Seiki Kuramitsu

Summary

Affiliation: Osaka University
Country: Japan

Publications

  1. pmc The role of ribonucleases in regulating global mRNA levels in the model organism Thermus thermophilus HB8
    Hiromasa Ohyama
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    BMC Genomics 15:386. 2014
  2. pmc Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems
    Rihito Morita
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Nucleic Acids 2010:179594. 2010
  3. pmc Structure and Function of the Small MutS-Related Domain
    Kenji Fukui
    RIKEN SPring 8 Center, Harima Institute, 1 1 1, Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Mol Biol Int 2011:691735. 2011
  4. ncbi request reprint [Structural proteomics of metabolism-related proteins]
    Seiki Kuramitsu
    Tanpakushitsu Kakusan Koso 53:604-7. 2008
  5. pmc A commensal symbiotic interrelationship for the growth of Symbiobacterium toebii with its partner bacterium, Geobacillus toebii
    Kwang Kim
    Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560 0043, Japan
    BMC Res Notes 4:437. 2011
  6. 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
  7. 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
  8. 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
  9. 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
  10. pmc Structure of RecJ exonuclease defines its specificity for single-stranded DNA
    Taisuke Wakamatsu
    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565 0871, Japan
    J Biol Chem 285:9762-9. 2010

Detail Information

Publications121 found, 100 shown here

  1. pmc The role of ribonucleases in regulating global mRNA levels in the model organism Thermus thermophilus HB8
    Hiromasa Ohyama
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    BMC Genomics 15:386. 2014
    ....
  2. pmc Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems
    Rihito Morita
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Nucleic Acids 2010:179594. 2010
    ..In this paper we give a broad overview of the whole DNA repair system and focus on the molecular basis of the repair machineries, particularly in Thermus thermophilus HB8...
  3. pmc Structure and Function of the Small MutS-Related Domain
    Kenji Fukui
    RIKEN SPring 8 Center, Harima Institute, 1 1 1, Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Mol Biol Int 2011:691735. 2011
    ..In this paper, we review the biochemical characteristics and structures of the Smr domains as well as cellular functions of the Smr-containing proteins...
  4. ncbi request reprint [Structural proteomics of metabolism-related proteins]
    Seiki Kuramitsu
    Tanpakushitsu Kakusan Koso 53:604-7. 2008
  5. pmc A commensal symbiotic interrelationship for the growth of Symbiobacterium toebii with its partner bacterium, Geobacillus toebii
    Kwang Kim
    Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka 560 0043, Japan
    BMC Res Notes 4:437. 2011
    ..Here, we investigated the interrelationship between these two bacteria for growth of S. toebii using different cell-free extracts of G. toebii...
  6. 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...
  7. 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...
  8. 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
  9. 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...
  10. pmc Structure of RecJ exonuclease defines its specificity for single-stranded DNA
    Taisuke Wakamatsu
    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565 0871, Japan
    J Biol Chem 285:9762-9. 2010
    ..In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism...
  11. 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...
  12. pmc Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins
    Yuri Uemura
    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565 0871, Japan
    FEBS Lett 587:2669-74. 2013
    ..GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins...
  13. doi request reprint Two dNTP triphosphohydrolases from Pseudomonas aeruginosa possess diverse substrate specificities
    Ryosuke Mega
    Graduate School of Frontier Biological Sciences, Osaka University, Osaka, Japan
    FEBS J 276:3211-21. 2009
    ..coli and T. thermophilus enzymes. On the basis of these results, we propose that the dNTP triphosphohydrolase family should be classified into at least three subfamilies...
  14. ncbi request reprint Crystal structure of family 5 uracil-DNA glycosylase bound to DNA
    Hiromichi Kosaka
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Mol Biol 373:839-50. 2007
    ..Based on no significant open-closed conformational change upon binding to DNA, we propose a "slide-in" mechanism for initial damage recognition...
  15. 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...
  16. 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...
  17. pmc Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia
    Tadashi Nakai
    RIKEN Harima Institute at SPring 8, Mikazuki, Sayo, Hyogo, Japan
    EMBO J 24:1523-36. 2005
    ..These results provide insights into the molecular basis of nonketotic hyperglycinemia...
  18. 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
    ....
  19. pmc Phenylacetyl coenzyme A is an effector molecule of the TetR family transcriptional repressor PaaR from Thermus thermophilus HB8
    Keiko Sakamoto
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Bacteriol 193:4388-95. 2011
    ..thermophilus FadR, which is involved in fatty acid degradation. The CoA moiety of PA-CoA may bind to the center of the PaaR molecule, in a manner similar to the binding of the CoA moiety of acyl-CoA to FadR...
  20. pmc A novel single-stranded DNA-specific 3'-5' exonuclease, Thermus thermophilus exonuclease I, is involved in several DNA repair pathways
    Atsuhiro Shimada
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043 and RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Nucleic Acids Res 38:5692-705. 2010
    ..Consequently, we concluded that TTHB178 is a novel 3'-5' ssExo that functions in various DNA repair systems in cooperation with or independently of RecJ. We named TTHB178 as T. thermophilus exonuclease I...
  21. 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...
  22. 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...
  23. doi request reprint The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA
    Shuhei Nakane
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Mol Biol 417:179-96. 2012
    ..The ability to bind to either syn-dNTP or anti-dNTP and the involvement of a Theorell-Chance mechanism are key aspects of the strong nucleotide-binding and efficient gap-filling activities of ttPolX...
  24. ncbi request reprint Thermus thermophilus MutS2, a MutS paralogue, possesses an endonuclease activity promoted by MutL
    Kenji Fukui
    Department of Biology, Graduate School of Science, Osaka University, 1 1 Machikaneyamacho, Toyonaka, Osaka 560 0043
    J Biochem 135:375-84. 2004
    ..ttMutS2 incises not only oligo dsDNA but also plasmid DNA, suggesting that ttMutS2 possesses an endonuclease activity. At low concentrations, the incision activity was not retained, but was promoted by T. thermophilus MutL...
  25. doi request reprint Bound nucleotide controls the endonuclease activity of mismatch repair enzyme MutL
    Kenji Fukui
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    J Biol Chem 283:12136-45. 2008
    ..Complementation experiments revealed that the endonuclease activity of ttMutL and its regulation by ATP binding are necessary for DNA repair in vivo...
  26. doi request reprint Structural and functional characterization of the transcriptional repressor CsoR from Thermus thermophilus HB8
    Keiko Sakamoto
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Microbiology 156:1993-2005. 2010
    ..The non-conserved H70 residue in the metal-binding motif of T. thermophilus CsoR is important for its DNA-binding affinity and metal-ion responsiveness...
  27. doi request reprint An alkyltransferase-like protein from Thermus thermophilus HB8 affects the regulation of gene expression in alkylation response
    Rihito Morita
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Biochem 150:327-39. 2011
    ..These results suggest that TTHA1564 might act as a transcriptional regulator. The results of DNA microarray analysis also implied that the alkylating agent induced oxidation stress in addition to alkylation stress...
  28. pmc Evidence for ATP-dependent structural rearrangement of nuclease catalytic site in DNA mismatch repair endonuclease MutL
    Tatsuya Yamamoto
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    J Biol Chem 286:42337-48. 2011
    ..Our data contribute toward understanding the relationship between mutations in MutL homolog and human disease...
  29. 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...
  30. 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...
  31. ncbi request reprint Biochemical characterization of TT1383 from Thermus thermophilus identifies a novel dNTP triphosphohydrolase activity stimulated by dATP and dTTP
    Naoyuki Kondo
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka
    J Biochem 136:221-31. 2004
    ..This is, to our knowledge, the first report of a non-specific dNTPase that is activated by dNTP itself...
  32. 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...
  33. pmc Crystal structure of MutS2 endonuclease domain and the mechanism of homologous recombination suppression
    Kenji Fukui
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo gun, Hyogo, 679 5148, Japan
    J Biol Chem 283:33417-27. 2008
    ..The full-length of ttMutS2 digested the branched DNA structures at the junction. These results indicate that ttMutS2 suppresses homologous recombination through a novel mechanism involving resolution of early intermediates...
  34. 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...
  35. doi request reprint Transcription profile of Thermus thermophilus CRISPR systems after phage infection
    Yoshihiro Agari
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Mol Biol 395:270-81. 2010
    ..These findings will facilitate understanding of the host response mechanism following phage infection...
  36. pmc Structures of hypoxanthine-guanine phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8
    Mayumi Kanagawa
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:893-8. 2010
    ..The group II enzymes are characterized by an N-terminal extension with additional secondary elements and a long loop connecting the second alpha-helix and beta-strand compared with the group I enzymes...
  37. 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...
  38. pmc Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8
    Taisuke Wakamatsu
    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565 0871, Japan
    J Bacteriol 190:1108-17. 2008
    ..These results suggest that ADPRase-I and ADPRase-II enzymes have nearly identical catalytic mechanisms but different mechanisms of substrate recognition...
  39. doi request reprint A non-cold-inducible cold shock protein homolog mainly contributes to translational control under optimal growth conditions
    Toshiko Tanaka
    Department of Biological Sciences, Graduate School of Science, Osaka University, Japan
    FEBS J 279:1014-29. 2012
    ..We also report the nucleotide binding affinity of ttCsp1. Finally, we discuss the functions of non-cold-induced Csps and propose how they modulate the levels of specific proteins to suit the prevailing environmental conditions...
  40. ncbi request reprint Molecular mechanism of the Thermus thermophilus ADP-ribose pyrophosphatase from mutational and kinetic studies
    Takushi Ooga
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Biochemistry 44:9320-9. 2005
    ..Our results highlight the diversity within the nudix protein family in terms of substrate recognition and catalysis...
  41. pmc Inactivation of the DNA repair genes mutS, mutL or the anti-recombination gene mutS2 leads to activation of vitamin B1 biosynthesis genes
    Kenji Fukui
    RIKEN SPring 8 Center, Harima Institute, Kouto, Sayo gun, Hyogo, Japan
    PLoS ONE 6:e19053. 2011
    ..These results suggested that bacterial cells sense the accumulation of oxidative DNA damage or absence of DNA repair activity, and signal the information to the transcriptional regulation machinery for an ROS-detoxifying system...
  42. doi request reprint Close proximity of phosphorylation sites to ligand in the phosphoproteome of the extreme thermophile Thermus thermophilus HB8
    Yoshio Takahata
    Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
    Proteomics 12:1414-30. 2012
    ..In oligomeric proteins, 5 phosphorylation sites were found at the subunit interface. Based on these results, we propose a regulatory mechanism that involves Ser/Thr/Tyr phosphorylation in T. thermophilus HB8...
  43. 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...
  44. doi request reprint Crystal structure of the tandem-type universal stress protein TTHA0350 from Thermus thermophilus HB8
    Hitoshi Iino
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Biochem 150:295-302. 2011
    ..The loop interacting with ATP in the C-terminal domain is in a conformation quite different from that in the N-terminal domain...
  45. doi request reprint Acetylome with structural mapping reveals the significance of lysine acetylation in Thermus thermophilus
    Hiroki Okanishi
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Proteome Res 12:3952-68. 2013
    ..The structural mapping of acetylation sites provides new molecular insight into the role of lysine acetylation in the proteins. ..
  46. doi request reprint MutS stimulates the endonuclease activity of MutL in an ATP-hydrolysis-dependent manner
    Atsuhiro Shimada
    Department of Biological Sciences, Graduate School of Science, Osaka University, Suita, Osaka, Japan
    FEBS J 280:3467-79. 2013
    ..We concluded that ATP hydrolysis by MutS and MutL is involved in the mismatch-dependent activation of MutL endonuclease activity. ..
  47. 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...
  48. ncbi request reprint Simultaneous detection of N-terminal fragment ions in a protein mixture using a ruthenium(II) complex
    Akihiro Ito
    Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Rapid Commun Mass Spectrom 21:2647-53. 2007
    ..Application to unknown proteins from Thermus thermophilus HB8 with two-dimensional electrophoretic separation resulted in the successful determination of the N-terminal sequence and easy identification of the target protein...
  49. pmc Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus
    Takushi Ooga
    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    J Biol Chem 284:15549-56. 2009
    ..These results suggest a novel mechanism of ppGpp-mediated growth control by the functional relay between Ndx8 and SpoT activity as ppGpp scavengers...
  50. doi request reprint Characterization of C- and N-terminal domains of Aquifex aeolicus MutL endonuclease: N-terminal domain stimulates the endonuclease activity of C-terminal domain in a zinc-dependent manner
    Hitoshi Iino
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Biosci Rep 31:309-22. 2011
    ..On the basis of these results, we propose a model for the intramolecular regulatory mechanism of MutL endonuclease activity...
  51. ncbi request reprint Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by X-ray crystallography
    Tadashi Nakai
    RIKEN Harima Institute SPring 8, 1 1 1 Kouto, Mikazuki, Sayo gun, Hyogo 679 5148, Japan
    J Mol Biol 337:1011-33. 2004
    ..MOPA and of E1(ceim).lipoamide built from the above structures suggest that His273alpha and His129beta' are potential proton donors to the carbonyl group of a BCOA and to the proximal sulfur atom on the lipoamide, respectively...
  52. ncbi request reprint Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily
    Hirohito Ishikawa
    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    J Biochem 140:535-42. 2006
    ..We also detected nuclease activity of TTHA0252 against rRNAs of T. thermophilus. Our results reveal structural and functional aspects of novel RNase E-like enzymes with a beta-CASP fold...
  53. ncbi request reprint Insights into different dependence of dNTP triphosphohydrolase on metal ion species from intracellular ion concentrations in Thermus thermophilus
    Naoyuki Kondo
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    Extremophiles 12:217-23. 2008
    ..In addition, the proposed model of dNTPase activity induced by magnesium and multiple dNTPs was discussed based on the results obtained in this study...
  54. doi request reprint An O6-methylguanine-DNA methyltransferase-like protein from Thermus thermophilus interacts with a nucleotide excision repair protein
    Rihito Morita
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Biochem 144:267-77. 2008
    ..Interaction of TTHA1564 with UvrA was confirmed using a surface plasmon resonance assay. These results suggest the possible involvement of TTHA1564 in DNA repair pathways...
  55. 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...
  56. ncbi request reprint Crystallization and preliminary X-ray crystallographic studies of 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
    Acta Crystallogr D Biol Crystallogr 59:2294-6. 2003
    ..878, b = 106.367, c = 168.639 A. A homotetramer of HIBADH is likely to be present in the asymmetric unit, giving a V(M) of 3.0 A(3) Da(-1) and a solvent content of 59.3%...
  57. doi request reprint Integrated database of information from structural genomics experiments
    Yukuhiko Asada
    Protein Crystallography Research Group, RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Acta Crystallogr D Biol Crystallogr 69:914-9. 2013
    ..In addition, to enhance the use of data (i) and (ii) by general researchers in biosciences, a comprehensible user interface, Bacpedia (http://bacpedia.harima.riken.jp), has been developed...
  58. ncbi request reprint Crystallization and preliminary X-ray diffraction studies of nucleoside diphosphate kinase from Thermus thermophilus HB8
    Shunsaku Takeishi
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Acta Crystallogr D Biol Crystallogr 59:1843-5. 2003
    ..7 A(3) Da(-1). The crystals diffracted X-rays generated by the synchrotron at SPring-8 to at least 1.9 A resolution and were suitable for high-resolution X-ray crystal structure determination...
  59. ncbi request reprint Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins
    Takuya B Hiyama
    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 7:119-29. 2006
    ..The CoA interaction of the single-domain CoA-binding proteins is significantly different and much more extensive than that of the multi-subunit/multi-domain CoA-binding protein succinyl-CoA synthetase...
  60. ncbi request reprint X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7
    Yoshihiro Agari
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Proteins 70:1108-11. 2008
  61. 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...
  62. doi request reprint Very rapid induction of a cold shock protein by temperature downshift in Thermus thermophilus
    Ryosuke Mega
    Graduate School of Frontier Biosciences, Osaka University, 1 3 Yamadaoka, Suita, Osaka 565 0871, Japan
    Biochem Biophys Res Commun 399:336-40. 2010
    ..Thus, ttCSP2 is considered to act as a 'thermosensor' during temperature downshift through changes in its secondary structure...
  63. doi request reprint Unique substrate specificity of purine nucleoside phosphorylases from Thermus thermophilus
    Fumiaki Tomoike
    Graduate School of Frontier Biosciences, Osaka University, 1 3 Yamadaoka, Suita, Osaka 565 0871, Japan
    Extremophiles 17:505-14. 2013
    ..Sequence analysis further suggested most 6PNP and 3PNP enzymes in thermophilic species belonging to the Deinococcus-Thermus phylum share the same critical residues as tt6PNP and tt3PNP, respectively...
  64. ncbi request reprint The Nudix hydrolase Ndx1 from Thermus thermophilus HB8 is a diadenosine hexaphosphate hydrolase with a novel activity
    Takayoshi Iwai
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043
    J Biol Chem 279:21732-9. 2004
    ..Trp-26 was likely involved in enzyme-substrate interactions based on fluorescence measurements. Based on these results, the mechanism of substrate recognition and catalysis are discussed...
  65. doi request reprint Structural bases for the specific interactions between the E2 and E3 components of the Thermus thermophilus 2-oxo acid dehydrogenase complexes
    Tadashi Nakai
    RIKEN SPring 8 Center, Harima Institute, Sayo, Hyogo 679 5148, Japan
    J Biochem 143:747-58. 2008
    ..The buried intermolecular surfaces of the E3b*PSBDp/b and E3o*PSBDo complexes differ in size, shape and charge distribution and thus, these differences presumably confer the binding specificities for the complexes...
  66. pmc Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions
    Yoshiaki Kitamura
    RIKEN SPring 8 Center, Harima Institute, Sayo, Hyogo 679 5148, Japan
    Acta Crystallogr D Biol Crystallogr 65:1098-106. 2009
    ..The catalytic process accompanied by the cumulative conformational change has been elucidated based on the intermediate models in order to provide new insights regarding the details of the catalytic mechanism...
  67. doi request reprint TetR-family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation
    Yoshihiro Agari
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Microbiology 157:1589-601. 2011
    ..thermophilus HB8, medium-to-long straight-chain fatty acids can be used for metabolic energy under the control of FadR, although the major fatty acids found in this strain are iso- and anteiso-branched-chain (C15 and 17) fatty acids...
  68. ncbi request reprint Expression, purification, crystallization and preliminary X-ray studies of geranylgeranyl diphosphate synthase from Thermus thermophilus HB8
    Kazuya Nishio
    RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo gun, Hyogo 679 5148, Japan
    Acta Crystallogr D Biol Crystallogr 60:178-80. 2004
    ..88, c = 73.37 A. There were two homodimers in the asymmetric unit. A native data set was collected to 1.55 A resolution and a data set suitable for MAD phasing was collected to 2.40 A resolution on beamline BL40B2 at SPring-8...
  69. ncbi request reprint Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8
    Akio Ebihara
    RIKEN Harima Institute at SPring 8, Kouto, Mikazuki cho, Sayo gun, Hyogo, 679 5148, Japan
    J Struct Funct Genomics 6:21-32. 2005
    ..The presence of a possible Fe-His-Asp triad in the heme proximal site suggests that TT1485 functions as a novel heme peroxidase to detoxify hydrogen peroxide within the cell...
  70. ncbi request reprint High sequence-coverage detection of proteolytic peptides using a bis(terpyridine)ruthenium(II) complex
    Akihiro Ito
    Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Analyst 132:358-64. 2007
    ..Application of this method to a protein mixture (myoglobin, lysozyme and ubiquitin) successfully achieved high sequence-coverage characterization (>90%) of these proteins simultaneously...
  71. doi request reprint An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA
    Ryuichi Asano
    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
    Acta Crystallogr D Biol Crystallogr 67:149-55. 2011
    ..A mutation analysis showed that Lys267 in the C-terminal DNA-recognition loop plays an important role in DNA binding...
  72. pmc Nuclease activity of the MutS homologue MutS2 from Thermus thermophilus is confined to the Smr domain
    Kenji Fukui
    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Nucleic Acids Res 35:850-60. 2007
    ..Furthermore, the Smr domain alone was stable and functional in binding and incising DNA. It is noteworthy that an endonuclease activity is associated with a MutS homologue, which is generally thought to recognize specific DNA structures...
  73. pmc Role of RecJ-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation
    Taisuke Wakamatsu
    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565 0871, Japan
    J Biol Chem 286:2807-16. 2011
    ..These results suggested that these RecJ-like proteins act in recycling short oligonucleotides to mononucleotides and in controlling pAp concentrations in vivo...
  74. doi request reprint Whole-cell proteome reference maps of an extreme thermophile, Thermus thermophilus HB8
    Kwang Kim
    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
    Proteomics 12:3063-8. 2012
    ..On the other hand, volume quantification analysis revealed that proteins involved in the translational process, nucleotide metabolism, and central carbon metabolism were most abundantly expressed in the exponential phase...
  75. doi request reprint The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair
    Shuhei Nakane
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    DNA Repair (Amst) 11:906-14. 2012
    ..Furthermore, phenotypic analysis of ΔttpolX, ΔttendoIV, and ΔttpolX/ΔttendoIV using hydrogen peroxide and sodium nitrite supports the hypothesis that ttPolX functions as a backup for ttEndoIV in BER...
  76. ncbi request reprint Improved heterologous gene expression in Escherichia coli by optimization of the AT-content of codons immediately downstream of the initiation codon
    Takashi Nishikubo
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    J Biotechnol 120:341-6. 2005
    ..This result suggests that incorporation of AT-rich codons can be utilized as a general strategy for improving the expression efficiency of a recombinant protein...
  77. pmc In vivo, in vitro, and x-ray crystallographic analyses suggest the involvement of an uncharacterized triose-phosphate isomerase (TIM) barrel protein in protection against oxidative stress
    Shuhei Nakane
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    J Biol Chem 286:41636-46. 2011
    ..Our results suggest that TTHB071 protects the cell from oxidative stress, through controlling the metabolism of FMN, pyridoxal phosphate, or an analogous compound...
  78. ncbi request reprint Rapid and sensitive amino-acid sequencing of cloning Thermus thermophilus HB8 ferredoxin by proteomics
    Maki Kaneko
    Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043 Japan
    J Proteome Res 3:983-7. 2004
    ..The catalytic electron-transfer reactivity of the [7Fe-8S] ferredoxin between ferredoxin-NADP+ reductase and cytochrome c was recognized...
  79. ncbi request reprint Distinction of Leu and Ile Using a Ruthenium(II) complex by MALDI-LIFT-TOF/TOF-MS analysis
    Akihiro Ito
    Department of Macromolecular Science and Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Anal Chem 77:6618-24. 2005
    ..The method was applied to long-chain peptides and provided easy and rapid N-terminal sequencing...
  80. doi request reprint A single amino acid limits the substrate specificity of Thermus thermophilus uridine-cytidine kinase to cytidine
    Fumiaki Tomoike
    Graduate School of Frontier Biosciences, Osaka University, 1 3 Yamadaoka, Suita, Osaka, Japan
    Biochemistry 50:4597-607. 2011
    ..Thermophilus HB8. On the basis of these results, we discuss the pyrimidine-salvage pathway in T. thermophilus HB8...
  81. pmc Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity
    Shuhei Nakane
    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Nucleic Acids Res 37:2037-52. 2009
    ..Our findings provide a molecular insight into the functional domain organization of bacterial PolXs, especially the requirement of the PHP domain for 3'-5' exonuclease activity...
  82. ncbi request reprint Characterization of growth-supporting factors produced by Geobacillus toebii for the commensal thermophile Symbiobacterium toebii
    Joong Jae Kim
    Department of Biological Sciences, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka, Japan
    J Microbiol Biotechnol 18:490-6. 2008
    ..toebii, indicating that common SGSF materials are widely present in various bacterial strains...
  83. ncbi request reprint Solution structure of ribosomal protein L16 from Thermus thermophilus HB8
    Mitsuhiro Nishimura
    Graduate School of Pharmaceutical Sciences, Osaka University, 1 6 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Mol Biol 344:1369-83. 2004
    ..This suggests the direct participation of L16 as a part of the binding site for antibiotics...
  84. 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...
  85. ncbi request reprint The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors
    Yusaku Hioki
    Institute for Protein Research, Osaka University, Japan
    Eur J Biochem 271:2624-35. 2004
    ....
  86. ncbi request reprint An enzyme with a deep trefoil knot for the active-site architecture
    Osamu Nureki
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Japan
    Acta Crystallogr D Biol Crystallogr 58:1129-37. 2002
    ..On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA...
  87. ncbi request reprint Regulation mechanism of spin-orbit coupling in charge-transfer-induced luminescence of imidazopyrazinone derivatives
    Hiroshi Isobe
    Department of Chemistry and Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    J Am Chem Soc 130:132-49. 2008
    ..This will constitute a necessary condition for the high efficiency of chemi- and bioluminescence...
  88. ncbi request reprint Overproduction, crystallization and preliminary diffraction data of ADP-ribose pyrophosphatase from Thermus thermophilus HB8
    Sachiko Yoshiba
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Acta Crystallogr D Biol Crystallogr 59:1840-2. 2003
    ..50 A resolution from the apo form using synchrotron radiation and to 2.0 A resolution from the complexed form. Both crystals belong to space group P3(1)21 or P3(2)21 and contain one molecule in the asymmetric unit...
  89. ncbi request reprint Overproduction, crystallization and preliminary X-ray diffraction analysis of a quinone oxidoreductase from Thermus thermophilus HB8
    Yoshimitsu Shimomura
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Acta Crystallogr D Biol Crystallogr 58:1365-7. 2002
    ..The asymmetric unit has one protein subunit (V(M) = 3.2 A(3) Da(-1) and V(sol) = 0.62 for the apo form), indicating that the twofold axis of the dimeric protein and the crystallographic twofold axis coincide...
  90. ncbi request reprint Identification and characterization of a second chromophore of DNA photolyase from Thermus thermophilus HB27
    Takumi Ueda
    Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Biol Chem 280:36237-43. 2005
    ..Based on these results, we concluded that FMN acts as a highly efficient light harvester that gathers light and transfers the energy to FAD...
  91. ncbi request reprint Increased rigidity of domain structures enhances the stability of a mutant enzyme created by directed evolution
    Jun Hoseki
    Department of Biochemistry, Osaka Medical College, Takatsuki, Japan
    Biochemistry 42:14469-75. 2003
    ..The present results suggest that the 19 mutations of HTK stabilize KNT by affecting the dynamic behavior of the structure of this enzyme without significantly changing its static overall structure...
  92. 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...
  93. ncbi request reprint Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi)
    Keisuke Hamada
    Structural Biophysics Laboratory, Highthroughput Factory, Hyogo, Japan
    J Biol Chem 278:49183-90. 2003
    ..R5P bound as the ring-opened reaction intermediate clarified the high stereoselectivity of the catalysis and is consistent with an aldose-ketose conversion by Rpi that proceeds via a cis-enediolate intermediate...
  94. ncbi request reprint Structure of Thermus thermophilus HB8 H-protein of the glycine-cleavage system, resolved by a six-dimensional molecular-replacement method
    Tadashi Nakai
    RIKEN Harima Institute SPring 8, 1 1 1 Kouto, Mikazuki, Sayo gun, Hyogo 679 5148, Japan
    Acta Crystallogr D Biol Crystallogr 59:1610-8. 2003
    ..Meanwhile, the lipoyl-lysine arm of the T. thermophilus H-protein was found to be more flexible than that of the pea H-protein, supporting the hypothesis that H-protein does not form a stable complex with L-protein during the reaction...
  95. 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...
  96. 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...
  97. ncbi request reprint Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8
    Motoyuki Hattori
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Proteins 64:284-7. 2006
  98. pmc Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4 A resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily
    Makoto Nakabayashi
    Department of Life Science, Graduate School of Life Science, University of Hyogo, Himeji Institute of Technology, 3 2 1 Koto, Ako gun, Hyogo 678 1297, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:1027-31. 2005
    ..However, the size of the ligand-binding cavity is distinctly smaller than other START domain-containing proteins, suggesting that it catalyses the transfer of smaller ligand molecules...
  99. 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...
  100. ncbi request reprint Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus
    Tatsuhiko Someya
    Department of Industrial Chemistry, Faculty of Engineering, Chiba Institute of Technology, Chiba 275 0016, Japan
    FEBS Lett 535:94-100. 2003
    ..Its C-terminal sequence (20 residues), which is rich in basic residues, shows a poorly structured form, as often seen in isolated ribosomal proteins. The results are discussed in relation to the oligonucleotide binding fold...