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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
 
MeSH Review

Thermus

 
 
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Disease relevance of Thermus

 

High impact information on Thermus

  • In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate [6].
  • The crystal structure of intact elongation factor Tu (EF-Tu) from Thermus thermophilus has been determined and refined at an effective resolution of 1.7 A, with incorporation of data extending to 1.45 A [7].
  • The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution [8].
  • Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 A resolution [9].
  • Thermus RRF could also be activated by introducing surface substitutions in its anticodon arm-mimic region [10].
 

Chemical compound and disease context of Thermus

  • The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined [11].
  • The crystal structure of Thermus thermophilus elongation factor G without guanine nucleotide was determined to 2.85 A [12].
  • 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 [13].
  • The crystal structures of two ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I (Klentaq1) with a primer/template DNA and dideoxycytidine triphosphate, and that of a binary complex of the same enzyme with a primer/template DNA, were determined to a resolution of 2.3, 2.3 and 2.5 A, respectively [14].
  • In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes [15].
 

Biological context of Thermus

 

Anatomical context of Thermus

  • The influence of divalent metal ions on the intrinsic and kirromycin-stimulated GTPase activity in the absence of programmed ribosomes and on nucleotide binding affinity of elongation factor Tu (EF-Tu) from Thermus thermophilus prepared as the nucleotide- and Mg(2+)-free protein has been investigated [21].
  • Fluorescence resonance energy transfer analysis of protein translocase. SecYE from Thermus thermophilus HB8 forms a constitutive oligomer in membranes [22].
  • The soluble ATPase purified from an aerobic thermophilic eubacterium, Thermus thermophilus, was not a usual F1-ATPase but a V1-ATPase, a peripheral section of plasma membrane V-type ATPase (Yokoyama, K., Oshima, T., and Yoshida, M. (1990) J. Biol. Chem. 265, 21946-21950) [23].
  • glmS of Thermus thermophilus HB8: an essential gene for cell-wall synthesis identified immediately upstream of the S-layer gene [24].
  • Where the NADH-quinone reductase segment involved an energy-coupling site (e.g., in bovine heart and rat liver mitochondria, and in Paracoccus denitrificans, Escherichia coli, and Thermus thermophilus HB-8 membranes), DCCD acted as an inhibitor of ubiquinone reduction by NADH [25].
 

Gene context of Thermus

 

Analytical, diagnostic and therapeutic context of Thermus

  • Guided by x-ray crystal structures and molecular modeling, site-directed mutagenesis has been used to systematically invert the coenzyme specificity of Thermus thermophilus isopropylmalate dehydrogenase from a 100-fold preference for NAD to a 1000-fold preference for NADP [31].
  • The PCNA-binding domain was determined, and a hybrid DNA polymerase was constructed by grafting this domain onto the classical PCR enzyme from Thermus aquaticus, Taq DNA polymerase [32].
  • Molecular cloning of a ribonuclease H (RNase HI) gene from an extreme thermophile Thermus thermophilus HB8: a thermostable RNase H can functionally replace the Escherichia coli enzyme in vivo [33].
  • This Thermus ligase is similar to Thermus thermophilus HB8 ligase with respect to pH, salt, NAD+, divalent cation profiles and steady-state kinetics.However, the former is more discriminative toward T/G mismatches at the 3'-side of the ligation junction, as judged by the ratios of initial ligation rates of matched and mismatched substrates [34].
  • Purification, crystallization and preliminary X-ray analysis of inorganic pyrophosphatase from Thermus thermophilus [35].

References

  1. Crystal structure of a eukaryote/archaeon-like protyl-tRNA synthetase and its complex with tRNAPro(CGG). Yaremchuk, A., Cusack, S., Tukalo, M. EMBO J. (2000) [Pubmed]
  2. Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Závodszky, P., Kardos, J., Svingor, n.u.l.l., Petsko, G.A. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  3. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Min, B., Pelaschier, J.T., Graham, D.E., Tumbula-Hansen, D., Söll, D. Proc. Natl. Acad. Sci. U.S.A. (2002) [Pubmed]
  4. Enhancement of the thermostability of subtilisin E by introduction of a disulfide bond engineered on the basis of structural comparison with a thermophilic serine protease. Takagi, H., Takahashi, T., Momose, H., Inouye, M., Maeda, Y., Matsuzawa, H., Ohta, T. J. Biol. Chem. (1990) [Pubmed]
  5. Evidence for N coordination to Fe in the [2Fe-2S] clusters of Thermus Rieske protein and phthalate dioxygenase from Pseudomonas. Cline, J.F., Hoffman, B.M., Mims, W.B., LaHaie, E., Ballou, D.P., Fee, J.A. J. Biol. Chem. (1985) [Pubmed]
  6. Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase. Fukai, S., Nureki, O., Sekine, S., Shimada, A., Tao, J., Vassylyev, D.G., Yokoyama, S. Cell (2000) [Pubmed]
  7. Crystal structure of active elongation factor Tu reveals major domain rearrangements. Berchtold, H., Reshetnikova, L., Reiser, C.O., Schirmer, N.K., Sprinzl, M., Hilgenfeld, R. Nature (1993) [Pubmed]
  8. Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Nureki, O., Vassylyev, D.G., Katayanagi, K., Shimizu, T., Sekine, S., Kigawa, T., Miyazawa, T., Yokoyama, S., Morikawa, K. Science (1995) [Pubmed]
  9. Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Belrhali, H., Yaremchuk, A., Tukalo, M., Larsen, K., Berthet-Colominas, C., Leberman, R., Beijer, B., Sproat, B., Als-Nielsen, J., Grübel, G. Science (1994) [Pubmed]
  10. Elongation factor G participates in ribosome disassembly by interacting with ribosome recycling factor at their tRNA-mimicry domains. Ito, K., Fujiwara, T., Toyoda, T., Nakamura, Y. Mol. Cell (2002) [Pubmed]
  11. Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia. Nakai, T., Nakagawa, N., Maoka, N., Masui, R., Kuramitsu, S., Kamiya, N. EMBO J. (2005) [Pubmed]
  12. Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. AEvarsson, A., Brazhnikov, E., Garber, M., Zheltonosova, J., Chirgadze, Y., al-Karadaghi, S., Svensson, L.A., Liljas, A. EMBO J. (1994) [Pubmed]
  13. 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. Berthet-Colominas, C., Seignovert, L., Härtlein, M., Grotli, M., Cusack, S., Leberman, R. EMBO J. (1998) [Pubmed]
  14. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. Li, Y., Korolev, S., Waksman, G. EMBO J. (1998) [Pubmed]
  15. ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. Sekine, S., Nureki, O., Dubois, D.Y., Bernier, S., Chênevert, R., Lapointe, J., Vassylyev, D.G., Yokoyama, S. EMBO J. (2003) [Pubmed]
  16. Heat-inactivated proteins are rescued by the DnaK.J-GrpE set and ClpB chaperones. Motohashi, K., Watanabe, Y., Yohda, M., Yoshida, M. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
  17. Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity. Nishiyama, M., Matsubara, N., Yamamoto, K., Iijima, S., Uozumi, T., Beppu, T. J. Biol. Chem. (1986) [Pubmed]
  18. CbpA, a DnaJ homolog, is a DnaK co-chaperone, and its activity is modulated by CbpM. Chae, C., Sharma, S., Hoskins, J.R., Wickner, S. J. Biol. Chem. (2004) [Pubmed]
  19. A new type of NADH dehydrogenase specific for nitrate respiration in the extreme thermophile Thermus thermophilus. Cava, F., Zafra, O., Magalon, A., Blasco, F., Berenguer, J. J. Biol. Chem. (2004) [Pubmed]
  20. NMR study of repair mechanism of DNA photolyase by FAD-induced paramagnetic relaxation enhancement. Ueda, T., Kato, A., Ogawa, Y., Torizawa, T., Kuramitsu, S., Iwai, S., Terasawa, H., Shimada, I. J. Biol. Chem. (2004) [Pubmed]
  21. Mg2+ is not catalytically required in the intrinsic and kirromycin-stimulated GTPase action of Thermus thermophilus EF-Tu. Rutthard, H., Banerjee, A., Makinen, M.W. J. Biol. Chem. (2001) [Pubmed]
  22. Fluorescence resonance energy transfer analysis of protein translocase. SecYE from Thermus thermophilus HB8 forms a constitutive oligomer in membranes. Mori, H., Tsukazaki, T., Masui, R., Kuramitsu, S., Yokoyama, S., Johnson, A.E., Kimura, Y., Akiyama, Y., Ito, K. J. Biol. Chem. (2003) [Pubmed]
  23. Isolation of prokaryotic V0V1-ATPase from a thermophilic eubacterium Thermus thermophilus. Yokoyama, K., Akabane, Y., Ishii, N., Yoshida, M. J. Biol. Chem. (1994) [Pubmed]
  24. glmS of Thermus thermophilus HB8: an essential gene for cell-wall synthesis identified immediately upstream of the S-layer gene. Fernández-Herrero, L.A., Badet-Denisot, M.A., Badet, B., Berenguer, J. Mol. Microbiol. (1995) [Pubmed]
  25. Inhibition of NADH-ubiquinone reductase activity by N,N'-dicyclohexylcarbodiimide and correlation of this inhibition with the occurrence of energy-coupling site 1 in various organisms. Yagi, T. Biochemistry (1987) [Pubmed]
  26. An unusual mechanism of bacterial gene expression revealed for the RNase P protein of Thermus strains. Feltens, R., Gossringer, M., Willkomm, D.K., Urlaub, H., Hartmann, R.K. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  27. Crystal structure of elongation factor P from Thermus thermophilus HB8. Hanawa-Suetsugu, K., Sekine, S., Sakai, H., Hori-Takemoto, C., Terada, T., Unzai, S., Tame, J.R., Kuramitsu, S., Shirouzu, M., Yokoyama, S. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  28. Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase. Shimada, A., Nureki, O., Goto, M., Takahashi, S., Yokoyama, S. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  29. Methionyl-tRNA synthetase gene from an extreme thermophile, Thermus thermophilus HB8. Molecular cloning, primary-structure analysis, expression in Escherichia coli, and site-directed mutagenesis. Nureki, O., Muramatsu, T., Suzuki, K., Kohda, D., Matsuzawa, H., Ohta, T., Miyazawa, T., Yokoyama, S. J. Biol. Chem. (1991) [Pubmed]
  30. Crystal structure of the bovine mitochondrial elongation factor Tu.Ts complex. Jeppesen, M.G., Navratil, T., Spremulli, L.L., Nyborg, J. J. Biol. Chem. (2005) [Pubmed]
  31. Redesigning secondary structure to invert coenzyme specificity in isopropylmalate dehydrogenase. Chen, R., Greer, A., Dean, A.M. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  32. Elucidation of an archaeal replication protein network to generate enhanced PCR enzymes. Motz, M., Kober, I., Girardot, C., Loeser, E., Bauer, U., Albers, M., Moeckel, G., Minch, E., Voss, H., Kilger, C., Koegl, M. J. Biol. Chem. (2002) [Pubmed]
  33. Molecular cloning of a ribonuclease H (RNase HI) gene from an extreme thermophile Thermus thermophilus HB8: a thermostable RNase H can functionally replace the Escherichia coli enzyme in vivo. Itaya, M., Kondo, K. Nucleic Acids Res. (1991) [Pubmed]
  34. Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D. Tong, J., Cao, W., Barany, F. Nucleic Acids Res. (1999) [Pubmed]
  35. Purification, crystallization and preliminary X-ray analysis of inorganic pyrophosphatase from Thermus thermophilus. Obmolova, G., Kuranova, I., Teplyakov, A. J. Mol. Biol. (1993) [Pubmed]
 
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