Thermus thermophilus HB8

Summary

Alias: Thermus thermophilus ATCC 27634, Thermus thermophilus str. HB8, Thermus thermophilus strain HB8

Top Publications

  1. pmc Insights into translational termination from the structure of RF2 bound to the ribosome
    Albert Weixlbaumer
    Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Science 322:953-6. 2008
  2. ncbi The electron transfer complex between cytochrome c552 and the CuA domain of the Thermus thermophilus ba3 oxidase. A combined NMR and computational approach
    Lucia Muresanu
    Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, J W Goethe University, Marie Curie Strasse 9, D 60439 Frankfurt am Main, Germany
    J Biol Chem 281:14503-13. 2006
  3. pmc Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function
    Hasan Demirci
    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
    RNA 16:2319-24. 2010
  4. pmc Evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase
    G Buse
    Institut fur Biochemie, Rheinisch Westfälische Technische Hochschule Aachen, Germany
    Protein Sci 8:985-90. 1999
  5. pmc Structural basis for the mechanism of respiratory complex I
    John M Berrisford
    Medical Research Council Mitochondrial Biology Unit, Cambridge CB20XY, United Kingdom
    J Biol Chem 284:29773-83. 2009
  6. ncbi Crystal structure of the ribosome at 5.5 A resolution
    M M Yusupov
    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Science 292:883-96. 2001
  7. doi 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
  8. doi 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
  9. ncbi The path of messenger RNA through the ribosome
    G Z Yusupova
    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Cell 106:233-41. 2001
  10. pmc Overexpression, purification and characterization of RecJ protein from Thermus thermophilus HB8 and its core domain
    A Yamagata
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Nucleic Acids Res 29:4617-24. 2001

Research Grants

Patents

  1. Modified thermostable RecA protein, nucleic acid molecule encoding the protein, nucleic acid amplification method using the protein, and kit for nucleic acid amplification
  2. Modified thermostable RecA protein, nucleic acid molecule encoding the protein, nucleic acid amplification method using the protein, and kit for nucleic acid amplification
  3. Highly conserved genes and their use to generate probes and primers for detection of microorganisms
  4. Plants with increased yield
  5. Proteins associated with abiotic stress response and homologs
  6. The production methods of optically active arylglycine derivatives
  7. A solvent composition
  8. Process of producing L-vinylglycine derivatives
  9. Process for producing protein
  10. PROTEIN FROM EXTREME THERMOPHILE AND CRYSTALS THEREOF

Scientific Experts

Detail Information

Publications96

  1. pmc Insights into translational termination from the structure of RF2 bound to the ribosome
    Albert Weixlbaumer
    Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Science 322:953-6. 2008
    ..The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release...
  2. ncbi The electron transfer complex between cytochrome c552 and the CuA domain of the Thermus thermophilus ba3 oxidase. A combined NMR and computational approach
    Lucia Muresanu
    Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, J W Goethe University, Marie Curie Strasse 9, D 60439 Frankfurt am Main, Germany
    J Biol Chem 281:14503-13. 2006
    ..Based on these structures, the electron transfer pathway from the heme of cytochrome c552 to the CuA center of the ba3 oxidase has been predicted...
  3. pmc Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function
    Hasan Demirci
    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
    RNA 16:2319-24. 2010
    ..Our data indicate that the KsgA-directed methylations facilitate structural rearrangements in order to establish a functionally optimum subunit conformation during the final stages of ribosome assembly...
  4. pmc Evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase
    G Buse
    Institut fur Biochemie, Rheinisch Westfälische Technische Hochschule Aachen, Germany
    Protein Sci 8:985-90. 1999
    ..The early evolutionary invention of this unusual structure may have prevented damaging *OH-radical release at e(-)-transfer to dioxygen and thus have enabled O2 respiration...
  5. pmc Structural basis for the mechanism of respiratory complex I
    John M Berrisford
    Medical Research Council Mitochondrial Biology Unit, Cambridge CB20XY, United Kingdom
    J Biol Chem 284:29773-83. 2009
    ..Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines...
  6. ncbi Crystal structure of the ribosome at 5.5 A resolution
    M M Yusupov
    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Science 292:883-96. 2001
    ..The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement...
  7. doi 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
    The TTHB212 gene from extremely thermophilic bacterium Thermus thermophilus HB8 forms an operon with the upstream sigE gene encoding an extracytoplasmic function sigma factor, sigma(E), the sole alternative sigma factor of this strain, on ..
  8. doi 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...
  9. ncbi The path of messenger RNA through the ribosome
    G Z Yusupova
    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Cell 106:233-41. 2001
    ..The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting...
  10. pmc Overexpression, purification and characterization of RecJ protein from Thermus thermophilus HB8 and its core domain
    A Yamagata
    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560 0043, Japan
    Nucleic Acids Res 29:4617-24. 2001
    ..Both proteins have 5'-->3' exonuclease activity, which was enhanced by increasing the temperature to 50 degrees C. Mg(2+), Mn(2+) or Co(2+) ions were required to activate both proteins, whereas Ca(2+) and Zn(2+) had no effects...
  11. ncbi An open conformation of the Thermus thermophilus gyrase B ATP-binding domain
    Valerie Lamour
    Institut de Génétique et de Biologie Moléculaire, CNRS INSERM ULP, BP163, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
    J Biol Chem 277:18947-53. 2002
    ..All together, these results indicate how the subdomains may propagate conformational changes from the active site and provide crucial information for the design of more specific inhibitors...
  12. pmc The structure of the ribosome with elongation factor G trapped in the posttranslocational state
    Yong Gui Gao
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
    Science 326:694-9. 2009
    ..The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure...
  13. pmc Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
    Shuya Fukai
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo ku, Japan
    RNA 9:100-11. 2003
    ..Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction...
  14. ncbi Visualizing tmRNA entry into a stalled ribosome
    Mikel Valle
    Howard Hughes Medical Institute, Wadsworth Center, Health Research, Inc, Empire State Plaza, Albany, NY 12201 0509, USA
    Science 300:127-30. 2003
    ..The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA...
  15. doi 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
    ..We found that the PHP domain of Thermus thermophilus HB8 PolX (ttPolX) functions as two types of phosphoesterase in BER, including a 3'-phosphatase and an ..
  16. ncbi The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state
    Sukyeong Lee
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 115:229-40. 2003
    ..Taken together, we propose a mechanism by which an ATP-driven conformational change is coupled to a large coiled-coil motion, which is indispensable for protein disaggregation...
  17. ncbi 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
    ..Such organisms, including Thermus thermophilus HB8, often possess the so-called MutS2 protein, which is highly homologous to MutS but contains an extra C-..
  18. pmc The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping
    Hsin Yang Chang
    Department of Biochemistry, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Proc Natl Acad Sci U S A 106:16169-73. 2009
    ..These sites, however, cannot be located within the D-channel. These results along with structural considerations point to the A-propionate region of the active-site heme and surrounding water molecules as the proton-loading site...
  19. ncbi 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
    ..metal and product were investigated using crystal structures of ADPRase from an extreme thermophile, Thermus thermophilus HB8. Seven structures were determined, including that of the free enzyme, the Zn(2+)-bound enzyme, the binary ..
  20. ncbi Recognition of cognate transfer RNA by the 30S ribosomal subunit
    J M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 292:897-902. 2001
    ..The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs...
  21. pmc Mg(2+)-dependent gating of bacterial MgtE channel underlies Mg(2+) homeostasis
    Motoyuki Hattori
    Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, Japan
    EMBO J 28:3602-12. 2009
    ..These structural and functional results have clarified the control of Mg(2+) homeostasis through cooperative Mg(2+) binding to the MgtE cytosolic domain...
  22. ncbi The role of modifications in codon discrimination by tRNA(Lys)UUU
    Frank V Murphy
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nat Struct Mol Biol 11:1186-91. 2004
    ..These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG...
  23. pmc Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry
    Moo Jin Suh
    Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
    Proteomics 5:4818-31. 2005
    ..The extension of protein identification to additional bacterial strains can be useful in phylogenetic studies as well as in biomarker identification...
  24. ncbi Structure of the 70S ribosome complexed with mRNA and tRNA
    Maria Selmer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 313:1935-42. 2006
    ..The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation...
  25. ncbi Structural basis for messenger RNA movement on the ribosome
    Gulnara Yusupova
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, 67404 Illkirch Cedex, France
    Nature 444:391-4. 2006
    ....
  26. ncbi Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors
    Sean R Connell
    Institut fur Medizinische Physik und Biophysik, Charite Universitatsmedizin Berlin, Ziegelstrasse 5 9, 10117 Berlin, Germany
    Mol Cell 25:751-64. 2007
    ..Therefore, a network of interaction with the ribosome establishes the active GTP conformation of EF-G and thus facilitates GTP hydrolysis and tRNA translocation...
  27. pmc Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8
    Akeo Shinkai
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    J Bacteriol 189:3891-901. 2007
    The extremely thermophilic bacterium Thermus thermophilus HB8, which belongs to the phylum Deinococcus-Thermus, has an open reading frame encoding a protein belonging to the cyclic AMP (cAMP) receptor protein (CRP) family present in many ..
  28. ncbi Crystal structure of the ribosome recycling factor bound to the ribosome
    Albert Weixlbaumer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nat Struct Mol Biol 14:733-7. 2007
    ..This suggests that such changes are not a direct requirement for or consequence of RRF binding but possibly arise from the subsequent stabilization of a hybrid state of the ribosome...
  29. pmc Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome
    Rebecca M Voorhees
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 16:528-33. 2009
    ..They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer...
  30. doi Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex
    Naoto Ohtani
    Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
    Biochem J 412:517-26. 2008
    The genome of an extremely thermophilic bacterium, Thermus thermophilus HB8, contains a single ORF (open reading frame) encoding an RNase-HII-like sequence...
  31. doi Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding
    Shinya Kurata
    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 8656, Japan
    J Biol Chem 283:18801-11. 2008
    ..G base pair does not have classical U.G wobble geometry. These structures provide help to explain how the taum(5)U modification enables efficient decoding of UUG codons...
  32. doi 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
    ..b>Thermus thermophilus HB8 has an Ogt homologue, TTHA1564, but in this case an alanine residue replaces cysteine in the putative ..
  33. ncbi Molecular genetic and protein chemical characterization of the cytochrome ba3 from Thermus thermophilus HB8
    J A Keightley
    Los Alamos National Laboratory, New Mexico 87545, USA
    J Biol Chem 270:20345-58. 1995
    b>Thermus thermophilus HB8 cells grown under reduced dioxygen tensions contain a substantially increased amount of heme A, much of which appears to be due to the presence of the terminal oxidase, cytochrome ba3...
  34. pmc Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3
    Hong Jin
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
    Proc Natl Acad Sci U S A 108:15798-803. 2011
    ..The substantial conformational rearrangements in the complex are described and suggest how RF3, by stabilizing the hybrid state of the ribosome, facilitates the dissociation of class I release factors...
  35. doi Identification of novel genes regulated by the oxidative stress-responsive transcriptional activator SdrP in Thermus thermophilus HB8
    Yoshihiro Agari
    RIKEN SPring 8 Center, Harima Institute, Sayo, Hyogo, Japan
    FEMS Microbiol Lett 313:127-34. 2010
    The stationary phase-dependent regulatory protein (SdrP) from the extremely thermophilic bacterium, Thermus thermophilus HB8, a CRP/FNR family protein, is a transcription activator, whose expression increases in the stationary phase of ..
  36. ncbi Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase
    A Aberg
    European Molecular Biology Laboratory, Grenoble Outstation, France
    Biochemistry 36:3084-94. 1997
    ..Arg-259 thus substitutes for the divalent cation observed in seryl-tRNA synthetase and plays a crucial catalytic role in the mechanism of histidine activation...
  37. doi The architecture of respiratory complex I
    Rouslan G Efremov
    Medical Research Council Mitochondrial Biology Unit, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 0XY, UK
    Nature 465:441-5. 2010
    ....
  38. pmc The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid
    C Berthet-Colominas
    European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
    EMBO J 17:2947-60. 1998
    ....
  39. ncbi Cytochrome oxidase genes from Thermus thermophilus. Nucleotide sequence of the fused gene and analysis of the deduced primary structures for subunits I and III of cytochrome caa3
    M W Mather
    Biochemistry Section, Los Alamos National Laboratory, New Mexico 87545
    J Biol Chem 268:5395-408. 1993
    ..Possible topological and helix packing models are developed based on considerations of homology, hydropathy, and variability...
  40. pmc Domain organization and functional analysis of Thermus thermophilus MutS protein
    H Tachiki
    Department of Biology, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043, Japan
    Nucleic Acids Res 26:4153-9. 1998
    ..Among the proteolytic fragments, the B domain bound to dsDNA. On the basis of these results we have proposed the domain organization of T. thermophilus MutS and putative roles of these domains...
  41. doi A new understanding of the decoding principle on the ribosome
    Natalia Demeshkina
    Departement de Biologie et de Genomique Structurales, Institut de Genetique et de Biologie Moleculaire et Cellulaire, Illkirch 67400, France
    Nature 484:256-9. 2012
    ..This by itself, or with distortions in the codon-anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome...
  42. ncbi Lysine is synthesized through the alpha-aminoadipate pathway in Thermus thermophilus
    T Kosuge
    Institute of Applied Biochemistry, University of Tsukuba, Ibaraki, Japan
    FEMS Microbiol Lett 169:361-7. 1998
    ..These results indicate that lysine was synthesized through the alpha-aminoadipate pathway and not through the diaminopimelate pathway in T. thermophilus...
  43. pmc Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus
    T Soulimane
    Rheinisch Westfälische Technische Hochschule Aachen, Institut fur Biochemie, Pauwelsstrasse 30, D 52057 Aachen, Germany
    EMBO J 19:1766-76. 2000
    ..New aspects of the proton pumping mechanism could be identified...
  44. 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
    ..understand the cellular function of ssExos in DNA repair better, genes encoding ssExos were disrupted in Thermus thermophilus HB8 that seems to have only a single set of 5'-3' and 3'-5' ssExos unlike other model organisms...
  45. pmc The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE
    Cajetan Neubauer
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Cell 139:1084-95. 2009
    ..These structures provide detailed insight into the translational regulation on the bacterial ribosome by mRNA cleavage...
  46. ncbi Structure of the 30S ribosomal subunit
    B T Wimberly
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Nature 407:327-39. 2000
    ..The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography...
  47. ncbi Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog
    P Nissen
    Department of Biostructural Chemistry, Institute of Chemistry, Aarhus University, Denmark
    Science 270:1464-72. 1995
    ..The overall shape of the ternary complex is similar to that of the translocation factor, EF-G-GDP, and this suggests a novel mechanism involving "molecular mimicry" in the translational apparatus...
  48. pmc Primary structure of a novel subunit in ba3-cytochrome oxidase from Thermus thermophilus
    T Soulimane
    Rheinisch Westfälische Technische Hochschule Aachen, Institut fur Biochemie, Germany
    Protein Sci 9:2068-73. 2000
    ..The open reading frame encoding this new subunit IIa (cbaD) is located upstream of cbaB in the same operon as the genes for subunit I (cbaA) and subunit II (cbaB)...
  49. pmc How hibernation factors RMF, HPF, and YfiA turn off protein synthesis
    Yury S Polikanov
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Science 336:915-8. 2012
    ..The binding of RMF and HPF, but not YfiA, to the ribosome induces a conformational change of the 30S head domain that promotes 100S dimer formation...
  50. ncbi Cytochrome oxidase genes from Thermus thermophilus. Nucleotide sequence and analysis of the deduced primary structure of subunit IIc of cytochrome caa3
    M W Mather
    Biochemistry Section, Los Alamos National Laboratory, New Mexico 87545
    J Biol Chem 266:5025-35. 1991
    ....
  51. ncbi The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit
    D E Brodersen
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
    Cell 103:1143-54. 2000
    ..For each of these antibiotics, interactions with the 30S subunit suggest a mechanism for its effects on ribosome function...
  52. pmc Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3
    M Pioletti
    Max Planck Institut fur Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
    EMBO J 20:1829-39. 2001
    ....
  53. ncbi The chaperone function of ClpB from Thermus thermophilus depends on allosteric interactions of its two ATP-binding sites
    S Schlee
    Abteilung Physikalische Biochemie, Max Planck Institut fur molekulare Physiologie, Otto Hahn Strasse 11, Dortmund, D 44227, Germany
    J Mol Biol 306:889-99. 2001
    ....
  54. 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
    ..We found Thermus thermophilus HB8 PolX (ttPolX) has Mg(2+)/Mn(2+)-dependent DNA/RNA polymerase, Mn(2+)-dependent 3'-5' exonuclease and DNA-..
  55. doi 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...
  56. ncbi Crystal structure of the MgtE Mg2+ transporter
    Motoyuki Hattori
    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta cho, Midori ku, Yokohama shi, Kanagawa 226 8501, Japan
    Nature 448:1072-5. 2007
    ..Whether this presumed regulation controls gating of an ion channel or opening of a secondary active transporter remains to be determined...
  57. pmc Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1
    Thorsten Althoff
    Abteilung Strukturbiologie, Max Planck Institut fur Biophysik, Frankfurt, Germany
    EMBO J 30:4652-64. 2011
    ..The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred...
  58. pmc Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA
    Yoshitaka Bessho
    Genomic Sciences Center, Yokohama Institute, RIKEN 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Proc Natl Acad Sci U S A 104:8293-8. 2007
    ..Therefore, the tRNP may simulate a tRNA, both structurally and functionally, with respect to aminoacylation and ribosome entry...
  59. pmc Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme
    Bin Liu
    Department of Molecular Biology, The Scripps Research Institute, MB 8, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Biochemistry 48:820-6. 2009
    ..An unexpected optical absorption envelope at approximately 590 nm is also reported. This spectral feature is tentatively thought to arise from a five-coordinate, low-spin, ferrous heme a(3) that is trapped in the frozen crystals...
  60. ncbi Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements
    Andrei Korostelev
    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
    Cell 126:1065-77. 2006
    ..Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site...
  61. ncbi Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
    Leonid A Sazanov
    Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust MRC Building, Hills Road, Cambridge CB2 2XY, U K
    Science 311:1430-6. 2006
    ..The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex...
  62. ncbi Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly
    Manjuli R Sharma
    Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, New York 12201, USA
    Mol Cell 18:319-29. 2005
    ..Furthermore, Era makes contact with several assembly elements of the 30S subunit. These observations suggest a direct involvement of Era in the assembly and maturation of the 30S subunit...
  63. ncbi 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
    ..The three-dimensional structure of L16 from Thermus thermophilus HB8 was determined by NMR...
  64. ncbi The functional cycle and regulation of the Thermus thermophilus DnaK chaperone system
    D Klostermeier
    Abteilung Physikalische Biochemie, Max Planck Institut fur molekulare Physiologie, Rheinlanddamm 201, Dortmund, D 44139, Germany
    J Mol Biol 287:511-25. 1999
    ..The novel factor DafATth that mediates interaction of DnaKTth with DnaJTth would thus serve as a "template" to stabilise the ternary DnaKTth.DafATth.DnaJTth complex until it is replaced by substrate proteins under heat shock conditions...
  65. ncbi Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
    A P Carter
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Nature 407:340-8. 2000
    ..This work reveals the structural basis for the action of these antibiotics, and leads to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process...
  66. ncbi Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains
    Sławomir Dabrowski
    Technical University of Gdansk, Department of Microbiology, ul G Narutowicza 11 12, Poland
    Microbiology 148:3307-15. 2002
    ..This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life...
  67. pmc The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA
    T Martin Schmeing
    MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
    Science 326:688-94. 2009
    ..A series of conformational changes in EF-Tu and aminoacyl-tRNA suggests a communication pathway between the decoding center and the guanosine triphosphatase center of EF-Tu...
  68. ncbi Crystal structure of an initiation factor bound to the 30S ribosomal subunit
    A P Carter
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 291:498-501. 2001
    ..The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit...
  69. pmc Mismatch DNA recognition protein from an extremely thermophilic bacterium, Thermus thermophilus HB8
    S Takamatsu
    Department of Biology, Faculty of Science, Osaka University, Toyonaka, Japan
    Nucleic Acids Res 24:640-7. 1996
    The mutS gene, implicated in DNA mismatch repair, was cloned from an extremely thermophilic bacterium, Thermus thermophilus HB8. Its nucleotide sequence encoded a 819-amino acid protein with a molecular mass of 91.4 kDa...
  70. ncbi A distinct TthMutY bifunctional glycosylase that hydrolyzes not only adenine but also thymine opposite 8-oxoguanine in the hyperthermophilic bacterium, Thermus thermophilus
    Jung Ho Back
    Department of Advanced Technology Fusion, BMIC, Konkuk University, Gwangjin gu, Seoul 143 701, Republic of Korea
    DNA Repair (Amst) 5:894-903. 2006
    ..These results suggest that TthMutY may be an example of a novel class of bifunctional A/GO mismatch DNA glycosylase that can also remove thymine from T/GO mispair...
  71. ncbi Crystal structure of monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8
    Rie Omi
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Biochemistry 46:12618-27. 2007
    Monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8, which catalyzes the dephosphorylation of l-histidinol phosphate, belongs to the PHP family, together with the PHP domain of bacterial DNA polymerase III and ..
  72. pmc Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome
    Gregor Blaha
    Department of Molecular Biophysics, Yale University, New Haven, CT 06520, USA
    Science 325:966-70. 2009
    ..EF-P facilitates the proper positioning of the fMet-tRNA(i)(fMet) for the formation of the first peptide bond during translation initiation...
  73. pmc Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27
    Alexandra Friedrich
    Institut fur Genetik und Mikrobiologie, Ludwig Maximilians Universitat, Maria Ward Strasse 1a, D 80638 Munich, Germany
    Appl Environ Microbiol 68:745-55. 2002
    ..These results suggest that pili and natural transformation in T. thermophilus HB27 are functionally linked...
  74. doi Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus
    Takuya Ouchi
    Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
    Nat Chem Biol 9:277-83. 2013
    ..Phylogenetic analysis reveals that gene duplication events at different stages of evolution led to ArgX and LysX...
  75. ncbi Glycyl-tRNA synthetase from Thermus thermophilus--wide structural divergence with other prokaryotic glycyl-tRNA synthetases and functional inter-relation with prokaryotic and eukaryotic glycylation systems
    M H Mazauric
    UPR 9002 du CNRS, Institut de Biologie Moleculaire et Cellulaire, Strasbourg, France
    Eur J Biochem 251:744-57. 1998
    ..These features are discussed in the context of the phylogenic connections between prokaryotes, eukaryotes, and archaebacteria, and of the particular place of T. thermophilus in this phylogeny...
  76. ncbi Glutamyl-tRNA synthetase from Thermus thermophilus HB8. Molecular cloning of the gltX gene and crystallization of the overproduced protein
    O Nureki
    Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Japan
    Eur J Biochem 204:465-72. 1992
    The gene for the Glu-tRNA synthetase from an extreme thermophile, Thermus thermophilus HB8, was isolated using a synthetic oligonucleotide probe coding for the N-terminal amino acid sequence of Glu-tRNA synthetase...
  77. pmc Cloning, nucleotide sequence, and engineered expression of Thermus thermophilus DNA ligase, a homolog of Escherichia coli DNA ligase
    G Lauer
    BioTechnica Diagnostics, Inc, Cambridge, Massachusetts 02138
    J Bacteriol 173:5047-53. 1991
    ..We have engineered the expression of the T. thermophilus gene in Escherichia coli, and we show that E. coli proteins may be substantially removed from the thermostable ligase by a simple heat precipitation step...
  78. ncbi glmS of Thermus thermophilus HB8: an essential gene for cell-wall synthesis identified immediately upstream of the S-layer gene
    L A Fernandez-Herrero
    Centro de Biologia Molecular Severo Ochoa, Universidad Autonoma de Madrid, Spain
    Mol Microbiol 17:1-12. 1995
    A 30 kbp chromosomal region containing the S-layer gene (slpA) from Thermus thermophilus HB8 was cloned from a lambda phage gene library...
  79. pmc Crystal structure of inorganic pyrophosphatase from Thermus thermophilus
    A Teplyakov
    European Molecular Biology Laboratory, Hamburg, Germany
    Protein Sci 3:1098-107. 1994
    ..The observed oligomeric organization of T-PPase allows us to suggest a possible mechanism for the allosteric regulation of hexameric PPases...
  80. doi Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes
    Perrin Baker
    Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
    Biochemistry 51:1942-52. 2012
    ....
  81. ncbi Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus
    C A Kelly
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110
    Biochemistry 32:3913-22. 1993
    ..The possible contributions of these and other factors to protein thermostability in tMDH are discussed...
  82. ncbi Identification and purification of translation initiation factor 2 (IF2) from Thermus thermophilus
    H P Vornlocher
    Laboratorium fur Biochemie, Universitat Bayreuth, Germany
    Eur J Biochem 243:66-71. 1997
    ..Comparison with other bacterial IF2 sequences indicates a similar domain architecture in all bacterial IF2 proteins...
  83. ncbi A mutation at the interface between domains causes rearrangement of domains in 3-isopropylmalate dehydrogenase
    C Qu
    Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
    Protein Eng 10:45-52. 1997
    ..The larger side chain at the mutated site contributed to the thermostability of the mutant protein by enhancing the local packing of side chains, and also by shifting the backbone of the opposing domain...
  84. ncbi The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids
    B T Wimberly
    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City 84132, USA
    Structure 5:1187-98. 1997
    ..S7 regulates its own synthesis by binding to its own mRNA. This ability of S7 to bind both messenger and ribosomal RNAs makes determination of its mode of RNA recognition particularly interesting...
  85. doi Thermus thermophilus encodes an archaeal-like fructose-1,6-bisphosphatase: purification of native and recombinant protein for structural studies
    T Soulimane
    Paul Scherrer Institute, Biomolecular Research, Villigen PSI, Switzerland
    Protein Expr Purif 74:175-80. 2010
    ..Both native (dissolved crystals) and recombinant material have been characterised by SDS-PAGE, N-terminal sequencing and MALDI-MS...
  86. doi Crystal structure of N-acylamino acid racemase from Thermus thermophilus HB8
    Minoru Hayashida
    RIKEN SPring 8 Center at Harima Institute, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Proteins 71:519-23. 2008
  87. ncbi An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase
    C Briand
    IGBMC CNRS INSERM ULP, UPR 9004, Laboratoire de Biologie et Génomique Structurale, 1, rue Laurent Fries, Illkirch Cedex, C U de Strasbourg, B P 163, France
    J Mol Biol 299:1051-60. 2000
    ..Based on these data, a pathway for tRNA binding and recognition is proposed...
  88. pmc Isolation and purification of Thermus thermophilus HpaB by a crystallization approach
    Tewfik Soulimane
    Department of Chemical and Environmental Sciences and Materials and Surface Science Institute, University of Limerick, National Technology Park, Limerick, Ireland
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:352-6. 2010
    ..Subsequently, well shaped single crystals of the native enzyme that diffract to 1.82 A resolution were grown in sitting drops. They belong to the orthorhombic space group I222, with unit-cell parameters a = 91.3, b = 99.8, c = 131.7 A...
  89. pmc Crystal structure of a eukaryote/archaeon-like protyl-tRNA synthetase and its complex with tRNAPro(CGG)
    A Yaremchuk
    European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
    EMBO J 19:4745-58. 2000
    ..Considerable structural changes in tRNA and/or synthetase, which are probably induced by small substrates, are required to achieve the conformation active for aminoacylation...
  90. pmc Integrity of thermus thermophilus cytochrome c552 synthesized by Escherichia coli cells expressing the host-specific cytochrome c maturation genes, ccmABCDEFGH: biochemical, spectral, and structural characterization of the recombinant protein
    J A Fee
    Department of Biology, University of California at San Diego, La Jolla 92093, USA
    Protein Sci 9:2074-84. 2000
    ..This approach may be generally useful for expression of alien cytochrome c genes in E. coli...
  91. ncbi L22 ribosomal protein and effect of its mutation on ribosome resistance to erythromycin
    Natalia Davydova
    Institute of Protein Research, Moscow Region 142 290, Pushchino, Russia
    J Mol Biol 322:635-44. 2002
    ..It seems that erythromycin, while still being able to interact with one side of the tunnel but not reaching the other, is therefore unable to block the polypeptide growth in the drug-resistant ribosome...
  92. ncbi 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
    ....
  93. ncbi Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 showing functional importance of the dimeric state
    Michihiro Sugahara
    Highthroughput Factory, RIKEN Harima Institute at SPring 8, Hyogo, Japan
    Proteins 58:249-52. 2005
  94. ncbi Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM
    Partha P Datta
    Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, P O Box 509, Albany, New York 12201, USA
    Mol Cell 20:723-31. 2005
    ....
  95. ncbi Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation
    Jun Hyuck Lee
    Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500 712, Republic of Korea
    Biochem Biophys Res Commun 350:1044-9. 2006
    ..The binding of 3-PG (or maybe 1,3-BPG) disrupts this salt bridge and, in ternary complex, the formation of new salt bridge between Arg60 and Asp197 stabilizes the closed conformation...
  96. ncbi Enzymatic properties of futalosine hydrolase, an enzyme essential to a newly identified menaquinone biosynthetic pathway
    Tomoshige Hiratsuka
    Biotechnology Research Center, Toyama Prefectural University, Toyama, Japan
    Biosci Biotechnol Biochem 73:1137-41. 2009
    ..5 and 80 degrees C. The Km value was calculated to be 154.0+/-5.3 microM and the kcat value was 1.02/s. Recombinant TTHA0556 was slightly inhibited by hypoxanthine, with a Ki value of 1.1 mM...

Research Grants3

  1. Molecular mechanisms of transcription elongation
    Dmitry Vassylyev; Fiscal Year: 2009
    ..the facile translocation upon nucleotide addition, the effects of systematic variation of the scaffold components and substitutions of the key RNA polymerase residues that are highlighted by the structure will be analyzed ..
  2. CRYSTALLOGRAPHIC STRUCTURE OF MAMMALIAN MEMBRANE P450
    C Stout; Fiscal Year: 2002
    ..In addition, these studies will yield significant new information regarding modes of membrane binding, and may help to advance the methodology enabling the engineering of membrane proteins for structural studies. ..
  3. STRUCTURE, FUNCTION AND DYNAMICS OF TRANSHYDROGENASE
    C Stout; Fiscal Year: 2007
    ..unreadable] [unreadable]..

Patents17

  1. Modified thermostable RecA protein, nucleic acid molecule encoding the protein, nucleic acid amplification method using the protein, and kit for nucleic acid amplification
    Patent Number: WO2016013592-A; Date:2016-01-28
  2. Modified thermostable RecA protein, nucleic acid molecule encoding the protein, nucleic acid amplification method using the protein, and kit for nucleic acid amplification
    Patent Number: JP2016023179-A; Date:2016-02-08
  3. Highly conserved genes and their use to generate probes and primers for detection of microorganisms
    Patent Number: WO0123604-A2; Date:2001-04-05
  4. Plants with increased yield
    Patent Number: WO2009037279-A1; Date:2009-03-26
  5. Proteins associated with abiotic stress response and homologs
    Patent Number: WO2007110314-A; Date:2007-10-04
  6. The production methods of optically active arylglycine derivatives
    Patent Number: JP2008113560-A; Date:2008-05-22
  7. A solvent composition
    Patent Number: JP2008005797-A; Date:2008-01-17
  8. Process of producing L-vinylglycine derivatives
    Patent Number: JP2007295865-A; Date:2007-11-15
  9. Process for producing protein
    Patent Number: JP2005269935-A; Date:2005-10-06
  10. PROTEIN FROM EXTREME THERMOPHILE AND CRYSTALS THEREOF
    Patent Number: JP2004254621-A; Date:2004-09-16
  11. Proteins associated with abiotic stress response and homologs
    Patent Number: EP2221382-A2; Date:2010-08-25
  12. Process for the control of production of fine chemicals
    Patent Number: EP2199304-A1; Date:2010-06-23
  13. Process for the production of fine chemicals
    Patent Number: EP2194140-A2; Date:2010-06-09
  14. Plants with increased yield (nue)
    Patent Number: WO2010046221-A1; Date:2010-04-29
  15. Plants with increased yield
    Patent Number: WO2009106596-A2; Date:2009-09-03
  16. Process for the production of lutein
    Patent Number: EP2096177-A2; Date:2009-09-02
  17. Lipid metabolism proteins, combinations of lipid metabolism proteins and uses thereof
    Patent Number: WO2009077406-A1; Date:2009-06-25