S Yokoyama

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. doi request reprint Wide-range protein photo-crosslinking achieved by a genetically encoded N(ε)-(benzyloxycarbonyl)lysine derivative with a diazirinyl moiety
    Tatsuo Yanagisawa
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Mol Biosyst 8:1131-5. 2012
  2. ncbi request reprint [NMR for protein structure analysis]
    Fumiaki Hayashi
    Tanpakushitsu Kakusan Koso 49:1800-8. 2004
  3. ncbi request reprint Structural genomics projects in Japan
    S Yokoyama
    Genomic Sciences Center, RIKEN Yokohama Institute, Tsurumi, Japan
    Nat Struct Biol 7:943-5. 2000
  4. ncbi request reprint Protein expression systems for structural genomics and proteomics
    Shigeyuki Yokoyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Curr Opin Chem Biol 7:39-43. 2003
  5. ncbi request reprint [Large-scale structural proteomics project at RIKEN: present and future]
    Shigeyuki Yokoyama
    Tanpakushitsu Kakusan Koso 50:836-45. 2005
  6. ncbi request reprint Holliday junction binding activity of the human Rad51B protein
    Hiroshi Yokoyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 278:2767-72. 2003
  7. pmc Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305 8566, Japan
    Plant Cell 16:3448-59. 2004
  8. ncbi request reprint Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses
    Kanako Kuwasako
    Protein Research Group, RIKEN Genomic Sciences Center, Yokohama 230 0045, Japan
    Proteins 71:1617-36. 2008
  9. ncbi request reprint A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Insitute of Advanced Industrial Science and Technology, Tsukuba, Japan
    J Mol Biol 337:49-63. 2004
  10. ncbi request reprint Homologous pairing promoted by the human Rad52 protein
    W Kagawa
    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
    J Biol Chem 276:35201-8. 2001

Detail Information

Publications99

  1. doi request reprint Wide-range protein photo-crosslinking achieved by a genetically encoded N(ε)-(benzyloxycarbonyl)lysine derivative with a diazirinyl moiety
    Tatsuo Yanagisawa
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Mol Biosyst 8:1131-5. 2012
    ..The incorporated photo-crosslinker is able to react not only with residues as distant as about 15 Å but also with those in closer proximity, thus enabling "wide-range" photo-crosslinking of proteins...
  2. ncbi request reprint [NMR for protein structure analysis]
    Fumiaki Hayashi
    Tanpakushitsu Kakusan Koso 49:1800-8. 2004
  3. ncbi request reprint Structural genomics projects in Japan
    S Yokoyama
    Genomic Sciences Center, RIKEN Yokohama Institute, Tsurumi, Japan
    Nat Struct Biol 7:943-5. 2000
    ..The newest, the structural genomics project at the Biological Information Research Center, focuses on human membrane proteins...
  4. ncbi request reprint Protein expression systems for structural genomics and proteomics
    Shigeyuki Yokoyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Curr Opin Chem Biol 7:39-43. 2003
    ..Protein folding is still a major bottleneck in protein expression. Cell-based and cell-free methods for screening of suitable samples for structure determination have been developed for achieving a high success rate...
  5. ncbi request reprint [Large-scale structural proteomics project at RIKEN: present and future]
    Shigeyuki Yokoyama
    Tanpakushitsu Kakusan Koso 50:836-45. 2005
  6. ncbi request reprint Holliday junction binding activity of the human Rad51B protein
    Hiroshi Yokoyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 278:2767-72. 2003
    ..Therefore, the Rad51B protein may have a specific function in Holliday junction processing in the homologous recombinational repair pathway in humans...
  7. pmc Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305 8566, Japan
    Plant Cell 16:3448-59. 2004
    ..The locations of the DNA-contacting residues are also likely to be similar to those of the EcoRII DNA binding domain...
  8. ncbi request reprint Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses
    Kanako Kuwasako
    Protein Research Group, RIKEN Genomic Sciences Center, Yokohama 230 0045, Japan
    Proteins 71:1617-36. 2008
    ..Collectively, this study provides details for the protein-recognition mode of p14 and insight into the branch site recognition...
  9. ncbi request reprint A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Insitute of Advanced Industrial Science and Technology, Tsukuba, Japan
    J Mol Biol 337:49-63. 2004
    ..The electrostatic profile on the surface suggested that a continuous region, including all the conserved basic residues, is involved in the DNA binding, the mode of which is likely to be novel as well...
  10. ncbi request reprint Homologous pairing promoted by the human Rad52 protein
    W Kagawa
    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
    J Biol Chem 276:35201-8. 2001
    ..Our results reveal the striking similarity between HsRad52 and the Escherichia coli RecT protein, which functions in a RecA-independent recombination pathway...
  11. pmc Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA
    Y Tanaka
    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
    EMBO J 20:6612-8. 2001
    ..The overall bending angle is 59 degrees, which may be important for the centromere-specific chromatin structure...
  12. ncbi request reprint Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1
    Takashi Kinebuchi
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Mol Cell 14:363-74. 2004
    ..The inner patch binds both single-stranded and double-stranded DNAs, while the outer one binds single-stranded DNA. Based on these results, we propose a model for the interaction of the Dmc1 rings with DNA...
  13. pmc Structural basis of replication origin recognition by the DnaA protein
    Norie Fujikawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 31:2077-86. 2003
    ..These base-specific interactions explain how DnaA exhibits higher affinity for the strong DnaA boxes (R1, R2 and R4) than the weak DnaA boxes (R3 and M) in the replication origin...
  14. ncbi request reprint Identification of functional domains of the Escherichia coli SeqA protein
    Norie Fujikawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Biochem Biophys Res Commun 300:699-705. 2003
    ..Therefore, two essential SeqA activities, self-association and DNA-binding, are independently performed by the structurally distinct N-terminal and C-terminal domains, respectively...
  15. ncbi request reprint Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)
    Takeshi Maeda
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 279:13174-82. 2004
    ..On the other hand the tissue tumor marker MUC1 has a SEA domain belonging to another subfamily, and its GSVVV motif for proteolytic cleavage is located in the short loop connecting beta2 and beta3...
  16. pmc Solution structure of an Arabidopsis WRKY DNA binding domain
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305 8566, Japan
    Plant Cell 17:944-56. 2005
    ..Based on a profile of NMR chemical shift perturbations, we propose that the same strand enters the DNA groove and forms contacts with the DNA bases...
  17. doi request reprint Structures and evolutionary origins of plant-specific transcription factor DNA-binding domains
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    Plant Physiol Biochem 46:394-401. 2008
    ....
  18. pmc Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine
    Augen A Pioszak
    RIKEN Genomic Sciences Center, Yokohama, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:867-74. 2005
    ..The architecture of the active site is consistent with specific recognition of uridine and catalysis of methyl transfer to the 5-carbon position. The cleft is suitable in size and charge distribution for binding single-stranded RNA...
  19. ncbi request reprint Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form
    Wataru Kagawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, Japan
    Mol Cell 10:359-71. 2002
    ..A mutational analysis revealed that the amino acid residues located between the beta-beta-beta-alpha fold and the characteristic hairpin loop are essential for ssDNA and dsDNA binding...
  20. ncbi request reprint Cell-free synthesis of zinc-binding proteins
    Takayoshi Matsuda
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Struct Funct Genomics 7:93-100. 2006
    ..NMR analyses confirmed that correctly folded proteins were synthesized by the cell-free method. These results indicate that the cell-free method can be used to synthesize correctly folded and functional zinc-binding proteins...
  21. pmc Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein
    Norie Fujikawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 32:82-92. 2004
    ..This electron density, which may be due to a water molecule or a metal ion, can exist in the hemimethylated state, but not in the fully methylated state, because of steric clash with the additional methyl group...
  22. ncbi request reprint Structural and functional differences of SWIRM domain subtypes
    Misao Yoneyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Mol Biol 369:222-38. 2007
    ..We also solved the structure of the SANT domain of MYSM1, and demonstrated that it bound DNA with a similar mode to that of the c-Myb DNA-binding domain...
  23. ncbi request reprint Solution structure of the human parvulin-like peptidyl prolyl cis/trans isomerase, hPar14
    T Terada
    Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Mol Biol 305:917-26. 2001
    ..Therefore, the mechanism determining the substrate specificity seems to be different between hPar14 and hPin1...
  24. ncbi request reprint Crystal structure of 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis
    Takashi Wada
    Genomic Sciences Center, RIKEN Yokohama Institute, and Protein Design Laboratory, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 278:30022-7. 2003
    ..Assaying the enzyme showed that CDP-ME kinase will phosphorylate CDP-ME but not 4-(uridine 5'-diphospho)-2-C-methyl-D-erythritol, indicating the substrate pyrimidine moiety is involved in important interactions with the enzyme...
  25. ncbi request reprint Selenomethionine incorporation into a protein by cell-free synthesis
    Takanori Kigawa
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, 230 0045 Japan
    J Struct Funct Genomics 2:29-35. 2002
    ..Therefore, the cell-free synthesis system could become a powerful protein expression method for high-throughput structure determinations by X-ray crystallography...
  26. ncbi request reprint Crystal structure of the RUN domain of the RAP2-interacting protein x
    Mutsuko Kukimoto-Niino
    RIKEN Genomic Sciences Center, Yokohama 230 0045, Japan
    J Biol Chem 281:31843-53. 2006
    ..In the crystal the putative Rap2 binding site of the RPIPx RUN domain interacts with the extended segment in a segment-swapping manner...
  27. ncbi request reprint Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8
    Hiroaki Sakai
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Struct Biol 149:99-110. 2005
    ..ATP and GlnK.ADP, have also been determined. ATP/ADP binding within a cleft at the interface of two adjacent T. thermophilus GlnK monomers might affect the conformation of the T-loop...
  28. ncbi request reprint An Arabidopsis SBP-domain fragment with a disrupted C-terminal zinc-binding site retains its tertiary structure
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    FEBS Lett 580:2109-16. 2006
    ....
  29. ncbi request reprint Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis
    Hiroyuki Kishida
    Protein Design Laboratory, Graduate School of Integrated Science, Yokohama City University, 1 7 29 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Acta Crystallogr D Biol Crystallogr 59:23-31. 2003
    ..At the high resolution of the refinement (1.6 A) the positions and coordination of the magnesium ions in the active site are clearly seen...
  30. ncbi request reprint A structure-based strategy for discovery of small ligands binding to functionally unknown proteins: combination of in silico screening and surface plasmon resonance measurements
    Naoei Yoshitani
    Protein Research Group, RIKEN Genomic Sciences Center, Yokohama, Japan
    Proteomics 5:1472-80. 2005
    ..They would be leads for the development of specific inhibitors/drugs for At2g24940, and provide important clues toward elucidation of the protein function...
  31. ncbi request reprint Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    J Mol Biol 348:253-64. 2005
    ..The structure consists of five alpha-helices, possessing a novel fold dissimilar to known DBD structures. By a chemical-shift perturbation analysis, a region including the ein3-3 site is suggested to be involved in DNA binding...
  32. doi request reprint Structural basis for the recognition of nucleophosmin-anaplastic lymphoma kinase oncoprotein by the phosphotyrosine binding domain of Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target-2
    Seizo Koshiba
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Struct Funct Genomics 11:125-41. 2010
    ..Our results indicate that the higher binding activity of the phosphorylation-independent binding site is caused by additional hydrophobic interactions...
  33. ncbi request reprint Preparation of Escherichia coli cell extract for highly productive cell-free protein expression
    Takanori Kigawa
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Struct Funct Genomics 5:63-8. 2004
    ....
  34. ncbi request reprint Temperature-dependent biosynthesis of 2-thioribothymidine of Thermus thermophilus tRNA
    Naoki Shigi
    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2 42 Aomi, Koto ku, Tokyo 135 0064, Japan
    J Biol Chem 281:2104-13. 2006
    ..Furthermore, we found that another posttranscriptionally modified nucleoside, 1-methyladenosine at position 58, is required for the efficient 2-thiolation of ribothymidine 54 both in vivo and in vitro...
  35. ncbi request reprint Role of the N-terminal domain of the human DMC1 protein in octamer formation and DNA binding
    Takashi Kinebuchi
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    J Biol Chem 280:28382-7. 2005
    ..Therefore, the N-terminal domain of DMC1 is required for the formation of the octamer, which may support the proper DNA binding activity of the DMC1 protein...
  36. pmc Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii
    Ali D Malay
    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro, Tsurumi, Yokohama 230 0045, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 65:1227-33. 2009
    ..The key phosphate-binding residues in the active site of Mj-GAPDH are conserved in other archaeal GAPDH proteins. These residues undergo a conformational shift in response to occupancy of the inorganic phosphate site...
  37. ncbi request reprint Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus
    Paul Reay
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Proteins 56:40-51. 2004
    ....
  38. ncbi request reprint Human centromere protein B induces translational positioning of nucleosomes on alpha-satellite sequences
    Yoshinori Tanaka
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 280:41609-18. 2005
    ..Therefore, CENP-B may be a determinant for translational positioning of the centromere-specific nucleosomes through its binding to the nucleosomal CENP-B box...
  39. ncbi request reprint Solution structure of the mouse enhancer of rudimentary protein reveals a novel fold
    Hua Li
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Yokohama, Tsurumi, 230 0045, Japan
    J Biomol NMR 32:329-34. 2005
  40. pmc Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii
    Balasundaram Padmanabhan
    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro, Tsurumi, Yokohama 230 0045, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 65:1222-6. 2009
    ..The binding-site region of MjDHDPS is essentially similar to those found in other known DHDPS structures...
  41. ncbi request reprint Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation
    Kay Fukushima
    Protein Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22, Suehiro cho, Tsurumi, Yokohama, Kanagawa, Japan
    J Mol Biol 321:317-27. 2002
    ..Indeed, in DFF35, the amino acid sequence is truncated in the middle of the second alpha helix constituting the structure of DFF-C, and thus both the hydrophobic core and the cluster of negative charges are disrupted...
  42. pmc Structure of putative 4-amino-4-deoxychorismate lyase from Thermus thermophilus HB8
    Balasundaram Padmanabhan
    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1 7 22 Suehiro, Tsurumi, Yokohama 230 0045, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 65:1234-9. 2009
    ..1.3.38) from Escherichia coli suggest that the TTHA0621 protein may also possess 4-amino-4-deoxychorismate lyase activity...
  43. pmc Structural characterization of the ribosome maturation protein, RimM
    Sakura Suzuki
    RIKEN Genomic Sciences Center, Yokohama, Japan
    J Bacteriol 189:6397-406. 2007
    ....
  44. pmc The crystal structure of leucyl/phenylalanyl-tRNA-protein transferase from Escherichia coli
    Xuesong Dong
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Protein Sci 16:528-34. 2007
    ..The conserved residues in the central cavity of L/F-transferase suggest that this region is important for the enzyme catalysis...
  45. pmc Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics
    Y Kuroda
    Protein Research Group, Genomic Sciences Center, The Institute of Physical and Chemical Research RIKEN, Yokohama, Kanagawa, Japan
    Protein Sci 9:2313-21. 2000
    ....
  46. pmc Dictyostelium IQGAP-related protein specifically involved in the completion of cytokinesis
    H Adachi
    Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3 8 1 Komaba, Meguro ku, Tokyo 153
    J Cell Biol 137:891-8. 1997
    ..Thus, it is possible that Dictyostelium GAPA participates in the severing of the midbody by regulating the actin cytoskeleton through an interaction with a member of small GTPases...
  47. ncbi request reprint Estimation of radiative heat transfer using a geometric human model
    N Kakuta
    Laboratory of Advanced Biomedical Engineering and Life Sciences, Center for Collaborative Research, The University of Tokyo, Japan
    IEEE Trans Biomed Eng 48:324-31. 2001
    ..The distribution of the radiative heat transfer rates shows the characteristics of body shape and variations in posture...
  48. ncbi request reprint Genomic and spectral analyses of long to middle wavelength-sensitive visual pigments of common marmoset (Callithrix jacchus)
    S Kawamura
    Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, 113 0033, Tokyo, Japan
    Gene 269:45-51. 2001
    ..The 'tri-allelic single-locus X-chromosome' model operates under the unique phenomenon, known as blood chimerism...
  49. pmc Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3
    Ryoichi Arai
    Protein Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22, Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Protein Sci 15:373-7. 2006
    ..Since heat-stable dehalogenases can be used for the detoxification of halogenated aliphatic compounds, PH0459 will be a useful target for biotechnological research...
  50. doi request reprint The NMR solution structures of the five constituent cold-shock domains (CSD) of the human UNR (upstream of N-ras) protein
    Alexander K Goroncy
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    J Struct Funct Genomics 11:181-8. 2010
    ..It also lends support to the hypothesis that the UNR protein arose by repeated duplication of a protein that originally contained just one CSD, and that the proto-UNR protein acquired cysteine C46 by mutation during evolution...
  51. doi request reprint Coupled transcription and translation from polymerase chain reaction-amplified DNA in Drosophila Schneider 2 cell-free system
    Motoaki Wakiyama
    RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230 0045, Japan
    Anal Biochem 400:142-4. 2010
    ..FLAG-tagged human Argonaute2 and TRBP2 were successfully synthesized within 90 min in a reaction volume of less than 10 microl and were detected by the FLAG antibody...
  52. doi request reprint A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P
    Tatsuo Yanagisawa
    RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan
    Nat Struct Mol Biol 17:1136-43. 2010
    ..In vivo analyses indicate that the EF-P modification by GenX and YjeK is essential for cell survival...
  53. pmc NMR solution structures of actin depolymerizing factor homology domains
    Alexander K Goroncy
    RIKEN Systems and Structural Biology Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, Japan
    Protein Sci 18:2384-92. 2009
    ..The G-actin binding site of the ADF-H domain of human HIP-55-drebrin-like protein is absent and distorted in mouse GMF beta and GMF gamma...
  54. pmc A Rac GTPase-activating protein, MgcRacGAP, is a nuclear localizing signal-containing nuclear chaperone in the activation of STAT transcription factors
    Toshiyuki Kawashima
    Division of Cellular Therapy, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    Mol Cell Biol 29:1796-813. 2009
    ..Thus, MgcRacGAP functions as both a critical mediator of STAT's tyrosine phosphorylation and an NLS-containing nuclear chaperone of p-STATs...
  55. pmc Crystal structure of the human receptor activity-modifying protein 1 extracellular domain
    Seisuke Kusano
    RIKEN Systems and Structural Biology Center, Yokohama 230 0045, Japan
    Protein Sci 17:1907-14. 2008
    ..These results suggest that the hydrophobic patch participates in the interaction with CRLR and the formation of the ligand-binding pocket when it forms the CRLR.RAMP1 heterodimer...
  56. doi request reprint Crystal structures of fission yeast histone chaperone Asf1 complexed with the Hip1 B-domain or the Cac2 C terminus
    Ali D Malay
    Yokohama Institute, RIKEN, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 283:14022-31. 2008
    ..1/H4 in vertebrates) in a replication-dependent pathway, whereas Asf1 and HIRA/Hip1 assemble histones H3/H4 (H3.3/H4 in vertebrates) in a replication-independent pathway...
  57. pmc Solution structure of the antifreeze-like domain of human sialic acid synthase
    Toshiyuki Hamada
    RIKEN Genomic Sciences Center, Yokohama 230 0045, Japan
    Protein Sci 15:1010-6. 2006
    ....
  58. ncbi request reprint Solution structure of an atypical WW domain in a novel beta-clam-like dimeric form
    Satoshi Ohnishi
    Genomic Sciences Center, RIKEN, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    FEBS Lett 581:462-8. 2007
    ....
  59. pmc Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3
    Naoya Tochio
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Protein Sci 15:2534-43. 2006
    ..This concave surface includes the highly conserved Glu-Leu-Lys-Leu motif at the C terminus, indicating that it is important for the function of the KA1 domain...
  60. ncbi request reprint Crystal structure of human myo-inositol monophosphatase 2, the product of the putative susceptibility gene for bipolar disorder, schizophrenia, and febrile seizures
    Ryoichi Arai
    Protein Research Group, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Proteins 67:732-42. 2007
    ....
  61. ncbi request reprint Improving cell-free protein synthesis for stable-isotope labeling
    Takayoshi Matsuda
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, 230 0045, Japan
    J Biomol NMR 37:225-9. 2007
    ..These results indicate that the D-Glu system is a highly productive cell-free system that is especially useful for stable-isotope labeling of proteins...
  62. ncbi request reprint Solution structure determination of the two DNA-binding domains in the Schizosaccharomyces pombe Abp1 protein by a combination of dipolar coupling and diffusion anisotropy restraints
    Jun Kikuchi
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan
    J Biomol NMR 22:333-47. 2002
    ..DNA complex is ellipsoid. This extended form would facilitate the recognition of the two separate sites in the relatively long DNA sequence by the DNA-binding domains of Apb1...
  63. pmc Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set
    Satoshi Akanuma
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230 0045, Japan
    Proc Natl Acad Sci U S A 99:13549-53. 2002
    ..Therefore, the catalytic function associated with a relatively large protein may be achieved with a subset of the 20 amino acid. The converged sequence also implies simpler constituents for proteins in the early stage of evolution...
  64. pmc Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein
    Hitoshi Kurumizaka
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nucleic Acids Res 31:4041-50. 2003
    ..Superposition of the Xrcc3 Tyr139 and Phe249 residues on the RecA structure suggested that Tyr139 may function to ensure proper folding and Phe249 may be important to constitute the Rad51C-binding interface in Xrcc3...
  65. ncbi request reprint Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8
    Hiroaki Sakai
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, 230 0045, Japan
    J Mol Biol 332:729-40. 2003
    ..This observation strongly suggests that LysX is an ATP-utilizing enzyme that shares a common evolutionary ancestor with other ATP-grasp fold proteins possessing a carboxylate-amine/thiol ligase activity...
  66. ncbi request reprint Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesis
    Namthip Chumpolkulwong
    RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan
    Eur J Biochem 271:1127-34. 2004
    ..Furthermore, when 14 mouse cDNA sequences were used as test templates, the protein yields of nine templates in the K42T system were 1.2-2 times higher than that of the wild-type...
  67. ncbi request reprint Functional convergence of two lysyl-tRNA synthetases with unrelated topologies
    Takaho Terada
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Nat Struct Biol 9:257-62. 2002
    ....
  68. ncbi request reprint Homologous pairing and ring and filament structure formation activities of the human Xrcc2*Rad51D complex
    Hitoshi Kurumizaka
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Biol Chem 277:14315-20. 2002
    ..In the presence of ssDNA, Xrcc2*Rad51D formed a filamentous structure, which is commonly observed among the human homologous pairing proteins, Rad51, Rad52, and Xrcc3*Rad51C...
  69. ncbi request reprint Crystal structure of the 2'-5' RNA ligase from Thermus thermophilus HB8
    Miyuki Kato
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Mol Biol 329:903-11. 2003
    ..In contrast, in the 2'-5' RNA ligase, the corresponding loops form an open conformation and are flexible. These characteristics may be due to the differences in the substrates, tRNA and ADP-ribose 1",2"-cyclic phosphate...
  70. pmc Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Angstroms resolution
    Ryoichi Arai
    Protein Research Group, RIKEN Yokohama Institute, Tsurumi ku, Yokohama, Japan
    Protein Sci 14:1888-93. 2005
    ..In addition, the putative phosphorylation sites are located at the start of the beta2-strand (Thr18) and at the start of the alpha1-helix (Ser24), implying that the phosphorylation might cause some structural changes...
  71. ncbi request reprint Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1
    Eiichi Mizohata
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Mol Biol 354:317-29. 2005
    ..The conformational flexibility near the intra-monomer disulfide linkage might be necessary for the dramatic structural rearrangements that occur in the catalytic cycle...
  72. pmc Unnatural base pairs for specific transcription
    T Ohtsuki
    Genomic Sciences Center, Exploratory Research for Advanced Technology (ERATO, Japan Science and Technology Corporation (JST, Institute of Physical and Chemical Research (RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
    Proc Natl Acad Sci U S A 98:4922-5. 2001
    ..The bulky dimethylamino group of x in the templates effectively eliminates noncognate pairing with the natural bases. These results enable RNA biosynthesis for the specific incorporation of unnatural nucleotides at the desired positions...
  73. ncbi request reprint Transformation potency of ErbB heterodimer signaling is determined by B-Raf kinase
    M Hatakeyama
    Bioinformatics Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Oncogene 23:5023-31. 2004
    ..The present study suggests that B-Raf kinase, which was specifically activated in the cells coexpressing ErbB1 and ErbB4 receptors, elevates total ERK activity within the cell and, therefore, can induce cellular transformation...
  74. pmc Homologous-pairing activity of the human DNA-repair proteins Xrcc3.Rad51C
    H Kurumizaka
    Genomic Sciences Center, RIKEN, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama shi, Kanagawa 230 0045, Japan
    Proc Natl Acad Sci U S A 98:5538-43. 2001
    ..Rad51C. Electron microscopic observations revealed that Xrcc3.Rad51C and Rad51C formed similar filamentous structures with circular single-stranded DNA...
  75. 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
    ....
  76. ncbi request reprint Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex
    Dmitry Temiakov
    Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, New York 11203 2098, USA
    Acta Crystallogr D Biol Crystallogr 59:185-7. 2003
    ..An unambiguous molecular-replacement solution was found using the C-terminal portion of the T7 RNA polymerase structure from the early initiation complex as a search model. Model building and structure refinement are now in progress...
  77. ncbi request reprint Mutational separation of two pathways for editing by a class I tRNA synthetase
    Tamara L Hendrickson
    The Scripps Research Institute and, The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Mol Cell 9:353-62. 2002
    ..These results are consistent with a molecular model that shows that the single editing active site contains two valyl binding pockets, one specific for each substrate...
  78. ncbi request reprint Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution
    Tahir H Tahirov
    High Throughput Factory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
    Nature 420:43-50. 2002
    ..The structure implies plausible mechanisms for the various phases of the transcription cycle, and reveals important structural similarities with the multisubunit RNA polymerases...
  79. ncbi request reprint [High-throughput cell-free protein expression system for structural genomics and proteomics studies]
    Takanori Kigawa
    Tanpakushitsu Kakusan Koso 47:1014-9. 2002
  80. 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...
  81. ncbi request reprint Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution
    Dmitry G Vassylyev
    Cellular Signaling Laboratory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
    Nature 417:712-9. 2002
    ..The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation...
  82. ncbi request reprint An unnatural base pair for incorporating amino acid analogs into proteins
    Ichiro Hirao
    Yokoyama CytoLogic Project, ERATO, JST, c o RIKEN, 2 1 Hirosawa, Wako Shi, Saitama 351 0198, Japan
    Nat Biotechnol 20:177-82. 2002
    ..This coupled transcription-translation system will permit the efficient synthesis of proteins with a tyrosine analog at the desired position...
  83. ncbi request reprint [Structure of the bacterial RNA polymerase holoenzyme]
    Shun ichi Sekine
    Tanpakushitsu Kakusan Koso 48:1-8. 2003
  84. doi request reprint A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin
    Shogo Ozaki
    Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
    J Biol Chem 283:8351-62. 2008
    ..These findings provide novel insights into mechanisms for pore-mediated origin unwinding, ATP/ADP-dependent regulation, and helicase loading of the initiation complex...
  85. pmc An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes
    Masatoshi Yoshimasu
    Cellular and Molecular Biology Laboratory, RIKEN, 2 1 Hirosawa, Wako Shi, Saitama 351 0198, Japan
    Nucleic Acids Res 31:1735-43. 2003
    ....
  86. ncbi request reprint Backbone 1H, 13C and 15N resonance assignments for the Mg2+-bound form of the Ca2+-binding photoprotein aequorin
    Wakana Ohashi
    J Biomol NMR 31:375-6. 2005
  87. 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...
  88. ncbi request reprint NMR structure of the N-terminal domain of SUMO ligase PIAS1 and its interaction with tumor suppressor p53 and A/T-rich DNA oligomers
    Seiji Okubo
    School of Pharmacy, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192 0392, Japan
    J Biol Chem 279:31455-61. 2004
    ..The three-dimensional structure and its binding duality are discussed in conjunction with the biological functions of PIAS1 as a SUMO ligase...
  89. ncbi request reprint Structural basis for substrate selection by t7 RNA polymerase
    Dmitry Temiakov
    Morse Institute for Molecular Genetics, Department of Microbiology, SUNY Health Science Center, 450 Clarkson Avenue, Brooklyn, New York 11203, USA
    Cell 116:381-91. 2004
    ..Modeling of multisubunit RNAPs suggests that this mechanism might be universal for all RNAPs...
  90. ncbi request reprint Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP
    Kanako Kuwasako
    Protein Research Group, Yokohama 230 0045, Japan
    Structure 14:1677-89. 2006
    ..Mutagenesis showed that this single Leu residue is the critical determinant for complex formation, which reveals the protein recognition mechanism in the subunit assembly...
  91. ncbi request reprint NMR assignment of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana
    David Pantoja-Uceda
    J Biomol NMR 29:207-8. 2004
  92. pmc Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure
    Mayuko Okabe
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    EMBO J 22:5918-27. 2003
    ....
  93. 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...
  94. ncbi request reprint A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription
    Yufeng Wei
    Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, New York, 10021, USA
    Nat Struct Mol Biol 14:653-61. 2007
    ..Thus, ETO-TAFH acts as a structural platform that can interchange negative and positive coregulatory proteins to control transcription...
  95. pmc The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes
    Kenji Keyamura
    Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812 8582, Japan
    Genes Dev 21:2083-99. 2007
    ..These results suggest an essential role for DiaA in the promotion of replication initiation in a cell cycle coordinated manner...
  96. 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...
  97. 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...
  98. 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...
  99. 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