Thermus thermophilus HB8

Summary

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

Top Publications

  1. Lee S, Sowa M, Watanabe Y, Sigler P, Chiu W, Yoshida M, et al. The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. Cell. 2003;115:229-40 pubmed
    ..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. ..
  2. Blaha G, Stanley R, Steitz T. Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science. 2009;325:966-70 pubmed publisher
    ..EF-P facilitates the proper positioning of the fMet-tRNA(i)(fMet) for the formation of the first peptide bond during translation initiation. ..
  3. Dabrowski S, Olszewski M, Piatek R, Brillowska Dabrowska A, Konopa G, Kur J. Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains. Microbiology. 2002;148:3307-15 pubmed
    ..This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life. ..
  4. Yusupova G, Yusupov M, Cate J, Noller H. The path of messenger RNA through the ribosome. Cell. 2001;106:233-41 pubmed
    ..The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting. ..
  5. Schlee S, Groemping Y, Herde P, Seidel R, Reinstein J. The chaperone function of ClpB from Thermus thermophilus depends on allosteric interactions of its two ATP-binding sites. J Mol Biol. 2001;306:889-99 pubmed
  6. Polikanov Y, Blaha G, Steitz T. How hibernation factors RMF, HPF, and YfiA turn off protein synthesis. Science. 2012;336:915-8 pubmed publisher
    ..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. ..
  7. Morita R, Nakagawa N, Kuramitsu S, Masui R. An O6-methylguanine-DNA methyltransferase-like protein from Thermus thermophilus interacts with a nucleotide excision repair protein. J Biochem. 2008;144:267-77 pubmed publisher
    ..b>Thermus thermophilus HB8 has an Ogt homologue, TTHA1564, but in this case an alanine residue replaces cysteine in the putative ..
  8. Ohtani N, Tomita M, Itaya M. Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex. Biochem J. 2008;412:517-26 pubmed publisher
    The genome of an extremely thermophilic bacterium, Thermus thermophilus HB8, contains a single ORF (open reading frame) encoding an RNase-HII-like sequence...
  9. Omi R, Goto M, Miyahara I, Manzoku M, Ebihara A, Hirotsu K. Crystal structure of monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8. Biochemistry. 2007;46:12618-27 pubmed
    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 ..
  10. Fukui K, Takahata Y, Nakagawa N, Kuramitsu S, Masui R. Analysis of a nuclease activity of catalytic domain of Thermus thermophilus MutS2 by high-accuracy mass spectrometry. Nucleic Acids Res. 2007;35:e100 pubmed
    ..The simultaneous identification of the innumerable fragments was achieved by the extremely high-accuracy of ESI-FT ICR MS. ..

Detail Information

Publications88

  1. Lee S, Sowa M, Watanabe Y, Sigler P, Chiu W, Yoshida M, et al. The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. Cell. 2003;115:229-40 pubmed
    ..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. ..
  2. Blaha G, Stanley R, Steitz T. Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science. 2009;325:966-70 pubmed publisher
    ..EF-P facilitates the proper positioning of the fMet-tRNA(i)(fMet) for the formation of the first peptide bond during translation initiation. ..
  3. Dabrowski S, Olszewski M, Piatek R, Brillowska Dabrowska A, Konopa G, Kur J. Identification and characterization of single-stranded-DNA-binding proteins from Thermus thermophilus and Thermus aquaticus - new arrangement of binding domains. Microbiology. 2002;148:3307-15 pubmed
    ..This ssDNA-binding domain was presumably present in the common ancestor to all three major branches of life. ..
  4. Yusupova G, Yusupov M, Cate J, Noller H. The path of messenger RNA through the ribosome. Cell. 2001;106:233-41 pubmed
    ..The mRNA enters the ribosome around position +13 to +15, the location of downstream pseudoknots that stimulate -1 translational frame shifting. ..
  5. Schlee S, Groemping Y, Herde P, Seidel R, Reinstein J. The chaperone function of ClpB from Thermus thermophilus depends on allosteric interactions of its two ATP-binding sites. J Mol Biol. 2001;306:889-99 pubmed
  6. Polikanov Y, Blaha G, Steitz T. How hibernation factors RMF, HPF, and YfiA turn off protein synthesis. Science. 2012;336:915-8 pubmed publisher
    ..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. ..
  7. Morita R, Nakagawa N, Kuramitsu S, Masui R. An O6-methylguanine-DNA methyltransferase-like protein from Thermus thermophilus interacts with a nucleotide excision repair protein. J Biochem. 2008;144:267-77 pubmed publisher
    ..b>Thermus thermophilus HB8 has an Ogt homologue, TTHA1564, but in this case an alanine residue replaces cysteine in the putative ..
  8. Ohtani N, Tomita M, Itaya M. Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex. Biochem J. 2008;412:517-26 pubmed publisher
    The genome of an extremely thermophilic bacterium, Thermus thermophilus HB8, contains a single ORF (open reading frame) encoding an RNase-HII-like sequence...
  9. Omi R, Goto M, Miyahara I, Manzoku M, Ebihara A, Hirotsu K. Crystal structure of monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8. Biochemistry. 2007;46:12618-27 pubmed
    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 ..
  10. Fukui K, Takahata Y, Nakagawa N, Kuramitsu S, Masui R. Analysis of a nuclease activity of catalytic domain of Thermus thermophilus MutS2 by high-accuracy mass spectrometry. Nucleic Acids Res. 2007;35:e100 pubmed
    ..The simultaneous identification of the innumerable fragments was achieved by the extremely high-accuracy of ESI-FT ICR MS. ..
  11. Korostelev A, Trakhanov S, Laurberg M, Noller H. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell. 2006;126:1065-77 pubmed
    ..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. ..
  12. Murphy F, Ramakrishnan V, Malkiewicz A, Agris P. The role of modifications in codon discrimination by tRNA(Lys)UUU. Nat Struct Mol Biol. 2004;11:1186-91 pubmed
    ..These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG. ..
  13. Fukui K, Masui R, Kuramitsu S. Thermus thermophilus MutS2, a MutS paralogue, possesses an endonuclease activity promoted by MutL. J Biochem. 2004;135:375-84 pubmed
    ..Such organisms, including Thermus thermophilus HB8, often possess the so-called MutS2 protein, which is highly homologous to MutS but contains an extra C-..
  14. Friedrich A, Prust C, Hartsch T, Henne A, Averhoff B. Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27. Appl Environ Microbiol. 2002;68:745-55 pubmed
    ..These results suggest that pili and natural transformation in T. thermophilus HB27 are functionally linked. ..
  15. Yamagata A, Masui R, Kakuta Y, Kuramitsu S, Fukuyama K. Overexpression, purification and characterization of RecJ protein from Thermus thermophilus HB8 and its core domain. Nucleic Acids Res. 2001;29:4617-24 pubmed
    ..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. ..
  16. Yaremchuk A, Tukalo M, Grøtli M, Cusack S. A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase. J Mol Biol. 2001;309:989-1002 pubmed
    ..T. thermophilus prolyl-tRNA synthetase appears to be the second class II aminoacyl-tRNA synthetase, after HisRS, to use a positively charged amino acid instead of a divalent cation to catalyse the amino acid activation reaction. ..
  17. Ng C, Lang K, Meenan N, Sharma A, Kelley A, Kleanthous C, et al. Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3. Nat Struct Mol Biol. 2010;17:1241-1246 pubmed publisher
    ..These residues activate the 16S rRNA for 2' OH-induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function. ..
  18. Carter A, Clemons W, Brodersen D, Morgan Warren R, Hartsch T, Wimberly B, et al. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science. 2001;291:498-501 pubmed
    ..The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit. ..
  19. Suh M, Hamburg D, Gregory S, Dahlberg A, Limbach P. Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry. Proteomics. 2005;5:4818-31 pubmed
    ..The extension of protein identification to additional bacterial strains can be useful in phylogenetic studies as well as in biomarker identification. ..
  20. Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, et al. Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal. J Biol Chem. 2004;279:37163-74 pubmed
    ..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 ..
  21. Althoff T, Mills D, Popot J, Kuhlbrandt W. Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1. EMBO J. 2011;30:4652-64 pubmed publisher
    ..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. ..
  22. Connell S, Takemoto C, Wilson D, Wang H, Murayama K, Terada T, et al. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol Cell. 2007;25:751-64 pubmed
    ..Therefore, a network of interaction with the ribosome establishes the active GTP conformation of EF-G and thus facilitates GTP hydrolysis and tRNA translocation. ..
  23. Chang H, Hemp J, Chen Y, Fee J, Gennis R. The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping. Proc Natl Acad Sci U S A. 2009;106:16169-73 pubmed publisher
    ..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. ..
  24. Gao Y, Selmer M, Dunham C, Weixlbaumer A, Kelley A, Ramakrishnan V. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science. 2009;326:694-9 pubmed publisher
    ..The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure. ..
  25. Hattori M, Tanaka Y, Fukai S, Ishitani R, Nureki O. Crystal structure of the MgtE Mg2+ transporter. Nature. 2007;448:1072-5 pubmed
    ..Whether this presumed regulation controls gating of an ion channel or opening of a secondary active transporter remains to be determined. ..
  26. Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G. A new understanding of the decoding principle on the ribosome. Nature. 2012;484:256-9 pubmed publisher
    ..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. ..
  27. Fukui K, Nakagawa N, Kitamura Y, Nishida Y, Masui R, Kuramitsu S. Crystal structure of MutS2 endonuclease domain and the mechanism of homologous recombination suppression. J Biol Chem. 2008;283:33417-27 pubmed publisher
    ..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. ..
  28. Neubauer C, Gao Y, Andersen K, Dunham C, Kelley A, Hentschel J, et al. The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell. 2009;139:1084-95 pubmed publisher
    ..These structures provide detailed insight into the translational regulation on the bacterial ribosome by mRNA cleavage. ..
  29. Milon P, Rodnina M. Kinetic control of translation initiation in bacteria. Crit Rev Biochem Mol Biol. 2012;47:334-48 pubmed publisher
  30. Yusupov M, Yusupova G, Baucom A, Lieberman K, Earnest T, Cate J, et al. Crystal structure of the ribosome at 5.5 A resolution. Science. 2001;292:883-96 pubmed
    ..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. ..
  31. Liu B, Chen Y, Doukov T, Soltis S, Stout C, Fee J. 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. Biochemistry. 2009;48:820-6 pubmed publisher
    ..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. ..
  32. Kurata S, Weixlbaumer A, Ohtsuki T, Shimazaki T, Wada T, Kirino Y, et al. Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding. J Biol Chem. 2008;283:18801-11 pubmed publisher
    ..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. ..
  33. Selmer M, Dunham C, Murphy F, Weixlbaumer A, Petry S, Kelley A, et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science. 2006;313:1935-42 pubmed
    ..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. ..
  34. Muresanu L, Pristovsek P, Lohr F, Maneg O, Mukrasch M, Rüterjans H, et al. The electron transfer complex between cytochrome c552 and the CuA domain of the Thermus thermophilus ba3 oxidase. A combined NMR and computational approach. J Biol Chem. 2006;281:14503-13 pubmed
    ..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. ..
  35. Nakane S, Nakagawa N, Kuramitsu S, Masui R. Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity. Nucleic Acids Res. 2009;37:2037-52 pubmed publisher
    ..We found Thermus thermophilus HB8 PolX (ttPolX) has Mg(2+)/Mn(2+)-dependent DNA/RNA polymerase, Mn(2+)-dependent 3'-5' exonuclease and DNA-..
  36. Schmeing T, Voorhees R, Kelley A, Gao Y, Murphy F, Weir J, et al. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science. 2009;326:688-694 pubmed publisher
    ..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. ..
  37. Sharma M, Barat C, Wilson D, Booth T, Kawazoe M, Hori Takemoto C, et al. Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly. Mol Cell. 2005;18:319-29 pubmed
    ..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. ..
  38. Nishimura M, Yoshida T, Shirouzu M, Terada T, Kuramitsu S, Yokoyama S, et al. Solution structure of ribosomal protein L16 from Thermus thermophilus HB8. J Mol Biol. 2004;344:1369-83 pubmed
    ..The three-dimensional structure of L16 from Thermus thermophilus HB8 was determined by NMR...
  39. Berrisford J, Sazanov L. Structural basis for the mechanism of respiratory complex I. J Biol Chem. 2009;284:29773-83 pubmed publisher
    ..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. ..
  40. Jin H, Kelley A, Ramakrishnan V. Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3. Proc Natl Acad Sci U S A. 2011;108:15798-803 pubmed publisher
    ..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. ..
  41. Agari Y, Kuramitsu S, Shinkai A. Identification of novel genes regulated by the oxidative stress-responsive transcriptional activator SdrP in Thermus thermophilus HB8. FEMS Microbiol Lett. 2010;313:127-34 pubmed publisher
    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 ..
  42. Pioletti M, Schlünzen F, Harms J, Zarivach R, Glühmann M, Avila H, et al. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J. 2001;20:1829-39 pubmed
  43. Voorhees R, Schmeing T, Kelley A, Ramakrishnan V. The mechanism for activation of GTP hydrolysis on the ribosome. Science. 2010;330:835-838 pubmed publisher
    ..The structure suggests a universal mechanism for GTPase activation and hydrolysis in translational GTPases on the ribosome. ..
  44. Ogle J, Brodersen D, Clemons W, Tarry M, Carter A, Ramakrishnan V. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science. 2001;292:897-902 pubmed
    ..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. ..
  45. Fukai S, Nureki O, Sekine S, Shimada A, Vassylyev D, Yokoyama S. Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase. RNA. 2003;9:100-11 pubmed
    ..Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction. ..
  46. Sakamoto K, Agari Y, Yokoyama S, Kuramitsu S, Shinkai A. Functional identification of an anti-sigmaE factor from Thermus thermophilus HB8. Gene. 2008;423:153-9 pubmed publisher
    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 ..
  47. Agari Y, Kashihara A, Yokoyama S, Kuramitsu S, Shinkai A. Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator. Mol Microbiol. 2008;70:60-75 pubmed publisher
    ..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. ..
  48. Weixlbaumer A, Petry S, Dunham C, Selmer M, Kelley A, Ramakrishnan V. Crystal structure of the ribosome recycling factor bound to the ribosome. Nat Struct Mol Biol. 2007;14:733-7 pubmed
    ..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. ..
  49. Bessho Y, Shibata R, Sekine S, Murayama K, Higashijima K, Hori Takemoto C, et al. Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc Natl Acad Sci U S A. 2007;104:8293-8 pubmed
    ..Therefore, the tRNP may simulate a tRNA, both structurally and functionally, with respect to aminoacylation and ribosome entry. ..
  50. Lamour V, Hoermann L, Jeltsch J, Oudet P, Moras D. An open conformation of the Thermus thermophilus gyrase B ATP-binding domain. J Biol Chem. 2002;277:18947-53 pubmed
    ..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. ..
  51. Fukui K, Kosaka H, Kuramitsu S, Masui R. Nuclease activity of the MutS homologue MutS2 from Thermus thermophilus is confined to the Smr domain. Nucleic Acids Res. 2007;35:850-60 pubmed
    ..It is noteworthy that an endonuclease activity is associated with a MutS homologue, which is generally thought to recognize specific DNA structures. ..
  52. Yusupova G, Jenner L, Rees B, Moras D, Yusupov M. Structural basis for messenger RNA movement on the ribosome. Nature. 2006;444:391-4 pubmed
  53. Back J, Park J, Chung J, Kim D, Han Y. A distinct TthMutY bifunctional glycosylase that hydrolyzes not only adenine but also thymine opposite 8-oxoguanine in the hyperthermophilic bacterium, Thermus thermophilus. DNA Repair (Amst). 2006;5:894-903 pubmed
    ..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. ..
  54. Voorhees R, Weixlbaumer A, Loakes D, Kelley A, Ramakrishnan V. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol. 2009;16:528-33 pubmed publisher
    ..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. ..
  55. Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R. The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. J Mol Biol. 2012;417:179-96 pubmed publisher
    ..Here, we show that Thermus thermophilus HB8 PolX (ttPolX) had strong binding affinity for Mg(2+)-dNTPs in the absence of DNA and that it follows a ..
  56. Efremov R, Baradaran R, Sazanov L. The architecture of respiratory complex I. Nature. 2010;465:441-5 pubmed publisher
  57. Shimada A, Masui R, Nakagawa N, Takahata Y, Kim K, Kuramitsu S, et al. A novel single-stranded DNA-specific 3'-5' exonuclease, Thermus thermophilus exonuclease I, is involved in several DNA repair pathways. Nucleic Acids Res. 2010;38:5692-705 pubmed publisher
    ..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...
  58. Jenner L, Demeshkina N, Yusupova G, Yusupov M. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat Struct Mol Biol. 2010;17:555-60 pubmed publisher
    ..These data allow rationalization of how modification deficiencies of ms(2)i(6)A37 in tRNAs may lead to shifts of the translational reading frame...
  59. Demirci H, Murphy F, Belardinelli R, Kelley A, Ramakrishnan V, Gregory S, et al. Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function. RNA. 2010;16:2319-24 pubmed publisher
    ..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...
  60. Nakane S, Nakagawa N, Kuramitsu S, Masui R. The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair. DNA Repair (Amst). 2012;11:906-14 pubmed publisher
    ..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 ..
  61. Brodersen D, Clemons W, Carter A, Morgan Warren R, Wimberly B, Ramakrishnan V. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell. 2000;103:1143-54 pubmed
    ..For each of these antibiotics, interactions with the 30S subunit suggest a mechanism for its effects on ribosome function...
  62. Petry S, Brodersen D, Murphy F, Dunham C, Selmer M, Tarry M, et al. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell. 2005;123:1255-66 pubmed publisher
    ..Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway...
  63. Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J. Visualizing tmRNA entry into a stalled ribosome. Science. 2003;300:127-30 pubmed publisher
    ..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...
  64. Klaholz B, Pape T, Zavialov A, Myasnikov A, Orlova E, Vestergaard B, et al. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature. 2003;421:90-4 pubmed publisher
    ..By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism...
  65. Rawat U, Zavialov A, Sengupta J, Valle M, Grassucci R, Linde J, et al. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature. 2003;421:87-90 pubmed publisher
    ..The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC...
  66. Weixlbaumer A, Jin H, Neubauer C, Voorhees R, Petry S, Kelley A, et al. Insights into translational termination from the structure of RF2 bound to the ribosome. Science. 2008;322:953-6 pubmed publisher
    ..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. ..
  67. Berthet Colominas C, Seignovert L, Hartlein M, Grotli M, Cusack S, Leberman R. 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. EMBO J. 1998;17:2947-60 pubmed
  68. Keightley J, Zimmermann B, Mather M, Springer P, Pastuszyn A, Lawrence D, et al. Molecular genetic and protein chemical characterization of the cytochrome ba3 from Thermus thermophilus HB8. J Biol Chem. 1995;270:20345-58 pubmed
    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...
  69. Aberg A, Yaremchuk A, Tukalo M, Rasmussen B, Cusack S. Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase. Biochemistry. 1997;36:3084-94 pubmed
    ..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. ..
  70. Schmeing T, Voorhees R, Kelley A, Ramakrishnan V. How mutations in tRNA distant from the anticodon affect the fidelity of decoding. Nat Struct Mol Biol. 2011;18:432-6 pubmed publisher
    ..Our results also suggest that each native tRNA will adopt a unique conformation when delivered to the ribosome that allows accurate decoding. ..
  71. Klostermeier D, Seidel R, Reinstein J. The functional cycle and regulation of the Thermus thermophilus DnaK chaperone system. J Mol Biol. 1999;287:511-25 pubmed
    ..DafATth.DnaJTth complex until it is replaced by substrate proteins under heat shock conditions. ..
  72. Fukui K, Nishida M, Nakagawa N, Masui R, Kuramitsu S. Bound nucleotide controls the endonuclease activity of mismatch repair enzyme MutL. J Biol Chem. 2008;283:12136-45 pubmed publisher
    ..Complementation experiments revealed that the endonuclease activity of ttMutL and its regulation by ATP binding are necessary for DNA repair in vivo. ..
  73. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark B, et al. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science. 1995;270:1464-72 pubmed
    ..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. ..
  74. Soulimane T, Than M, Dewor M, Huber R, Buse G. Primary structure of a novel subunit in ba3-cytochrome oxidase from Thermus thermophilus. Protein Sci. 2000;9:2068-73 pubmed
    ..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). ..
  75. Carter A, Clemons W, Brodersen D, Morgan Warren R, Wimberly B, Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 2000;407:340-8 pubmed
    ..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. ..
  76. Hattori M, Iwase N, Furuya N, Tanaka Y, Tsukazaki T, Ishitani R, et al. Mg(2+)-dependent gating of bacterial MgtE channel underlies Mg(2+) homeostasis. EMBO J. 2009;28:3602-12 pubmed publisher
    ..These structural and functional results have clarified the control of Mg(2+) homeostasis through cooperative Mg(2+) binding to the MgtE cytosolic domain. ..
  77. Soulimane T, Buse G, Bourenkov G, Bartunik H, Huber R, Than M. Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus. EMBO J. 2000;19:1766-76 pubmed
    ..New aspects of the proton pumping mechanism could be identified. ..
  78. Buse G, Soulimane T, Dewor M, Meyer H, Blüggel M. Evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase. Protein Sci. 1999;8:985-90 pubmed
    ..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. ..
  79. Chen Y, Hunsicker Wang L, Pacoma R, Luna E, Fee J. A homologous expression system for obtaining engineered cytochrome ba3 from Thermus thermophilus HB8. Protein Expr Purif. 2005;40:299-318 pubmed
    ..We have cloned the complete cba operon of Thermus thermophilus HB8 in an Escherichia coli/T. thermophilus shuttle vector...
  80. Kosuge T, Hoshino T. Lysine is synthesized through the alpha-aminoadipate pathway in Thermus thermophilus. FEMS Microbiol Lett. 1998;169:361-7 pubmed
    ..These results indicate that lysine was synthesized through the alpha-aminoadipate pathway and not through the diaminopimelate pathway in T. thermophilus. ..
  81. Mather M, Springer P, Hensel S, Buse G, Fee J. 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. J Biol Chem. 1993;268:5395-408 pubmed
    ..Possible topological and helix packing models are developed based on considerations of homology, hydropathy, and variability. ..
  82. Mather M, Springer P, Fee J. Cytochrome oxidase genes from Thermus thermophilus. Nucleotide sequence and analysis of the deduced primary structure of subunit IIc of cytochrome caa3. J Biol Chem. 1991;266:5025-35 pubmed
  83. Wimberly B, Brodersen D, Clemons W, Morgan Warren R, Carter A, Vonrhein C, et al. Structure of the 30S ribosomal subunit. Nature. 2000;407:327-39 pubmed
    ..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. ..
  84. Takamatsu S, Kato R, Kuramitsu S. Mismatch DNA recognition protein from an extremely thermophilic bacterium, Thermus thermophilus HB8. Nucleic Acids Res. 1996;24:640-7 pubmed
    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...
  85. Tachiki H, Kato R, Masui R, Hasegawa K, Itakura H, Fukuyama K, et al. Domain organization and functional analysis of Thermus thermophilus MutS protein. Nucleic Acids Res. 1998;26:4153-9 pubmed
    ..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. ..
  86. Sazanov L, Hinchliffe P. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science. 2006;311:1430-6 pubmed
    ..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. ..
  87. Shinkai A, Kira S, Nakagawa N, Kashihara A, Kuramitsu S, Yokoyama S. Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8. J Bacteriol. 2007;189:3891-901 pubmed
    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 ..
  88. Wakamatsu T, Nakagawa N, Kuramitsu S, Masui R. Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8. J Bacteriol. 2008;190:1108-17 pubmed
    ADP-ribose (ADPR) is one of the main substrates of Nudix proteins. Among the eight Nudix proteins of Thermus thermophilus HB8, we previously determined the crystal structure of Ndx4, an ADPR pyrophosphatase (ADPRase)...