Pyrococcus furiosus DSM 3638

Summary

Alias: Pyrococcus furiosus DSM3638, Pyrococcus furiosus str. DSM 3638, Pyrococcus furiosus strain DSM 3638

Top Publications

  1. Grünberg S, Bartlett M, Naji S, Thomm M. Transcription factor E is a part of transcription elongation complexes. J Biol Chem. 2007;282:35482-90 pubmed
    ..These results demonstrate the presence of TFE in early elongation complexes and suggest a role of TFE in stabilization of the transcription bubble during elongation. ..
  2. Liu L, Komori K, Ishino S, Bocquier A, Cann I, Kohda D, et al. The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus. J Biol Chem. 2001;276:45484-90 pubmed
    ..furiosus, in a similar fashion to the eukaryotic polymerase alpha-primase complex. ..
  3. Blake P, Park J, Zhou Z, Hare D, Adams M, Summers M. Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci. 1992;1:1508-21 pubmed
    ..However, P. furiosus Rd contains several unique structural elements, including at least four additional hydrogen bonds and three potential electrostatic interactions.(ABSTRACT TRUNCATED AT 400 WORDS) ..
  4. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K. Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition. Structure. 2001;9:197-204 pubmed
    ..This model accounts for how Hjc recognizes and resolves the junction DNA in a specific manner. Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA. ..
  5. Fujikane R, Komori K, Shinagawa H, Ishino Y. Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus. J Biol Chem. 2005;280:12351-8 pubmed
    ..The Hjm helicase may play a central role in the repair systems of organisms living in extreme environments. ..
  6. Fujikane R, Shinagawa H, Ishino Y. The archaeal Hjm helicase has recQ-like functions, and may be involved in repair of stalled replication fork. Genes Cells. 2006;11:99-110 pubmed
    ..The functional interaction of Hjm with PCNA for its helicase activity further suggests that the Hjm works at stalled replication forks, as a member of the reconstituted replisomes to restart replication. ..
  7. Naji S, Grünberg S, Thomm M. The RPB7 orthologue E' is required for transcriptional activity of a reconstituted archaeal core enzyme at low temperatures and stimulates open complex formation. J Biol Chem. 2007;282:11047-57 pubmed
    ..Analyses of the kinetic stabilities of open complexes revealed an unexpected E'-independent role of TFE in the stabilization of open complexes. ..
  8. Kim S, Kim D, Kim J, Kang L, Cho H. Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus. Int J Biol Macromol. 2008;42:356-61 pubmed publisher
    ..This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases. ..
  9. Hopkins B, Paull T. The P. furiosus mre11/rad50 complex promotes 5' strand resection at a DNA double-strand break. Cell. 2008;135:250-60 pubmed publisher
    ..This work elucidates how the conserved Mre11/Rad50 complex promotes DNA end resection in archaea and may serve as a model for DSB processing in eukaryotes. ..
  10. Xu Y, Amero C, Pulukkunat D, Gopalan V, Foster M. Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-R. J Mol Biol. 2009;393:1043-55 pubmed publisher
    ..These findings provide valuable new insights into mechanisms of RNP assembly and serve as important steps towards a three-dimensional model of this ancient RNP enzyme. ..

Detail Information

Publications135 found, 100 shown here

  1. Grünberg S, Bartlett M, Naji S, Thomm M. Transcription factor E is a part of transcription elongation complexes. J Biol Chem. 2007;282:35482-90 pubmed
    ..These results demonstrate the presence of TFE in early elongation complexes and suggest a role of TFE in stabilization of the transcription bubble during elongation. ..
  2. Liu L, Komori K, Ishino S, Bocquier A, Cann I, Kohda D, et al. The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus. J Biol Chem. 2001;276:45484-90 pubmed
    ..furiosus, in a similar fashion to the eukaryotic polymerase alpha-primase complex. ..
  3. Blake P, Park J, Zhou Z, Hare D, Adams M, Summers M. Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci. 1992;1:1508-21 pubmed
    ..However, P. furiosus Rd contains several unique structural elements, including at least four additional hydrogen bonds and three potential electrostatic interactions.(ABSTRACT TRUNCATED AT 400 WORDS) ..
  4. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K. Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition. Structure. 2001;9:197-204 pubmed
    ..This model accounts for how Hjc recognizes and resolves the junction DNA in a specific manner. Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA. ..
  5. Fujikane R, Komori K, Shinagawa H, Ishino Y. Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus. J Biol Chem. 2005;280:12351-8 pubmed
    ..The Hjm helicase may play a central role in the repair systems of organisms living in extreme environments. ..
  6. Fujikane R, Shinagawa H, Ishino Y. The archaeal Hjm helicase has recQ-like functions, and may be involved in repair of stalled replication fork. Genes Cells. 2006;11:99-110 pubmed
    ..The functional interaction of Hjm with PCNA for its helicase activity further suggests that the Hjm works at stalled replication forks, as a member of the reconstituted replisomes to restart replication. ..
  7. Naji S, Grünberg S, Thomm M. The RPB7 orthologue E' is required for transcriptional activity of a reconstituted archaeal core enzyme at low temperatures and stimulates open complex formation. J Biol Chem. 2007;282:11047-57 pubmed
    ..Analyses of the kinetic stabilities of open complexes revealed an unexpected E'-independent role of TFE in the stabilization of open complexes. ..
  8. Kim S, Kim D, Kim J, Kang L, Cho H. Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus. Int J Biol Macromol. 2008;42:356-61 pubmed publisher
    ..This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases. ..
  9. Hopkins B, Paull T. The P. furiosus mre11/rad50 complex promotes 5' strand resection at a DNA double-strand break. Cell. 2008;135:250-60 pubmed publisher
    ..This work elucidates how the conserved Mre11/Rad50 complex promotes DNA end resection in archaea and may serve as a model for DSB processing in eukaryotes. ..
  10. Xu Y, Amero C, Pulukkunat D, Gopalan V, Foster M. Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-R. J Mol Biol. 2009;393:1043-55 pubmed publisher
    ..These findings provide valuable new insights into mechanisms of RNP assembly and serve as important steps towards a three-dimensional model of this ancient RNP enzyme. ..
  11. Chen W, Xu Y, Cho I, Oruganti S, Foster M, Gopalan V. Cooperative RNP assembly: complementary rescue of structural defects by protein and RNA subunits of archaeal RNase P. J Mol Biol. 2011;411:368-83 pubmed publisher
  12. Day M, Hsu B, Joshua Tor L, Park J, Zhou Z, Adams M, et al. X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci. 1992;1:1494-507 pubmed
    ..The influence of these and other features upon the thermostability of the P. furiosus protein is discussed. ..
  13. Blake P, Park J, Bryant F, Aono S, Magnuson J, Eccleston E, et al. Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR. Biochemistry. 1991;30:10885-95 pubmed
    ..These interactions, which are not present in rubredoxins from mesophilic organisms, may prevent the beta-sheet from "unzipping" at elevated temperatures. ..
  14. Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y. 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. Proc Natl Acad Sci U S A. 1999;96:8873-8 pubmed
    ..These results support the notion that the formation and resolution of Holliday junction is the common mechanism of homologous recombination in the three domains of life. ..
  15. Strop P, Mayo S. Contribution of surface salt bridges to protein stability. Biochemistry. 2000;39:1251-5 pubmed
    ..5 kcal mol(-)(1). The entropic cost of making a surface salt bridge involving the protein's backbone is reduced, since the backbone has already been immobilized upon protein folding. ..
  16. Nishino T, Komori K, Ishino Y, Morikawa K. X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease: similarity between its endonuclease domain and restriction enzymes. Structure. 2003;11:445-57 pubmed
    ..Simultaneous disruptions of both interfaces result in their dissociation into separate monomers, with strikingly reduced endonuclease activities. ..
  17. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K. Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing. Structure. 2005;13:143-53 pubmed
    ..Hence, our findings provide a structural basis for the functional mechanisms of this helicase/nuclease family. ..
  18. Wilson R, Bohlen C, Foster M, Bell C. Structure of Pfu Pop5, an archaeal RNase P protein. Proc Natl Acad Sci U S A. 2006;103:873-8 pubmed
    ..NMR spectra have been used to map the interaction of Pop5 with Pfu Rpp30. The data presented permit tantalizing hypotheses regarding the role of this protein subunit shared by archaeal and eukaryotic RNase P. ..
  19. Roovers M, Hale C, Tricot C, Terns M, Terns R, Grosjean H, et al. Formation of the conserved pseudouridine at position 55 in archaeal tRNA. Nucleic Acids Res. 2006;34:4293-301 pubmed
    ..While we cannot unequivocally assign the function from our results, both possibilities represent unexpected functions of these proteins as discussed herein. ..
  20. Griese J, Hopfner K. Structure and DNA-binding activity of the Pyrococcus furiosus SMC protein hinge domain. Proteins. 2011;79:558-68 pubmed publisher
    ..The ssDNA-binding activity of its hinge domain might play a role in the DNA-loading process of the prokaryotic SMC complex during replication. ..
  21. Song J, Smith S, Hannon G, Joshua Tor L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science. 2004;305:1434-7 pubmed
    ..quot; The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage...
  22. Murshudov G, Vagin A, Dodson E. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr. 1997;53:240-55 pubmed publisher
    ..The results derived using the maximum-likelihood residual are consistently better than those obtained from least-squares refinement...
  23. Nishino T, Komori K, Ishino Y, Morikawa K. Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: asymmetric DNA binding and cleavage mechanisms. Structure. 2005;13:1183-92 pubmed publisher
    ..Upon binding to DNA, Hef nuclease disrupts base pairs near the cleavage site. It is most likely that this bipartite binding mode is conserved in the XPF/Rad1/Mus81 nuclease family...
  24. Tatur J, Hagedoorn P, Overeijnder M, Hagen W. A highly thermostable ferritin from the hyperthermophilic archaeal anaerobe Pyrococcus furiosus. Extremophiles. 2006;10:139-48 pubmed
    ..No apparent melting temperature was found up to 120 degrees C. The extreme thermostability of PfFtn has potential value for biotechnological applications...
  25. Rashid R, Liang B, Baker D, Youssef O, He Y, Phipps K, et al. Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. Mol Cell. 2006;21:249-60 pubmed publisher
    ..We have also identified a dyskeratosis congenita mutation cluster site within a modeled dyskerin structure...
  26. Li L, Ye K. Crystal structure of an H/ACA box ribonucleoprotein particle. Nature. 2006;443:302-7 pubmed
  27. Tsai H, Pulukkunat D, Woznick W, Gopalan V. Functional reconstitution and characterization of Pyrococcus furiosus RNase P. Proc Natl Acad Sci U S A. 2006;103:16147-52 pubmed
    ..Results from our kinetic and footprinting studies on Pfu RNase P, together with insights from recent structures of bacterial RPRs, provide a framework for appreciating the role of multiple Rpps in archaeal RNase P...
  28. Xue S, Wang R, Yang F, Terns R, Terns M, Zhang X, et al. Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Mol Cell. 2010;39:939-49 pubmed publisher
  29. Klein B, Bose D, Baker K, Yusoff Z, Zhang X, Murakami K. RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proc Natl Acad Sci U S A. 2011;108:546-50 pubmed publisher
    ..These structures reveal that the cellular RNA polymerases also use a strategy of encircling DNA to enhance its processivity as commonly observed for many nucleic acid processing enzymes including DNA polymerases and helicases...
  30. Armache J, Anger A, Marquez V, Franckenberg S, Frohlich T, Villa E, et al. Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution. Nucleic Acids Res. 2013;41:1284-93 pubmed publisher
    ..Collectively, these findings suggest insights into the evolution of eukaryotic ribosomal proteins through increased copy number and binding site promiscuity...
  31. Kyrpides N, Ouzounis C. The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus. Trends Biochem Sci. 1995;20:140-1 pubmed
  32. Riera J, Robb F, Weiss R, Fontecave M. Ribonucleotide reductase in the archaeon Pyrococcus furiosus: a critical enzyme in the evolution of DNA genomes?. Proc Natl Acad Sci U S A. 1997;94:475-8 pubmed
  33. Tahirov T, Oki H, Tsukihara T, Ogasahara K, Yutani K, Libeu C, et al. High-resolution crystals of methionine aminopeptidase from Pyrococcus furiosus obtained by water-mediated transformation. J Struct Biol. 1998;121:68-72 pubmed publisher
    ..75 A, without change or reduction of crystal mosaicity, and improvement in stability to X-ray radiation. The water-mediated transformation also appears to relieve the problem of nonisomorphism among the original MAP-Pfu crystals...
  34. Grunden A, Ghosh M, Adams M. Proline dipeptidase from Pyrococcus furiosus. Methods Enzymol. 2001;330:433-45 pubmed
  35. Story S, Shah C, Jenney F, Adams M. Characterization of a novel zinc-containing, lysine-specific aminopeptidase from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol. 2005;187:2077-83 pubmed publisher
    ..Based on its amino acid sequence, KAP is part of the M18 family of peptidases and represents the first prokaryotic member of this family. KAP is also the first lysine-specific aminopeptidase to be purified from an archaeon...
  36. Gurha P, Gupta R. Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA. RNA. 2008;14:2521-7 pubmed publisher
    ..The homology of eukaryal Pus10 with archaeal Pus10 suggests that the former may also have a tRNA Psi54 synthase activity...
  37. Hu Y, Faham S, Roy R, Adams M, Rees D. Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus: the 1.85 A resolution crystal structure and its mechanistic implications. J Mol Biol. 1999;286:899-914 pubmed publisher
    ..Similarities in the active site structures between FOR and the unrelated molybdoenzyme aldehyde oxidoreductase from Desulfovibrio gigas suggest that both enzymes utilize a common mechanism for aldehyde oxidation...
  38. Ma K, Adams M. Ferredoxin:NADP oxidoreductase from Pyrococcus furiosus. Methods Enzymol. 2001;334:40-5 pubmed
  39. Arndt J, Hao B, Ramakrishnan V, Cheng T, Chan S, Chan M. Crystal structure of a novel carboxypeptidase from the hyperthermophilic archaeon Pyrococcus furiosus. Structure. 2002;10:215-24 pubmed
    ..The roles for these conserved residues in the catalytic mechanism are inferred based on modeling and their location. ..
  40. Massant J, Verstreken P, Durbecq V, Kholti A, Legrain C, Beeckmans S, et al. Metabolic channeling of carbamoyl phosphate, a thermolabile intermediate: evidence for physical interaction between carbamate kinase-like carbamoyl-phosphate synthetase and ornithine carbamoyltransferase from the hyperthermophile Pyrococcus furiosus. J Biol Chem. 2002;277:18517-22 pubmed
    ..Therefore, by physically interacting with each other, CKase and OTCase prevent the thermodenaturation of carbamoyl phosphate in the aqueous cytoplasmic environment...
  41. Porcelli M, Moretti M, Concilio L, Forte S, Merlino A, Graziano G, et al. S-adenosylhomocysteine hydrolase from the archaeon Pyrococcus furiosus: biochemical characterization and analysis of protein structure by comparative molecular modeling. Proteins. 2005;58:815-25 pubmed publisher
    ..Interestingly, all these residues are fairly well conserved in hyperthermophilic AdoHcyHDs but not in mesophilic ones, thus suggesting a common adaptation mechanism at high temperatures...
  42. Marco Marín C, Escamilla Honrubia J, Rubio V. First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis. Biochim Biophys Acta. 2005;1747:271-5 pubmed
    ..95 angstroms), and the asymmetric unit contained two monomers, with 52% solvent content. The self-rotation function suggests that the enzyme is hexameric, which agrees with biochemical studies on bacterial UMPKs. ..
  43. Kanai A, Sato A, Imoto J, Tomita M. Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein. Biochem J. 2006;393:373-9 pubmed publisher
  44. Gandini R, Reichenbach T, Tan T, Divne C. Structural basis for dolichylphosphate mannose biosynthesis. Nat Commun. 2017;8:120 pubmed publisher
    ..Here the authors report the structure of dolichylphosphate mannose synthase in complex with bound nucleotide and donor to provide insight into the mechanism of Dol-P-Man synthesis. ..
  45. Mathur E, Adams M, Callen W, Cline J. The DNA polymerase gene from the hyperthermophilic marine archaebacterium, Pyrococcus furiosus, shows sequence homology with alpha-like DNA polymerases. Nucleic Acids Res. 1991;19:6952 pubmed
  46. Britton K, Baker P, Borges K, Engel P, Pasquo A, Rice D, et al. Insights into thermal stability from a comparison of the glutamate dehydrogenases from Pyrococcus furiosus and Thermococcus litoralis. Eur J Biochem. 1995;229:688-95 pubmed
    ..One hot spot for the accumulation of exchanges lies close to a region of the molecule involved in its conformational flexibility and these changes may modulate the dynamics of this enzyme and thereby contribute to increased stability...
  47. Ma K, Schicho R, Kelly R, Adams M. Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase: evidence for a sulfur-reducing hydrogenase ancestor. Proc Natl Acad Sci U S A. 1993;90:5341-4 pubmed
    ..It is suggested that the function of some form of ancestral hydrogenase was S0 reduction rather than, or in addition to, the reduction of protons...
  48. Villeret V, Clantin B, Tricot C, Legrain C, Roovers M, Stalon V, et al. The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures. Proc Natl Acad Sci U S A. 1998;95:2801-6 pubmed
    ..The present crystallographic analysis of PF OTCase provides a structural illustration that oligomerization can play a major role in extreme thermal stabilization...
  49. DiRuggiero J, Brown J, Bogert A, Robb F. DNA repair systems in archaea: mementos from the last universal common ancestor?. J Mol Evol. 1999;49:474-84 pubmed
  50. Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K. Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI. J Mol Biol. 2000;300:889-901 pubmed publisher
    ..For the double-strand break, the two strands in the DNA duplex were cleaved by PI-PfuI with different efficiencies. We suggest that the cleavage of each strand is catalyzed by each of the two non-equivalent active sites...
  51. Maher M, Ghosh M, Grunden A, Menon A, Adams M, Freeman H, et al. Structure of the prolidase from Pyrococcus furiosus. Biochemistry. 2004;43:2771-83 pubmed publisher
    ..The final R and R(free) values are 0.24 and 0.28, respectively...
  52. Marco Mar n C, Gil Ortiz F, Rubio V. The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis. J Mol Biol. 2005;352:438-54 pubmed publisher
  53. Wang X, Lee H, Sugar F, Jenney F, Adams M, Prestegard J. PF0610, a novel winged helix-turn-helix variant possessing a rubredoxin-like Zn ribbon motif from the hyperthermophilic archaeon, Pyrococcus furiosus. Biochemistry. 2007;46:752-61 pubmed publisher
    ..furiosus. The discovery of this novel structure represents the addition of another branch to the winged HTH protein family and could contribute to our understanding of transcription regulatory processes in P. furiosus...
  54. Carte J, Wang R, Li H, Terns R, Terns M. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 2008;22:3489-96 pubmed publisher
    ..cas6 is one of the most widely distributed CRISPR-associated genes. Our findings indicate that Cas6 functions in the generation of CRISPR-derived guide RNAs in numerous bacteria and archaea...
  55. Croyle M, Bhattacharya A, Gordon D, Maurer R. Analysis of the organization and nucleotide sequence of the chromosomal gene for the beta-subunit of rat thyrotropin. DNA. 1986;5:299-304 pubmed
    ..Southern blot analysis of total genomic DNA demonstrated that the rat genome contains sequences similar to the cloned gene, suggesting that no rearrangements occurred during the cloning process. ..
  56. Creti R, Sterpetti P, Bocchetta M, Ceccarelli E, Cammarano P. Chromosomal organization and nucleotide sequence of the fus-gene encoding elongation factor 2 (EF-2) of the hyperthermophilic archaeum Pyrococcus woesei. FEMS Microbiol Lett. 1995;126:85-90 pubmed
    ..The Pyrococcus EF-2(G) equivalent factor is somewhat closer to the eukaryal than to the bacterial homolog, and also shares with the former the C-terminal sequence required for ADP ribosylation of EF-2 by Diphtheria toxin. ..
  57. Tsunasawa S, Nakura S, Tanigawa T, Kato I. Pyrrolidone carboxyl peptidase from the hyperthermophilic Archaeon Pyrococcus furiosus: cloning and overexpression in Escherichia coli of the gene, and its application to protein sequence analysis. J Biochem. 1998;124:778-83 pubmed
    ..in abstracts of the "International Congress on Exthermophiles '98" p. 58 (1998)]. To elucidate their contribution to the hyperthermostability of these enzymes, further structural studies are required...
  58. Komori K, Miyata T, DiRuggiero J, Holley Shanks R, Hayashi I, Cann I, et al. Both RadA and RadB are involved in homologous recombination in Pyrococcus furiosus. J Biol Chem. 2000;275:33782-90 pubmed publisher
    ..These results suggest that RadB has important roles in homologous recombination in Archaea and may regulate the cleavage reactions of the branch-structured DNA...
  59. Powers S, Robinson C, Robinson A. Denaturation of an extremely stable hyperthermophilic protein occurs via a dimeric intermediate. Extremophiles. 2007;11:179-89 pubmed
    ..The extremely high stability is thus derived from a combination of oligomeric interactions and subunit folding. ..
  60. Liu W, Vierke G, Wenke A, Thomm M, Ladenstein R. Crystal structure of the archaeal heat shock regulator from Pyrococcus furiosus: a molecular chimera representing eukaryal and bacterial features. J Mol Biol. 2007;369:474-88 pubmed publisher
    ..Molecular docking and mutational analyses suggested a novel binding mode in which the major specific contacts occur at the minor groove interacting with the strongly basic wing containing a cluster of three arginine residues...
  61. Fislage M, Roovers M, Münnich S, Droogmans L, Versées W. Crystallization and preliminary X-ray crystallographic analysis of putative tRNA-modification enzymes from Pyrococcus furiosus and Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:1432-5 pubmed publisher
    ..2 Å resolution. The protein encoded by the gene ttc1157 from the eubacterium Thermus thermophilus was crystallized in the trigonal space group P3(2)21. A complete data set was collected to 2.05 Å resolution. ..
  62. Zwickl P, Fabry S, Bogedain C, Haas A, Hensel R. Glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaebacterium Pyrococcus woesei: characterization of the enzyme, cloning and sequencing of the gene, and expression in Escherichia coli. J Bacteriol. 1990;172:4329-38 pubmed
    ..The coding gene of P. woesei was expressed at a high level in Escherichia coli, thus providing an ideal basis for detailed structural and functional studies of that enzyme. ..
  63. Dong G, Vieille C, Savchenko A, Zeikus J. Cloning, sequencing, and expression of the gene encoding extracellular alpha-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl Environ Microbiol. 1997;63:3569-76 pubmed
    ..With a half-life of 13 h at 98 degrees C, the P. furiosus enzyme was significantly more thermostable than the commercially available Bacillus licheniformis alpha-amylase (Taka-therm)...
  64. Dabrowski S, Kur J. Cloning and expression in Escherichia coli of the recombinant his-tagged DNA polymerases from Pyrococcus furiosus and Pyrococcus woesei. Protein Expr Purif. 1998;14:131-8 pubmed publisher
    ..The enzymes were characterized and displayed high DNA polymerase activity and thermostability. This bacterial expression system appears to be the method of choice for production of Pfu or Pwo DNA polymerases...
  65. Furumoto H, Taguchi A, Morinaga T, Itoh T. 5S rRNA binding proteins from the hyperthermophilic archaeon, Pyrococcus furiosus. FEBS Lett. 2000;486:195-9 pubmed
    ..coli and Northwestern analysis showed the N-terminal region of PfL18, including the conserved arginine-rich region, to have a significant role in 5S rRNA-PfL18 interaction. ..
  66. Augustin M, Huber R, Kaiser J. Crystal structure of a DNA-dependent RNA polymerase (DNA primase). Nat Struct Biol. 2001;8:57-61 pubmed publisher
    ..In this first structure of a complete protein of the archaeal/eukaryotic primase family, the arrangement of the catalytically active residues resembles the active sites of various DNA polymerases that are unrelated in fold...
  67. Hopfner K, Karcher A, Craig L, Woo T, Carney J, Tainer J. Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell. 2001;105:473-85 pubmed
    ..furiosus MR reveal a dual functional complex consisting of a (Mre11)2/(Rad50)2 heterotetrameric DNA processing head and a double coiled-coil linker...
  68. Mayanagi K, Miyata T, Oyama T, Ishino Y, Morikawa K. Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus. J Struct Biol. 2001;134:35-45 pubmed publisher
    ..furiosus DNA polymerase I in vitro. The 3D reconstruction of RFCS with catalytic activity provides important insights into the organization mechanism and the functional state of the RFC complex...
  69. Griffith S, Sawaya M, Boutz D, Thapar N, Katz J, Clarke S, et al. Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate. J Mol Biol. 2001;313:1103-16 pubmed publisher
    ..Manual and computer-based docking studies on different isomers help explain how the enzyme uses steric effects to make the critical distinction between normal L-aspartyl and age-damaged L-isoaspartyl and D-aspartyl residues...
  70. Lee S, Surma M, Seitz S, Hausner W, Thomm M, Boos W. Characterization of the TrmB-like protein, PF0124, a TGM-recognizing global transcriptional regulator of the hyperthermophilic archaeon Pyrococcus furiosus. Mol Microbiol. 2007;65:305-18 pubmed publisher
    ..However, the TGM motif was not essential for TrmBL1 binding. We conclude that TrmBL1 is a global sugar-sensing transcriptional regulator controlling the genes of transport systems and of sugar-metabolizing enzymes...
  71. Akita M, Adachi A, Takemura K, Yamagami T, Matsunaga F, Ishino Y. Cdc6/Orc1 from Pyrococcus furiosus may act as the origin recognition protein and Mcm helicase recruiter. Genes Cells. 2010;15:537-52 pubmed publisher
    ..However, some other function is required for the functional loading of this helicase to start the unwinding of the replication fork DNA...
  72. Kado Y, Inoue T, Ishikawa K. Structure of hyperthermophilic ?-glucosidase from Pyrococcus furiosus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:1473-9 pubmed publisher
  73. Kim Y, Kim Y, Oh B. Crystal structure and nucleic acid-binding activity of the CRISPR-associated protein Csx1 of Pyrococcus furiosus. Proteins. 2013;81:261-70 pubmed publisher
    ..In this study, we report the crystal structure of PF1127, a Cas protein of Pyrococcus furiosus DSM 3638 that is composed of 480 amino acids and belongs to the Csx1 family...
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    ..Further mutational analysis of the two conserved (but non-Cmr2-binding) glycine-rich loops of Cmr3 identified a region that is likely involved in assembly or the RNA cleavage function of the Cmr complex...
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    ..Given that PfRecJ is associated with the GINS complex, a central nexus in archaeal DNA replication fork, we speculate that PfRecJ proofreads the RNA primer in vivo. ..
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    ..0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal. ..
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    ..Collectively, the findings indicate that invader silencing by Type III-B CRISPR-Cas systems relies both on RNA and DNA nuclease activities from the Cmr effector complex as well as on the affiliated, trans-acting Csx1 endoribonuclease. ..
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    ..The deduced amino acid sequence displayed strong homology to the alpha-amylase A of Dictyoglomus thermophilum, an obligately anaerobic, extremely thermophilic bacterium. Evolutionary implications of this homology are discussed...
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    ..The crystal packing reveals a beta-sheet interaction, which supports the suggestion that P. furiosus ferredoxin is a functional dimer. The extraordinary thermostability of P. furiosus ferredoxin is further discussed...
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    ..This L-Met binding mode is different from that observed for L-Met binding [CoCo(EcMetAP-I)]. Therefore, the catalytic mechanisms of type-I MetAPs may differ somewhat from type-II enzymes when a dinuclear metalloactive site is present. ..
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    ..At the optimum growth temperature of P. woesei (100 degrees C) and M. fervidus (83 degrees C), the 3-phosphoglycerate kinases show half-lives of inactivation of only 28 min and 44 min, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)..
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    ..Based on the presence of conserved sequence motifs and the substrate specificity of the P. furiosus fructose-1,6-bisphosphatase, we propose that this enzyme belongs to a new family, class IV fructose-1,6-bisphosphatase...
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    ..However, the interfaces between catalytic trimers in the dodecameric oligomer are mainly hydrophobic and also involve aromatic-aromatic and cation-pi interactions...
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    ..This is the first report in Archaea of an unusual polyamine APC that is proposed to play a role in stress adaptation...
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    ..Only the thermophilic tRNase Z shows in addition activity toward intron containing pre-tRNAs, 5' extended precursors, the phosphodiester bis(p-nitrophenyl)phosphate (bpNPP) and the glyoxalase II substrate S-D-lactoylglutathion (SLG)...
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