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Disease relevance of Pyrococcus


High impact information on Pyrococcus

  • To clarify functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair, we report Pyrococcus furiosus Mre11 crystal structures, revealing a protein phosphatase-like, dimanganese binding domain capped by a unique domain controlling active site access [6].
  • Analysis of the three-dimensional structure of ACE shows that it bears little similarity to that of carboxypeptidase A, but instead resembles neurolysin and Pyrococcus furiosus carboxypeptidase--zinc metallopeptidases with no detectable sequence similarity to ACE [7].
  • Superoxide reductase from the hyperthermophilic anaerobe Pyrococcus furiosus uses electrons from reduced nicotinamide adenine dinucleotide phosphate, by way of rubredoxin and an oxidoreductase, to reduce superoxide to hydrogen peroxide, which is then reduced to water by peroxidases [8].
  • The crystal structure of the tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) from Pyrococcus furiosus, a hyperthermophilic archaeon (formerly archaebacterium) that grows optimally at 100 degrees C, has been determined at 2.3 angstrom resolution by means of multiple isomorphous replacement and multiple crystal form averaging [9].
  • Here it is shown that the archaebacterium Pyrococcus woesei expresses a protein with structural and functional similarity to eukaryotic TBP molecules [10].

Chemical compound and disease context of Pyrococcus


Biological context of Pyrococcus

  • The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures [16].
  • The intracellular protease from Pyrococcus horikoshii (PH1704) and PfpI from Pyrococcus furiosus are members of a class of intracellular proteases that have no sequence homology to any other known protease family [17].
  • When each of the gene products was phylogenetically analyzed, we found that genes evolutionarily-related to the lysine biosynthetic genes in T. thermophilus were all present in a hyperthermophilic and anaerobic archaeon, Pyrococcus horikoshii, and formed a gene cluster in a manner similar to that in T. thermophilus [18].
  • In the genome of Pyrococcus genes encoding putative homologues of eucaryal transcription factors TATA-binding protein (TBP) and TFIIB have been detected [19].
  • The predicted amino acid sequence of inhA showed low similarity to that of an intracellular protease in Pyrococcus horikoshii (PH1704), and an active cysteine residue in the protease was conserved in the isonitrile hydratase at the corresponding position (Cys-101) [20].

Associations of Pyrococcus with chemical compounds


Gene context of Pyrococcus

  • To clarify RAD51 interactions controlling homologous recombination, we report here the crystal structure of the full-length RAD51 homolog from Pyrococcus furiosus [26].
  • To address this, transcription initiation complexes have been formed with Pyrococcus furiosus transcription factors (TBP and TFB1), RNA polymerase, and a linear DNA fragment containing a strong promoter [27].
  • DJ-1 is structurally most similar to the monomer subunit of protease I, the intracellular cysteine protease from Pyrococcus horikoshii, and belongs to the Class I glutamine amidotransferase-like superfamily [28].
  • Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation [29].
  • Only two proteins homologous to subunits of eukaryotic replication factor C (RFC) have been detected in Pyrococcus abyssi (Pab) [30].

Analytical, diagnostic and therapeutic context of Pyrococcus


  1. A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea. Komori, K., Sakae, S., Shinagawa, H., Morikawa, K., Ishino, Y. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
  2. Redox properties of rubredoxin variants as a function of solvent composition and temperature: investigation of monopolar and dipolar interactions. Zheng, H., Kellog, S.J., Erickson, A.E., Dubauskie, N.A., Smith, E.T. J. Biol. Inorg. Chem. (2003) [Pubmed]
  3. Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Lazaridis, T., Lee, I., Karplus, M. Protein Sci. (1997) [Pubmed]
  4. Novel bifunctional hyperthermostable carboxypeptidase/aminoacylase from Pyrococcus horikoshii OT3. Ishikawa, K., Ishida, H., Matsui, I., Kawarabayasi, Y., Kikuchi, H. Appl. Environ. Microbiol. (2001) [Pubmed]
  5. Simultaneous detection of different Rhizobium strains marked with either the Escherichia coli gusA gene or the Pyrococcus furiosus celB gene. Sessitsch, A., Wilson, K.J., Akkermans, A.D., de Vos, W.M. Appl. Environ. Microbiol. (1996) [Pubmed]
  6. Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Hopfner, K.P., Karcher, A., Craig, L., Woo, T.T., Carney, J.P., Tainer, J.A. Cell (2001) [Pubmed]
  7. Crystal structure of the human angiotensin-converting enzyme-lisinopril complex. Natesh, R., Schwager, S.L., Sturrock, E.D., Acharya, K.R. Nature (2003) [Pubmed]
  8. Anaerobic microbes: oxygen detoxification without superoxide dismutase. Jenney, F.E., Verhagen, M.F., Cui, X., Adams, M.W. Science (1999) [Pubmed]
  9. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Chan, M.K., Mukund, S., Kletzin, A., Adams, M.W., Rees, D.C. Science (1995) [Pubmed]
  10. The TATA-binding protein: a general transcription factor in eukaryotes and archaebacteria. Rowlands, T., Baumann, P., Jackson, S.P. Science (1994) [Pubmed]
  11. Kinetic and structural characterization of manganese(II)-loaded methionyl aminopeptidases. D'souza, V.M., Swierczek, S.I., Cosper, N.J., Meng, L., Ruebush, S., Copik, A.J., Scott, R.A., Holz, R.C. Biochemistry (2002) [Pubmed]
  12. Cloning and sequencing of a gene from the archaeon Pyrococcus furiosus with high homology to a gene encoding phosphoenolpyruvate synthetase from Escherichia coli. Jones, C.E., Fleming, T.M., Piper, P.W., Littlechild, J.A., Cowan, D.A. Gene (1995) [Pubmed]
  13. Molecular and phylogenetic characterization of pyruvate and 2-ketoisovalerate ferredoxin oxidoreductases from Pyrococcus furiosus and pyruvate ferredoxin oxidoreductase from Thermotoga maritima. Kletzin, A., Adams, M.W. J. Bacteriol. (1996) [Pubmed]
  14. The 3-phosphoglycerate kinase of the hyperthermophilic archaeum Pyrococcus woesei produced in Escherichia coli: loss of heat resistance due to internal translation initiation and its restoration by site-directed mutagenesis. Hess, D., Hensel, R. Gene (1996) [Pubmed]
  15. Cloning, purification, crystallization and preliminary crystallographic analysis of galactokinase from Pyrococcus furiosus. de Geus, D., Hartley, A.P., Sedelnikova, S.E., Glynn, S.E., Baker, P.J., Verhees, C.H., van der Oost, J., Rice, D.W. Acta Crystallogr. D Biol. Crystallogr. (2003) [Pubmed]
  16. The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures. Villeret, V., Clantin, B., Tricot, C., Legrain, C., Roovers, M., Stalon, V., Glansdorff, N., Van Beeumen, J. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  17. Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-A resolution. Du, X., Choi, I.G., Kim, R., Wang, W., Jancarik, J., Yokota, H., Kim, S.H. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  18. A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis. Nishida, H., Nishiyama, M., Kobashi, N., Kosuge, T., Hoshino, T., Yamane, H. Genome Res. (1999) [Pubmed]
  19. Two transcription factors related with the eucaryal transcription factors TATA-binding protein and transcription factor IIB direct promoter recognition by an archaeal RNA polymerase. Hausner, W., Wettach, J., Hethke, C., Thomm, M. J. Biol. Chem. (1996) [Pubmed]
  20. Isonitrile hydratase from Pseudomonas putida N19-2. Cloning, sequencing, gene expression, and identification of its active acid residue. Goda, M., Hashimoto, Y., Takase, M., Herai, S., Iwahara, Y., Higashibata, H., Kobayashi, M. J. Biol. Chem. (2002) [Pubmed]
  21. Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. Charron, C., Roy, H., Blaise, M., Giegé, R., Kern, D. EMBO J. (2003) [Pubmed]
  22. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. Schmitt, E., Moulinier, L., Fujiwara, S., Imanaka, T., Thierry, J.C., Moras, D. EMBO J. (1998) [Pubmed]
  23. Enzymes and proteins from organisms that grow near and above 100 degrees C. Adams, M.W. Annu. Rev. Microbiol. (1993) [Pubmed]
  24. The carbamate kinase-like carbamoyl phosphate synthetase of the hyperthermophilic archaeon Pyrococcus furiosus, a missing link in the evolution of carbamoyl phosphate biosynthesis. Durbecq, V., Legrain, C., Roovers, M., Piérard, A., Glansdorff, N. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  25. Femtosecond dynamics of rubredoxin: tryptophan solvation and resonance energy transfer in the protein. Zhong, D., Pal, S.K., Zhang, D., Chan, S.I., Zewail, A.H. Proc. Natl. Acad. Sci. U.S.A. (2002) [Pubmed]
  26. Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. Shin, D.S., Pellegrini, L., Daniels, D.S., Yelent, B., Craig, L., Bates, D., Yu, D.S., Shivji, M.K., Hitomi, C., Arvai, A.S., Volkmann, N., Tsuruta, H., Blundell, T.L., Venkitaraman, A.R., Tainer, J.A. EMBO J. (2003) [Pubmed]
  27. Topography of the euryarchaeal transcription initiation complex. Bartlett, M.S., Thomm, M., Geiduschek, E.P. J. Biol. Chem. (2004) [Pubmed]
  28. The crystal structure of DJ-1, a protein related to male fertility and Parkinson's disease. Honbou, K., Suzuki, N.N., Horiuchi, M., Niki, T., Taira, T., Ariga, H., Inagaki, F. J. Biol. Chem. (2003) [Pubmed]
  29. Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation. Bagautdinov, B., Kuroishi, C., Sugahara, M., Kunishima, N. J. Mol. Biol. (2005) [Pubmed]
  30. Replication factor C from the hyperthermophilic archaeon Pyrococcus abyssi does not need ATP hydrolysis for clamp-loading and contains a functionally conserved RFC PCNA-binding domain. Henneke, G., Gueguen, Y., Flament, D., Azam, P., Querellou, J., Dietrich, J., Hübscher, U., Raffin, J.P. J. Mol. Biol. (2002) [Pubmed]
  31. Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization. Liu, L., Iwata, K., Kita, A., Kawarabayasi, Y., Yohda, M., Miki, K. J. Mol. Biol. (2002) [Pubmed]
  32. Characterization of PCR products from bacilli using electrospray ionization FTICR mass spectrometry. Muddiman, D.C., Wunschel, D.S., Liu, C., Pasa-Tolić, L., Fox, K.F., Fox, A., Anderson, G.A., Smith, R.D. Anal. Chem. (1996) [Pubmed]
  33. Participation of the disulfide bridge in the redox cycle of the ferredoxin from the hyperthermophile Pyrococcus furiosus: 1H nuclear magnetic resonance time resolution of the four redox states at ambient temperature. Gorst, C.M., Zhou, Z.H., Ma, K., Teng, Q., Howard, J.B., Adams, M.W., La Mar, G.N. Biochemistry (1995) [Pubmed]
  34. Persistence of tertiary structure in 7.9 M guanidinium chloride: the case of endo-beta-1,3-glucanase from Pyrococcus furiosus. Chiaraluce, R., Van Der Oost, J., Lebbink, J.H., Kaper, T., Consalvi, V. Biochemistry (2002) [Pubmed]
  35. Purification, crystallization and preliminary crystallographic analysis of the glycine-cleavage system component T-protein from Pyrococcus horikoshii OT3. Lokanath, N.K., Kuroishi, C., Okazaki, N., Kunishima, N. Acta Crystallogr. D Biol. Crystallogr. (2004) [Pubmed]
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