi, Kigawa, Takanori, Yokoyama, Shigeyuki
We developed an effective strategy to restrict the amino acid usage in a relatively large protein to a reduced set with conservation of its in vivo function. The 213-residue Escherichia coli orotate...
The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus
Kawaguchi, Shin-ichi, Müller, Jörg, Linde, Dirk, Kuramitsu, Seiki, Shibata, Takehiko, Inoue, Yorinao, ...
The CsaA protein was first characterized in Bacillus subtilis as a molecular chaperone with export-related activities. Here we report the 2.0 Å-resolution crystal structure of the Thermus...
Renault, Louis, Kerjan, Pierre, Pasqualato, Sebastiano, Ménétrey, Julie, Robinson, Jean-Charles, Kawaguchi, Shin-ichi, ...
The EMAPII (endothelial monocyte-activating polypeptide II) domain is a tRNA-binding domain associated with several aminoacyl-tRNA synthetases, which becomes an independent domain with inflammatory...
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...
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding
Sekine, Shun-ichi, Nureki, Osamu, Dubois, Daniel Y., Bernier, Stéphane, Chênevert, Robert, Lapointe, Jacques, ...
Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including...
An NMR study on the interaction of Escherichia coli DinI with RecA–ssDNA complexes
Yoshimasu, Masatoshi, Aihara, Hideki, Ito, Yutaka, Rajesh, Sundaresan, Ishibe, Satoko, Mikawa, Tsutomu, ...
The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co-...
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...
Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein
Kurumizaka, Hitoshi, Enomoto, Rima, Nakada, Maki, Eda, Keiko, Yokoyama, Shigeyuki, Shibata, Takehiko
The Xrcc3 protein, which is required for the homologous recombinational repair of damaged DNA, forms a complex with the Rad51C protein in human cells. Mutations in either the Xrcc3 or Rad51C gene...
Okabe, Mayuko, Tomita, Kozo, Ishitani, Ryuichiro, Ishii, Ryohei, Takeuchi, Nono, Arisaka, Fumio, ...
CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase], a template-independent RNA polymerase, adds the defined ‘cytidine–cytidine–adenosine’ sequence onto the 3′ end of tRNA. The...
Takai, Kazuyuki, Yokoyama, Shigeyuki
Many tRNA molecules that recognize the purine-ending codons but not the pyrimidine-ending codons have a modified uridine at the wobble position, in which a methylene carbon is attached directly to...
Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein
Fujikawa, Norie, Kurumizaka, Hitoshi, Nureki, Osamu, Tanaka, Yoshinori, Yamazoe, Mitsuyoshi, Hiraga, Sota, ...
The Escherichia coli SeqA protein recognizes the 11 hemimethylated G-mA-T-C sites in the oriC region of the chromosome, and prevents replication over-initiation within one cell cycle. The crystal...
Yokoyama, Hiroshi, Sarai, Naoyuki, Kagawa, Wataru, Enomoto, Rima, Shibata, Takehiko, Kurumizaka, Hitoshi, ...
The Rad51B, Rad51C, Rad51D and Xrcc2 proteins are Rad51 paralogs, and form a complex (BCDX2 complex) in mammalian cells. Mutant cells defective in any one of the Rad51-paralog genes exhibit...
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...
Sakamoto, Kensaku, Ishimaru, Satoshi, Kobayashi, Takatsugu, Walker, James R., Yokoyama, Shigeyuki
The Escherichia coli argU10(Ts) mutation in the argU gene, encoding the minor tRNAArg species for the rare codons AGA and AGG, causes pleiotropic defects, including growth inhibition at high...
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...
Kobayashi, Takatsugu, Sakamoto, Kensaku, Takimura, Tetsuo, Sekine, Ryo, Vincent, Kelly, Kamata, Kenji, ...
The genetic code in a eukaryotic system has been expanded by the engineering of Escherichia coli tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically...
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...
Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs
Moriyama, Kei, Kimoto, Michiko, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
Direct site-specific biotinylation of RNA molecules was achieved by specific transcription mediated by unnatural base pairs. Unnatural base pairs between 2-amino-6-(2-thienyl)purine (denoted by s)...
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...
Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain
Sakata, Eri, Yamaguchi, Yoshiki, Kurimoto, Eiji, Kikuchi, Jun, Yokoyama, Shigeyuki, Yamada, Shingo, ...
Parkin, a product of the causative gene of autosomal-recessive juvenile parkinsonism (AR-JP), is a RING-type E3 ubiquitin ligase and has an amino-terminal ubiquitin-like (Ubl) domain. Although a...
Kitamura, Aya, Muto, Yutaka, Watanabe, Satoru, Kim, Insil, Ito, Takuhiro, Nishiya, Yoichi, ...
In the second step of the two consecutive transesterifications of the self-splicing reaction of the group I intron, the conserved guanosine at the 3' terminus of the intron (omegaG) binds to the...
Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase
FUKAI, SHUYA, NUREKI, OSAMU, SEKINE, SHUN-ICHI, SHIMADA, ATSUSHI, VASSYLYEV, DMITRY G., YOKOYAMA, SHIGEYUKI
The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNAVal, with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based...
Minagawa, Asako, Takaku, Hiroaki, Ishii, Ryohei, Takagi, Masamichi, Yokoyama, Shigeyuki, Nashimoto, Masayuki
Thermotoga maritima tRNase Z cleaves pre-tRNAs containing the 74CCA76 sequence precisely after the A76 residue to create the mature 3′ termini. Its crystal structure has revealed a four-layer...
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein
Sarai, Naoyuki, Kagawa, Wataru, Kinebuchi, Takashi, Kagawa, Ako, Tanaka, Kozo, Miyagawa, Kiyoshi, ...
The process of homologous recombination is indispensable for both meiotic and mitotic cell division, and is one of the major pathways for double-strand break (DSB) repair. The human Rad54B protein,...
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....
Analysis of the role of Aurora B on the chromosomal targeting of condensin I
Takemoto, Ai, Murayama, Akiko, Katano, Miyuki, Urano, Takeshi, Furukawa, Koichi, Yokoyama, Shigeyuki, ...
During mitosis, chromosome condensation takes place, which entails the conversion of interphase chromatin into compacted mitotic chromosomes. Condensin I is a five-subunit protein complex that plays...
Transcription Activation Mediated by a Cyclic AMP Receptor Protein from Thermus thermophilus HB8▿ §
Shinkai, Akeo, Kira, Satoshi, Nakagawa, Noriko, Kashihara, Aiko, Kuramitsu, Seiki, Yokoyama, Shigeyuki
The extremely thermophilic bacterium Thermus thermophilus HB8, which belongs to the phylum Deinococcus-Thermus, has an open reading frame encoding a protein belonging to the cyclic AMP (cAMP)...
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...
Fukunaga, Ryuya, Ishitani, Ryuichiro, Nureki, Osamu, Yokoyama, Shigeyuki
The leucyl-tRNA synthetase (LeuRS) from P. horikoshii has been overexpressed in Escherichia coli and purified, and cocrystallizations with each of the tRNALeu isoacceptors have been attempted....
Padmanabhan, Balasundaram, Scharlock, Maria, Tong, Kit I., Nakamura, Yoshihiro, Kang, Moon-Il, Kobayashi, Akira, ...
Keap1-DC (Kelch/double-glycine repeat and C-terminal region) of mouse Keap1 has been overexpressed in E. coli, purified and crystallized using the vapour-diffusion method.
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...
Fluorescent probing for RNA molecules by an unnatural base-pair system
Kimoto, Michiko, Mitsui, Tsuneo, Harada, Yoko, Sato, Akira, Yokoyama, Shigeyuki, Hirao, Ichiro
Fluorescent labeling of nucleic acids is widely used in basic research and medical applications. We describe the efficient site-specific incorporation of a fluorescent base analog,...
Umehara, Takashi, Otta, Yumi, Tsuganezawa, Keiko, Matsumoto, Takehisa, Tanaka, Akiko, Horikoshi, Masami, ...
The histone chaperone cia1 from fission yeast has been overexpressed in E. coli, purified and crystallized using the vapour-diffusion method.
Negative regulation of condensin I by CK2-mediated phosphorylation
Takemoto, Ai, Kimura, Keiji, Yanagisawa, Junn, Yokoyama, Shigeyuki, Hanaoka, Fumio
Condensin I, which plays an essential role in mitotic chromosome assembly and segregation in vivo, constrains positive supercoils into DNA in the presence of adenosine triphosphate in vitro....
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...
Cytoplasmic destruction of p53 by the endoplasmic reticulum-resident ubiquitin ligase ‘Synoviolin'
Yamasaki, Satoshi, Yagishita, Naoko, Sasaki, Takeshi, Nakazawa, Minako, Kato, Yukihiro, Yamadera, Tadayuki, ...
Synoviolin, also called HRD1, is an E3 ubiquitin ligase and is implicated in endoplasmic reticulum -associated degradation. In mammals, Synoviolin plays crucial roles in various physiological and...
Wakiyama, Motoaki, Takimoto, Koji, Ohara, Osamu, Yokoyama, Shigeyuki
MicroRNAs (miRNAs) are incorporated into miRNP complexes and regulate protein expression post-transcriptionally through binding to 3′-untranslated regions of target mRNAs. Here we describe a...
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...
Keyamura, Kenji, Fujikawa, Norie, Ishida, Takuma, Ozaki, Shogo, Su’etsugu, Masayuki, Fujimitsu, Kazuyuki, ...
Escherichia coli DiaA is a DnaA-binding protein that is required for the timely initiation of chromosomal replication during the cell cycle. In this study, we determined the crystal structure of DiaA...
Tong, Kit I., Padmanabhan, Balasundaram, Kobayashi, Akira, Shang, Chengwei, Hirotsu, Yosuke, Yokoyama, Shigeyuki, ...
Nrf2 is the regulator of the oxidative/electrophilic stress response. Its turnover is maintained by Keap1-mediated proteasomal degradation via a two-site substrate recognition mechanism in which two...
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...
Computer-aided NMR assay for detecting natively folded structural domains
Hondoh, Takayuki, Kato, Atsushi, Yokoyama, Shigeyuki, Kuroda, Yutaka
Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of...
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...
Ebihara, Akio, Yao, Min, Masui, Ryoji, Tanaka, Isao, Yokoyama, Shigeyuki, Kuramitsu, Seiki
We have determined the crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 at 1.9 Å resolution. This protein is a member of the Escherichia coli ygcH sequence family,...
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...
Reconstitution reveals the functional core of mammalian eIF3
Masutani, Mamiko, Sonenberg, Nahum, Yokoyama, Shigeyuki, Imataka, Hiroaki
Eukaryotic translation initiation factor (eIF)3 is the largest eIF (∼650 kDa), consisting of 10–13 different polypeptide subunits in mammalian cells. To understand the role of each subunit, we...
Padmanabhan, Balasundaram, Tong, Kit I., Kobayashi, Akira, Yamamoto, Masayuki, Yokoyama, Shigeyuki
The structure of mouse Keap1-DC complexed with the DLG motif peptide of Nrf2 transcription factor was determined at 1.9 Å resolution. The structure showed that the peptide binds to Keap1-DC at the...
Structural and functional analyses of the DMC1-M200V polymorphism found in the human population
Hikiba, Juri, Hirota, Kouji, Kagawa, Wataru, Ikawa, Shukuko, Kinebuchi, Takashi, Sakane, Isao, ...
The M200V polymorphism of the human DMC1 protein, which is an essential, meiosis-specific DNA recombinase, was found in an infertile patient, raising the question of whether this homozygous human...
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′...
Kumarevel, Thirumananseri, Nakano, Noboru, Ponnuraj, Karthe, Gopinath, Subash C. B., Sakamoto, Keiko, Shinkai, Akeo, ...
Genome analyses have revealed that members of the Lrp/AsnC family of transcriptional regulators are widely distributed among prokaryotes, including both bacteria and archaea. These regulatory...
Vassylyeva, Marina N., Mori, Hiroyuki, Tsukazaki, Tomoya, Yokoyama, Shigeyuki, Tahirov, Tahir H., Ito, Koreaki, ...
The SecA ATPase from T. thermophilus was cloned, expressed, purified and crystallized. Complete diffraction data sets were collected for two crystal forms at 2.8 and 3.5 Å resolution,...
Structure of the stand-alone RAM-domain protein from Thermus thermophilus HB8
Nakano, Noboru, Okazaki, Nobuo, Satoh, Shinya, Takio, Koji, Kuramitsu, Seiki, Shinkai, Akeo, ...
The crystal structure of the stand-alone RAM domain from T. thermophilus HB8 has been determined at 2.4 Å resolution. The structure revealed that five dimers are arranged to form a ring.
Yanagisawa, Tatsuo, Ishii, Ryohei, Fukunaga, Ryuya, Nureki, Osamu, Yokoyama, Shigeyuki
Pyrrolysyl-tRNA synthetase (PylRS) from M. mazei has been overexpressed in an N-terminally truncated form PylRS(c270) in Escherichia coli, purified to homogeneity and crystallized by the hanging-drop...
Biochemical analysis of the N-terminal domain of human RAD54B
Sarai, Naoyuki, Kagawa, Wataru, Fujikawa, Norie, Saito, Kengo, Hikiba, Juri, Tanaka, Kozo, ...
The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less...
Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain
Hatayama, Minoru, Tomizawa, Tadashi, Sakai-Kato, Kumiko, Bouvagnet, Patrice, Kose, Shingo, Imamoto, Naoko, ...
Disruptions in ZIC3 cause heterotaxy, a congenital anomaly of the left–right axis. ZIC3 encodes a nuclear protein with a zinc finger (ZF) domain that contains five tandem C2H2 ZF motifs. Missense...
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,...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Baba, Seiki, Chen, Lirong, Liu, Zhi-Jie, ...
The molybdenum-cofactor biosynthesis protein C from T. thermophilus has been crystallized in two different space groups, P21 and R32; the crystals diffracted to 1.9 and 1.75 Å resolution,...
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...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Baba, Seiki, Kuroishi, Chizu, Ebihara, Akio, ...
DHNA synthetase from G. kaustophilus has been cloned, expressed, purified and crystallized.
Fukunaga, Ryuya, Yokoyama, Shigeyuki
The N- and C-terminal fragments of alanyl-tRNA synthetase from the archaeon A. fulgidus have been crystallized.
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...
Nakamura, Yoshihiro, Umehara, Takashi, Tanaka, Akiko, Horikoshi, Masami, Padmanabhan, Balasundaram, Yokoyama, Shigeyuki
The complex of the non-ATPase subunit Nas6 with the C-terminal domain of the ATPase subunit Rpt3 of the 26S proteasome from S. cerevisiae was co-expressed in E. coli and purified to homogeneity. The...
An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules
Kimoto, Michiko, Kawai, Rie, Mitsui, Tsuneo, Yokoyama, Shigeyuki, Hirao, Ichiro
Toward the expansion of the genetic alphabet, we present an unnatural base pair system for efficient PCR amplification, enabling the site-specific incorporation of extra functional components into...
Oki, Kenji, Sakamoto, Kensaku, Kobayashi, Takatsugu, Sasaki, Hiroshi M., Yokoyama, Shigeyuki
To guarantee specific tRNA and amino acid pairing, several aminoacyl-tRNA synthetases correct aminoacylation errors by deacylating or “editing” misaminoacylated tRNA. A previously developed...
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Ohmori, Miwa, Agari, Kazuko, Kitamura, Yoshiaki, ...
The molybdopterin synthase from T. thermophilus HB8 was cloned, expressed, purified and crystallized. The crystals belong to space group P21 and diffracted to a resolution of 1.64 Å.
Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8
Kanaujia, Shankar Prasad, Ranjani, Chellamuthu Vasuki, Jeyakanthan, Jeyaraman, Nishida, Masami, Kitamura, Yoshiaki, Baba, Seiki, ...
The glucose dehydrogenase (GDH) protein from T. thermophilus HB8 was cloned, expressed, purified and crystallized. GDH crystals belong to space group P21 and diffract to 1.9 Å resolution.
Inagaki, Eiji, Ohshima, Noriyasu, Sakamoto, Keiko, Babayeva, Nigar D., Kato, Hiroaki, Yokoyama, Shigeyuki, ...
A crystal structure of NADP+-bound T. thermophilus Δ1-pyrroline-5-carboxylate dehydrogenase refined to 1.55 Å resolution is reported. The structure provides structural insights into the mechanism...
Umehara, Takashi, Wakamori, Masatoshi, Tanaka, Akiko, Padmanabhan, Balasundaram, Yokoyama, Shigeyuki
The C-terminal bromodomain of human BRD2 was cloned, expressed, purified and crystallized. A complete diffraction data set has been collected to 1.80 Å resolution.
Ishii, Ryohei, Minagawa, Asako, Takaku, Hiroaki, Takagi, Masamichi, Nashimoto, Masayuki, Yokoyama, Shigeyuki
The crystal structure of T. maritima tRNase Z has been determined at 1.97 Å. The structure shows the flexible arm and the fully metal-binding active site.
Kumarevel, Thirumananseri, Tanaka, Tomoyuki, Umehara, Takashi, Yokoyama, Shigeyuki
ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global...
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...
Kanai, Akio, Sato, Asako, Fukuda, Yoko, Okada, Kiyoshi, Matsuda, Takashi, Sakamoto, Taiichi, ...
Using an expression protein library of a hyperthermophilic archaeon, Pyrococcus furiosus, we identified a gene (PF0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase...
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...
Crystal structure of human selenocysteine tRNA
Itoh, Yuzuru, Chiba, Shiho, Sekine, Shun-ichi, Yokoyama, Shigeyuki
Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNASec) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNASec. tRNASec has a 9-bp...
Nakano, Noboru, Kumarevel, Thirumananseri, Matsunaga, Emiko, Shinkai, Akeo, Kuramitsu, Seiki, Yokoyama, Shigeyuki
A putative member of the Lrp/AsnC family of transcriptional regulators, ST1022 from S. tokodaii strain 7, has been purified and crystallized in the absence and presence of the effector l-glutamine. A...
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...