Shigeyuki Yokoyama

Summary

Affiliation: RIKEN Brain Science Institute
Country: Japan

Publications

  1. pmc A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.)
    Tatsuo Yanagisawa
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, 230 0045, Japan
    J Struct Funct Genomics 16:25-41. 2015
  2. pmc Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2
    Hiroaki Tanabe
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    J Struct Funct Genomics 16:11-23. 2015
  3. pmc Development of a hexahistidine-3× FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris
    Toshiaki Higo
    Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi, Yokohama, Kanagawa, 230 0045, Japan
    J Struct Funct Genomics 15:191-9. 2014
  4. pmc Crystal structures of the S6K1 kinase domain in complexes with inhibitors
    Hideaki Niwa
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, 230 0045, Japan
    J Struct Funct Genomics 15:153-64. 2014
  5. pmc Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine
    Mitsuo Kuratani
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    J Struct Funct Genomics 15:173-80. 2014
  6. pmc Crystal structure of the eukaryotic translation initiation factor 2A from Schizosaccharomyces pombe
    Kazuhiro Kashiwagi
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo, 113 0033, Japan
    J Struct Funct Genomics 15:125-30. 2014
  7. pmc Tertiary structure of bacterial selenocysteine tRNA
    Yuzuru Itoh
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nucleic Acids Res 41:6729-38. 2013
  8. pmc Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1)
    Aya Kitamura
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Biol Chem 287:43950-60. 2012
  9. pmc Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis
    Balasundaram Padmanabhan
    Department of Biophysics, National Institute of Mental Health and Neuro Sciences NIMHANS, Bangalore 560029, India
    BMC Struct Biol 13:10. 2013
  10. ncbi request reprint Ectodomain structures of the CGRP and AM receptors
    Seisuke Kusano
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Curr Protein Pept Sci 14:375-85. 2013

Collaborators

Detail Information

Publications71

  1. pmc A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.)
    Tatsuo Yanagisawa
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, 230 0045, Japan
    J Struct Funct Genomics 16:25-41. 2015
    ..Therefore, we propose that MM1309 functions as either a guardian protein that protects the Cys moiety from oxidation or an alternative translation factor for Cys-tRNA(Cys). ..
  2. pmc Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2
    Hiroaki Tanabe
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    J Struct Funct Genomics 16:11-23. 2015
    ..X-ray diffraction data sets were obtained at resolutions of 2.8 and 2.4 Å, respectively. ..
  3. pmc Development of a hexahistidine-3× FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris
    Toshiaki Higo
    Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi, Yokohama, Kanagawa, 230 0045, Japan
    J Struct Funct Genomics 15:191-9. 2014
    ..The method described here will be widely useful for the rapid and large-scale preparation of crystallization grade eukaryotic multi-subunit protein complexes. ..
  4. pmc Crystal structures of the S6K1 kinase domain in complexes with inhibitors
    Hideaki Niwa
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, 230 0045, Japan
    J Struct Funct Genomics 15:153-64. 2014
    ..Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein. The structural features required for the specific binding of inhibitors are discussed...
  5. pmc Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine
    Mitsuo Kuratani
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    J Struct Funct Genomics 15:173-80. 2014
    ..aeolicus, T. thermophilus, and P. abyssi...
  6. pmc Crystal structure of the eukaryotic translation initiation factor 2A from Schizosaccharomyces pombe
    Kazuhiro Kashiwagi
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo, 113 0033, Japan
    J Struct Funct Genomics 15:125-30. 2014
    ..Highly conserved residues are concentrated in the positively-charged top face, suggesting the importance of this face for interactions with nucleic acids or other initiation factors. ..
  7. pmc Tertiary structure of bacterial selenocysteine tRNA
    Yuzuru Itoh
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nucleic Acids Res 41:6729-38. 2013
    ..kandleri SerRS lacks interactions with A. aeolicus tRNA(Sec) in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNA(Sec) to enter the SerRS catalytic site. ..
  8. pmc Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1)
    Aya Kitamura
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Biol Chem 287:43950-60. 2012
    ..aeolicus contains the 5-mnm group attached to the C5 atom of U34. Taken together, these results support the recent proposal of an alternative MnmC1-independent shortcut pathway for producing mnm(5)U34 in tRNAs...
  9. pmc Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis
    Balasundaram Padmanabhan
    Department of Biophysics, National Institute of Mental Health and Neuro Sciences NIMHANS, Bangalore 560029, India
    BMC Struct Biol 13:10. 2013
    ..In the anaerobic pathway of cobalamin (vitamin B12) synthesis, the CbiT enzyme plays two roles, as a cobalt-precorrin-7 C15-methyltransferase and a C12-decarboxylase, to produce the intermediate, cobalt-precorrin 8...
  10. ncbi request reprint Ectodomain structures of the CGRP and AM receptors
    Seisuke Kusano
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Curr Protein Pept Sci 14:375-85. 2013
    ..These structural features of the ectodomains are consistent with mutagenesis results, and are useful to further examine the binding modes of the peptide ligands to the full-length CGRP and AM₁ receptors...
  11. pmc Mathematical model for empirically optimizing large scale production of soluble protein domains
    Eisuke Chikayama
    Genomic Sciences Center RIKEN, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    BMC Bioinformatics 11:113. 2010
    ..Here, we report a mathematical model for empirically optimizing the cost of large-scale domain production in proteomics research...
  12. ncbi request reprint Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA
    Mitsuo Kuratani
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Mol Biol 375:1064-75. 2008
    ..However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate...
  13. pmc Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
    Takatsugu Kobayashi
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Proc Natl Acad Sci U S A 102:1366-71. 2005
    ..These results demonstrate that the amino acid-binding pocket on the 37V195C mutant is optimized for specific 3-iodo-L-tyrosine recognition...
  14. ncbi request reprint Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability
    Neratur K Lokanath
    Highthroughput Factory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo gun, Hyogo 679 5148, Japan
    Acta Crystallogr D Biol Crystallogr 60:1816-23. 2004
    ..From these results, it is concluded that the oligomeric state of 2-deoxyribose-5-phosphate aldolase is important for the thermostability and not for the catalytic function...
  15. ncbi request reprint Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8
    Neratur K Lokanath
    Highthroughput Factory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo gun, Hyogo 679 5148, Japan
    J Mol Biol 352:905-17. 2005
    ..A kinetic study confirms that this enzyme has strict substrate specificity for 3-hydroxyisobutyrate and serine, but it cannot distinguish the chirality of the substrates. Lys165 is likely the catalytic residue of the enzyme...
  16. doi request reprint Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins
    Akio Ebihara
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Proteins 71:2097-101. 2008
  17. ncbi request reprint Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal
    Sachiko Yoshiba
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    J Biol Chem 279:37163-74. 2004
    ..This water molecule is situated at an ideal position to carry out nucleophilic attack on the adenosyl phosphate, as it is 3.6 A away from the target phosphorus and almost in line with the scissile bond...
  18. ncbi request reprint Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii
    Yuzuru Itoh
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    RNA Biol 5:169-77. 2008
    ..Two sulfate ions are bound to the channel, suggesting that the tRNA 3' region might bind to the channel...
  19. pmc Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding
    Thirumananseri Kumarevel
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Nucleic Acids Res 36:4808-20. 2008
    ....
  20. ncbi request reprint Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase
    Ryuya Fukunaga
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Mol Biol 359:901-12. 2006
    ..The T233A and H319A mutants have detectable editing activities against the cognate isoleucine...
  21. doi request reprint Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin
    Mitsuo Kuratani
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Mol Biol 401:323-33. 2010
    ..We also discuss previous genetic and biochemical data on human NSUN2/hTrm4/Misu and archaeal PAB1947 methyltransferase, based on the structure of M. jannaschii Trm4...
  22. pmc Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase
    Hiroshi M Sasaki
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo 113 0033, Japan
    Proc Natl Acad Sci U S A 103:14744-9. 2006
    ..In particular, the replacement of Asn-217 abolished the activity, revealing its absolute requirement for the catalysis...
  23. doi request reprint Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator
    Yoshihiro Agari
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Mol Microbiol 70:60-75. 2008
    ..coli CRP. Based on the properties of the SdrP-regulated genes found in this study, it is speculated that SdrP is involved in nutrient and energy supply, redox control, and polyadenylation of mRNA...
  24. doi request reprint Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation
    Sakurako Goto-Ito
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
    Nat Struct Mol Biol 16:1109-15. 2009
    ..This interaction by D1 lowers the K(m) value for tRNA, enabling the D2-D3 catalysis. Thus, we propose that aTrm5 provides the tertiary structure checkpoint in tRNA maturation...
  25. ncbi request reprint Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis
    Sakurako Goto-Ito
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Acta Crystallogr D Biol Crystallogr 63:1059-68. 2007
    ..On the basis of the surface properties, a docking model of P. horikoshii TYW1, the tRNA, the FeS clusters and the AdoMet molecule was constructed, with the nucleoside at position 37 of tRNA flipped out from the canonical tRNA structure...
  26. ncbi request reprint Crystal structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase
    Eiji Inagaki
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Mol Biol 362:490-501. 2006
    ..8 A, 1.9 A, and 1.4 A resolution, respectively. The solved structures suggest an overall view of the P5CDh catalytic mechanism and provide insights into the P5CDh deficiencies in the case of the human type II hyperprolinemia...
  27. ncbi request reprint Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme
    Ryuichiro Ishitani
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Cell 113:383-94. 2003
    ..Consequently, the enzyme precisely locates the exposed G15 in the active site, by counting the nucleotide number from G1 to G15 in the lambda form...
  28. doi request reprint Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5
    Sakurako Goto-Ito
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo ku, Tokyo 113 0033, Japan
    Proteins 72:1274-89. 2008
    ..The positive charges on the surface of D2-D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2-D3 region plays the major role in tRNA methylation...
  29. ncbi request reprint Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8
    Jun Hoseki
    RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki, Sayo gun, Hyogo 679 5148, Japan
    J Mol Biol 333:515-26. 2003
    ..coli MUG (family 2). These results suggest that the mechanism by which family 4 UDGs remove uracils from DNA is similar to that of family 1 enzymes...
  30. ncbi request reprint Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus
    Ryuya Fukunaga
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Mol Biol 370:128-41. 2007
    ..One of the three strictly conserved Cys residues (Cys39, Cys42, or Cys247), of one subunit may play a crucial role in the catalysis in the active site of the other subunit...
  31. ncbi request reprint Crystal structure of purine nucleoside phosphorylase from Thermus thermophilus
    Tahir H Tahirov
    Highthroughput Factory, RIKEN Harima Institute, 1 1 1 Kouto, Mikazuki cho, Sayo gun, Hyogo 679 5148, Japan
    J Mol Biol 337:1149-60. 2004
    ..The obtained experimental data suggest that the catalytic properties of the T.thermophilus enzyme are reminiscent of the trimeric rather than hexameric purine nucleoside phosphorylases...
  32. pmc Crystallization screening test for the whole-cell project on Thermus thermophilus HB8
    Hitoshi Iino
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:487-91. 2008
    ..The structures of 360 of 944 purified proteins have been successfully determined through the combined use of an HTS-80 and a TERA...
  33. ncbi request reprint Thermodynamic basis for the stabilities of three CutA1s from Pyrococcus horikoshii,Thermus thermophilus, and Oryza sativa, with unusually high denaturation temperatures
    Masahide Sawano
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Biochemistry 47:721-30. 2008
    ....
  34. ncbi request reprint Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion
    Takatsugu Kobayashi
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nat Struct Biol 10:425-32. 2003
    ..Based on this finding, we created a mutant TyrRS that aminoacylates the amber suppressor tRNA with C34 65 times more efficiently than does the wild-type enzyme...
  35. ncbi request reprint Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase
    Shun ichi Sekine
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Structure 14:1791-9. 2006
    ..These structures, together with our previously described structures, reveal that tRNA plays a crucial role in accurate positioning of both L-glutamate and ATP, thus driving the amino acid activation...
  36. ncbi request reprint Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase
    Wataru Iwasaki
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Mol Biol 360:329-42. 2006
    ..We performed a mutational analysis of this particular arginine residue, and confirmed its significance in the tRNA recognition...
  37. doi request reprint Functional identification of an anti-sigmaE factor from Thermus thermophilus HB8
    Keiko Sakamoto
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Gene 423:153-9. 2008
    ..Thus, TTHB212 protein was identified as an anti-sigma(E) factor. These findings indicate that T. thermophilus HB8 has a regulatory system involving sigma(E) and anti-sigma(E) factors...
  38. pmc Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog
    Kenji Oki
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Proc Natl Acad Sci U S A 105:13298-303. 2008
    ..Thus, the editing-domain transplantation achieved unambiguous pairing between the tRNA and the nonnatural amino acid in an expanded genetic code...
  39. ncbi request reprint Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer
    Yuko Hisanaga
    Structural Biophysics Laboratory, RIKEN Harima Institute at SPring 8, Sayo, Hyogo, Japan
    J Biol Chem 279:31717-26. 2004
    ..Based on these high resolution crystal structures, we propose a unidirectional Bi Uni Uni Bi Ping-Pong mechanism for the two-step acylation by ttLC-FACS...
  40. ncbi request reprint A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI
    Naoki Kunishima
    Highthroughput Factory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Sayo gun, Hyogo 679 5148, Japan
    J Mol Biol 352:212-28. 2005
    ....
  41. ncbi request reprint The putative DNA-binding protein Sto12a from the thermoacidophilic archaeon Sulfolobus tokodaii contains intrachain and interchain disulfide bonds
    Akeo Shinkai
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Mol Biol 372:1293-304. 2007
    ..This is a novel fold among winged-helix DNA-binding proteins. Possible DNA-binding interactions of the Sto12a protein are discussed based on the crystal structure of Sto12a and comparisons to other winged-helix DNA-binding proteins...
  42. ncbi request reprint A two-unnatural-base-pair system toward the expansion of the genetic code
    Ichiro Hirao
    Research Center for Advanced Science and Technology, The University of Tokyo, 4 6 1 Komaba, Meguro ku, Tokyo 153 8904, Japan
    J Am Chem Soc 126:13298-305. 2004
    ..These unnatural-base-pair studies provide valuable information for understanding the mechanisms of replication and transcription...
  43. ncbi request reprint Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase
    Takatsugu Kobayashi
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Mol Biol 346:105-17. 2005
    ..After the amino acid activation, the KMSKS loop adopts the semi-open form again to accept the CCA end of tRNA for the aminoacyl transfer reaction...
  44. ncbi request reprint Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain 7
    Thirumananseri Kumarevel
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Struct Biol 161:9-17. 2008
    ..We also show the protein-DNA interactions by biochemical methods. Our molecular modeling analysis suggested that Asp88 and Arg90 are the key residues in ST1710 involved in the protein-DNA interactions...
  45. pmc Structure of a UPF0150-family protein from Thermus thermophilus HB8
    Nobuo Okazaki
    RIKEN SPring 8 Center, Harima Institute, Sayo, Hyogo 679 5148, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:173-7. 2007
    ..Based on the properties and functions of structural homologues of the TTHA0281 monomer, the TTHA0281 protein is speculated to be involved in RNA metabolism, including RNA binding and cleavage...
  46. ncbi request reprint Site-specific functionalization of proteins by organopalladium reactions
    Koichiro Kodama
    Department of Biophysics and Biochemistry, School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Chembiochem 8:232-8. 2007
    ..Site-specific biotinylations of the Ras protein were confirmed by Western blot and LC-MS/MS...
  47. ncbi request reprint Hyper-thermostability of CutA1 protein, with a denaturation temperature of nearly 150 degrees C
    Tomoyuki Tanaka
    RIKEN SPring 8 Center, Harima Institute, Kouto, Sayo, Hyogo 679 5148, Japan
    FEBS Lett 580:4224-30. 2006
    ....
  48. pmc Expression, purification, crystallization and preliminary X-ray diffraction analysis of galactokinase from Pyrococcus horikoshii
    Eiji Inagaki
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:169-71. 2006
    ..57 A, beta = 109.8 degrees. The ternary complex form was isomorphous with the apo form, except for the length of the a axis. The galactokinase activity of the enzyme was confirmed and the kinetic parameters at 323 K were determined...
  49. doi request reprint Site-specific incorporation of 4-iodo-L-phenylalanine through opal suppression
    Koichiro Kodama
    Department of Biophysics and Biochemistry, School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo, Tokyo
    J Biochem 148:179-87. 2010
    ..The 4-iodo-l-phenylalanine residue can be used for the chemoselective modification of proteins. This method will contribute to advancements in protein engineering studies with non-natural amino acid substitutions...
  50. ncbi request reprint Crystal structures of tyrosyl-tRNA synthetases from Archaea
    Mitsuo Kuratani
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Mol Biol 355:395-408. 2006
    ..In addition, a non-proline cis peptide bond, which is involved in the tRNA binding, is conserved among the archaeal TyrRSs...
  51. ncbi request reprint A new protein engineering approach combining chemistry and biology, part I; site-specific incorporation of 4-iodo-L-phenylalanine in vitro by using misacylated suppressor tRNAPhe
    Koichiro Kodama
    Department of Biophysics and Biochemistry, School of Science The University of Tokyo, 7 3 1 Hongo Bunkyo ku, Tokyo 113 0033, Japan
    Chembiochem 7:1577-81. 2006
    ..coli cell-free system. Our approach will find wide application in protein engineering since an aryl iodide tag on proteins can be used for site-specific functionalization of proteins...
  52. ncbi request reprint Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa
    Toru Sengoku
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Tokyo 113 0033, Japan
    Cell 125:287-300. 2006
    ..This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures...
  53. doi request reprint Crystal structure of TTHA0061, an uncharacterized protein from Thermus thermophilus HB8, reveals a novel fold
    Tomoyuki Tanaka
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Biochem Biophys Res Commun 400:258-64. 2010
    ..Differential scanning calorimetry analysis suggested that the thermostability of TTHA0061 increased at pH ranges of 5.8-6.2, perhaps due to the abundance of glutamic acid residues...
  54. ncbi request reprint Stabilization due to dimer formation of phosphoribosyl anthranilate isomerase from Thermus thermophilus HB8: X-ray Analysis and DSC experiments
    Junichiro Taka
    RIKEN Harima Institute at SPring8, 1 1 1 Kohto, Mikazukicho, Sayo, Hyogo 679 5148
    J Biochem 137:569-78. 2005
    ....
  55. doi request reprint Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures
    Satoshi Arai
    Department of Chemistry, Graduate School of Science, Chiba University, 1 33 Yayoi cho, Inage, Chiba 263 8522, Japan
    Nature 493:703-7. 2013
    ..To our knowledge, these asymmetric structures represent the first high-resolution view of the rotational mechanism of V(1)-ATPase...
  56. doi request reprint Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon
    Ryuya Fukunaga
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Biochem Biophys Res Commun 372:480-5. 2008
    ..9muM and 0.111s(-1)). The triple mutant SepRS and the tRNA with the PaUA anticodon represent a specific pair for the site-specific incorporation of phosphoserine into proteins in response to the UADs codon within mRNA...
  57. pmc Identification of promoters recognized by RNA polymerase-sigmaE holoenzyme from Thermus thermophilus HB8
    Akeo Shinkai
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Bacteriol 189:8758-64. 2007
    ..With the combination of in vitro transcription assay and GeneChip technology, we identified three promoters recognized by sigma(E). The predicted consensus promoter sequence for sigma(E) is 5'-CA(A/T)(A/C)C(A/C)-N(15)-CCGTA-3'...
  58. ncbi request reprint Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii
    Ryuya Fukunaga
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Acta Crystallogr D Biol Crystallogr 63:390-400. 2007
    ..The glycine-rich loop is located near the active site and may be involved in substrate recognition and/or catalysis...
  59. ncbi request reprint Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1
    Thirumananseri Kumarevel
    RIKEN SPring 8 Center, Harima Institute, Sayo, Hyogo 679 5148, Japan
    Proteins 71:1156-62. 2008
    ..In addition, we showed that Ape10b2 binds to 16 and 39 bp duplex DNAs with high affinity. On the basis of our analyses, we have created a putative protein-DNA complex model...
  60. pmc ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding
    Shun ichi Sekine
    Cellular Signaling Laboratory and Structurome Group, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
    EMBO J 22:676-88. 2003
    ..Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite...
  61. ncbi request reprint An efficient unnatural base pair for a base-pair-expanded transcription system
    Tsuneo Mitsui
    Research Center for Advanced Science and Technology, The University of Tokyo, 4 6 1 Komaba, Meguro ku, Tokyo 153 8904, Japan
    J Am Chem Soc 127:8652-8. 2005
    ..This specific transcription allows the large-scale preparation of artificial RNAs and can be combined with other systems to simultaneously incorporate several different components into a transcript...
  62. ncbi request reprint Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative
    Yoko Tanaka
    Department of Biology, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Biochem 138:263-75. 2005
    ..Superimpositioning of the structures indicates the imidazole ring of His110 is rotated, implying concomitant proton transfer to the ribose ring O4'. Based on these structural data we propose a novel reaction mechanism for GTPCH1...
  63. doi request reprint Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein
    Shunsuke Tagami
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Nature 468:978-82. 2010
    ..The ratcheted state might also be associated with other aspects of transcription, such as RNAP translocation and transcription termination...
  64. ncbi request reprint Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis
    Naoyuki Kondo
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    Acta Crystallogr D Biol Crystallogr 63:230-9. 2007
    ..Recognition of the triphosphate moiety crucial for the activity might be attained by highly conserved positively charged residues. The possible mode of dNTP binding is discussed in light of the structure...
  65. doi request reprint Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA
    Hirofumi Nakagawa
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Proteins 81:1232-44. 2013
    ..A positively charged surface that includes the catalytic site and the two zinc fingers is likely to provide the tRNA-binding site...
  66. pmc ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators
    Thirumananseri Kumarevel
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Nucleic Acids Res 37:4723-35. 2009
    ..Conserved wHtH loop residues interacting with the bound DNA and mutagenic analysis indicated that R89, R90 and K91 were important for DNA recognition. Significantly, the bound DNA exhibited a new binding mechanism...
  67. pmc Biochemical and structural studies on the high affinity of Hsp70 for ADP
    Akihiko Arakawa
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
    Protein Sci 20:1367-79. 2011
    ..In ADP-ATP exchange, the slow ADP dissociation might be rate-limiting. However, the nucleotide-exchange factors actually enhance ADP release by disrupting the Mg(2+) ion-mediated network...
  68. ncbi request reprint Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus
    Mitsuo Kuratani
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Biol Chem 280:16002-8. 2005
    ..This cavity contains many conserved amino acid residues that are likely to be involved in either catalysis or tRNA binding. We made a docking model of TadA with the tRNA anticodon stem loop...
  69. ncbi request reprint Cold denaturation of ubiquitin at high pressure
    Ryo Kitahara
    RIKEN SPring 8 Center, RIKEN Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Magn Reson Chem 44:S108-13. 2006
    ..8-5.8 (kJ/Kmol), which is consistent with the fact that the denaturation takes place from a mixture of N and I at 2 kbar rather than from pure N at 1 bar...
  70. pmc Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization
    Masahiro Naganuma
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    Proc Natl Acad Sci U S A 106:8489-94. 2009
    ..The helical subdomain mediates dimerization by forming a helix-loop-helix zipper. The globular subdomain, which is important for the aminoacylation and editing activities, has a positively-charged face suitable for tRNA binding...
  71. pmc Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain
    Akio Ebihara
    RIKEN SPring 8 Center, Harima Institute, Hyogo 679 5148, Japan
    Protein Sci 15:1494-9. 2006
    ..This report shows that TTHB192 and its sequence homologs adopt an RNA recognition motif-like domain and provides the first testable functional hypothesis for this protein family...