Thermococcus kodakarensis KOD1

Summary

Alias: Pyrococcus sp. (strain KOD1), Pyrococcus sp. KOD1, Thermococcus kodakaraensis KOD1, Thermococcus kodakarensis str. KOD1, Thermococcus kodakarensis strain KOD1

Top Publications

  1. Rashid N, Morikawa M, Imanaka T. A RecA/RAD51 homologue from a hyperthermophilic archaeon retains the major RecA domain only. Mol Gen Genet. 1996;253:397-400 pubmed
    ..Recombinant Pk-REC was fully active and complemented the ultraviolet light sensitivity of an E. coli recA mutant strain. ..
  2. Yan Z, Fujiwara S, Kohda K, Takagi M, Imanaka T. In vitro stabilization and in vivo solubilization of foreign proteins by the beta subunit of a chaperonin from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1. Appl Environ Microbiol. 1997;63:785-9 pubmed
    ..These results suggest that the beta subunit plays a major role in chaperonin activity and is functional without the alpha subunit...
  3. Adul Rahman R, Jongsareejit B, Fujiwara S, Imanaka T. Characterization of recombinant glutamine synthetase from the hyperthermophilic archaeon Pyrococcus sp. strain KOD1. Appl Environ Microbiol. 1997;63:2472-6 pubmed
    ..8 for the synthetase reaction and pH 7.2 for the transferase reaction). Of the various nucleoside triphosphates tested, GTP as well as ATP was involved in the synthetase reaction...
  4. Takagi M, Nishioka M, Kakihara H, Kitabayashi M, Inoue H, Kawakami B, et al. Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Appl Environ Microbiol. 1997;63:4504-10 pubmed
    ..These characteristics enabled the KOD DNA polymerase to perform a more accurate PCR in a shorter reaction time...
  5. Higashibata H, Fujiwara S, Takagi M, Imanaka T. Analysis of DNA compaction profile and intracellular contents of archaeal histones from Pyrococcus kodakaraensis KOD1. Biochem Biophys Res Commun. 1999;258:416-24 pubmed
    ..These results suggest that HpkB plays a major role to protect double stranded DNA from thermal denaturation in vivo...
  6. Fukui T, Eguchi T, Atomi H, Imanaka T. A membrane-bound archaeal Lon protease displays ATP-independent proteolytic activity towards unfolded proteins and ATP-dependent activity for folded proteins. J Bacteriol. 2002;184:3689-98 pubmed
    ..Lon from Thermococcus kodakaraensis KOD1 (Lon(Tk)) is a 70-kDa protein with an N-terminal ATPase domain belonging to the AAA(+) superfamily ..
  7. Chemnitz Galal W, Pan M, Kelman Z, Hurwitz J. Characterization of DNA primase complex isolated from the archaeon, Thermococcus kodakaraensis. J Biol Chem. 2012;287:16209-19 pubmed publisher
    ..Supplementation of such reactions with the DNA primase complex supported lagging strand formation as well...
  8. Kuba Y, Ishino S, Yamagami T, Tokuhara M, Kanai T, Fujikane R, et al. Comparative analyses of the two proliferating cell nuclear antigens from the hyperthermophilic archaeon, Thermococcus kodakarensis. Genes Cells. 2012;17:923-37 pubmed publisher
    ..The sensitivities of the ?pcna2 mutant strain to ultraviolet irradiation (UV), methyl methanesulfonate (MMS) and mitomycin C (MMC) were indistinguishable from those of the wild-type strain. ..
  9. Alsina C, Faijes M, Planas A. Glycosynthase-type GH18 mutant chitinases at the assisting catalytic residue for polymerization of chitooligosaccharides. Carbohydr Res. 2019;478:1-9 pubmed publisher
    ..From the selected enzymes, the Thermococcus kodakaraensis ChiA D1022A mutant gave the best results, with the formation of insoluble polymers in 45% yield (w/w) and containing about 55% of the target DP10 product. ..

More Information

Publications146 found, 100 shown here

  1. Oyama T, Ishino S, Fujino S, Ogino H, Shirai T, Mayanagi K, et al. Architectures of archaeal GINS complexes, essential DNA replication initiation factors. BMC Biol. 2011;9:28 pubmed publisher
  2. Louvel H, Kanai T, Atomi H, Reeve J. The Fur iron regulator-like protein is cryptic in the hyperthermophilic archaeon Thermococcus kodakaraensis. FEMS Microbiol Lett. 2009;295:117-28 pubmed
    ..kodakaraensis diphtheria toxin regulator (DtxR) homolog may control the expression of the major iron acquisition effectors, while its inactivation enabled higher resistance to iron deficiency. ..
  3. Pham B, Jia B, Lee S, Ying S, Kwak J, Cheong G. Chaperone-Like Activity of a Bacterioferritin Comigratory Protein from Thermococcus kodakaraensis KOD1. Protein Pept Lett. 2015;22:443-8 pubmed
    ..Prx subfamily member, and specifically a bacterioferritin comigratory protein from hyperthermophilic Thermococcus kodakaraensis KOD1 (TkBcp), was overexpressed, purified and characterized...
  4. Gorlas A, Marguet E, Gill S, Geslin C, Guigner J, Guyot F, et al. Sulfur vesicles from Thermococcales: A possible role in sulfur detoxifying mechanisms. Biochimie. 2015;118:356-64 pubmed publisher
    ..kodakaraensis produces less sulfur vesicles than T. prieurii, T. nautili does not produce such sulfur vesicles, suggesting that Thermococcales species exhibit significant differences in their sulfur metabolic pathways. ..
  5. Huber C, von Watzdorf J, Marx A. 5-methylcytosine-sensitive variants of Thermococcus kodakaraensis DNA polymerase. Nucleic Acids Res. 2016;44:9881-9890 pubmed
    ..Employing these findings in combination with a nucleotide, which is fluorescently labeled at the terminal phosphate, indicates the potential use of the mutant DNA polymerase in the detection of 5mC. ..
  6. Yamashita M, Xu J, Morokuma D, Hirata K, Hino M, Mon H, et al. Characterization of Recombinant Thermococcus kodakaraensis (KOD) DNA Polymerases Produced Using Silkworm-Baculovirus Expression Vector System. Mol Biotechnol. 2017;59:221-233 pubmed publisher
    ..Taken together, our results suggested that silkworm-BEVS can be used to express and purify efficient rKOD in a commercial way. ..
  7. Singh R, Feller A, Roovers M, Van Elder D, Wauters L, Droogmans L, et al. Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism. RNA. 2018;: pubmed publisher
  8. Klenk H, Schwass V, Lottspeich F, Zillig W. Nucleotide sequence of the genes encoding the three largest subunits of the DNA-dependent RNA polymerase from the archaeum Thermococcus celer. Nucleic Acids Res. 1992;20:4659 pubmed
  9. Foophow T, Tanaka S, Angkawidjaja C, Koga Y, Takano K, Kanaya S. Crystal structure of a subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis: requirement of a C-terminal beta-jelly roll domain for hyperstability. J Mol Biol. 2010;400:865-77 pubmed publisher
    ..We propose that attachment of a beta-jelly roll domain to the C-terminus is one of the strategies of the proteins from hyperthermophiles to adapt to high-temperature environment...
  10. Mao H, White S, Williamson J. A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex. Nat Struct Biol. 1999;6:1139-47 pubmed publisher
  11. Iida T, Furutani M, Nishida F, Maruyama T. FKBP-type peptidyl-prolyl cis-trans isomerase from a sulfur-dependent hyperthermophilic archaeon, Thermococcus sp. KS-1. Gene. 1998;222:249-55 pubmed
    ..Catalytic efficiency of this recombinant PPIase was 1.2-times higher with the substrate N-succinyl-A-L-P-F-p-nitroanilide than with N-succinyl-A-A-P-F-p-nitroanilide. ..
  12. Mao H, Williamson J. Local folding coupled to RNA binding in the yeast ribosomal protein L30. J Mol Biol. 1999;292:345-59 pubmed
    ..The exposed hydrophobic surface that is buried upon RNA binding may provide the energy necessary to drive secondary structure formation, and may account for the increased stability of b L30. ..
  13. Kwon S, Nishitani Y, Watanabe S, Hirao Y, Imanaka T, Kanai T, et al. Crystal structure of a [NiFe] hydrogenase maturation protease HybD from Thermococcus kodakarensis KOD1. Proteins. 2016;84:1321-7 pubmed publisher
    A [NiFe] hydrogenase maturation protease HybD from Thermococcus kodakarensis KOD1 (TkHybD) is involved in the cleavage of the C-terminal residues of [NiFe] hydrogenase large subunits by Ni recognition...
  14. Muroya A, Tsuchiya D, Ishikawa M, Haruki M, Morikawa M, Kanaya S, et al. Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses. Protein Sci. 2001;10:707-14 pubmed publisher
    ..The crystal structure of the Type 2 RNase H from Thermococcus kodakaraensis KOD1 has revealed that the N-terminal major domain adopts the RNase H fold, despite the poor sequence ..
  15. Kanai T, Ito S, Imanaka T. Characterization of a cytosolic NiFe-hydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol. 2003;185:1705-11 pubmed
    ..an NiFe-hydrogenase exclusively localized in the cytoplasm of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (T. kodakaraensis hydrogenase). A gene cluster encoding T...
  16. Kishimoto A, Kita A, Ishibashi T, Tomita H, Yokooji Y, Imanaka T, et al. Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis. Proteins. 2014;82:1924-36 pubmed publisher
    ..Based on these structures, we discuss the catalytic mechanism by which PPS produces phosphopantoyl adenylate, which is thought to be a reaction intermediate. ..
  17. Aono R, Sato T, Yano A, Yoshida S, Nishitani Y, Miki K, et al. Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J Bacteriol. 2012;194:6847-55 pubmed publisher
    ..The results strongly suggest that these enzymes are actually involved in the conversion of nucleoside monophosphates to 3-phosphoglycerate in T. kodakarensis. ..
  18. Rahman R, Fujiwara S, Takagi M, Imanaka T. Sequence analysis of glutamate dehydrogenase (GDH) from the hyperthermophilic archaeon Pyrococcus sp. KOD1 and comparison of the enzymatic characteristics of native and recombinant GDHs. Mol Gen Genet. 1998;257:338-47 pubmed
    ..Kinetic studies suggested that the reaction is biased towards glutamate production. KOD1-GDH utilized both coenzymes NADH and NADPH, as do most eukaryal GDHs...
  19. Kitabayashi M, Nishiya Y, Esaka M, Itakura M, Imanaka T. Gene cloning and function analysis of replication factor C from Thermococcus kodakaraensis KOD1. Biosci Biotechnol Biochem. 2003;67:2373-80 pubmed
    ..The RFC-like genes, arranged in tandem in the Thermococcus kodakaraensis KOD1 genome, were cloned individually and co-expressed in Escherichia coli cells. T...
  20. Lee H, Kim Y, Bae S, Jeon J, Lim J, Kang S, et al. Overexpression and characterization of a carboxypeptidase from the hyperthermophilic archaeon Thermococcus sp. NA1. Biosci Biotechnol Biochem. 2006;70:1140-7 pubmed
    ..This broad specificity was confirmed by C-terminal ladder sequencing of porcine N-acetyl-renin substrate by TNA1_CP. ..
  21. Ishino S, Nishi Y, Oda S, Uemori T, Sagara T, Takatsu N, et al. Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea. Nucleic Acids Res. 2016;44:2977-86 pubmed publisher
    ..The discovery of this endonuclease suggests the existence of a novel mismatch repair process, initiated by the double-strand break generated by the EndoMS endonuclease, in Archaea and some Bacteria. ..
  22. Rashid N, Imanaka H, Fukui T, Atomi H, Imanaka T. Presence of a novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase reveals a metabolic link between pentoses and central carbon metabolism in the hyperthermophilic archaeon Thermococcus kodakaraensis. J Bacteriol. 2004;186:4185-91 pubmed publisher
    ..this study, we have examined the presence of this metabolic link in the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. A search of the genome sequence of this strain revealed the presence of a closely related orthologue ..
  23. Briegel A, Oikonomou C, Chang Y, Kjær A, Huang A, Kim K, et al. Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis. EMBO Rep. 2017;18:1660-1670 pubmed publisher
    ..In addition to anchoring the lophotrichous bundle of archaella, the conical frustum associates with chemosensory arrays and ribosome-excluding material and may function as a polar organizing center for the coccoid cells. ..
  24. Watanabe S, Kawashima T, Nishitani Y, Kanai T, Wada T, Inaba K, et al. Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer. Proc Natl Acad Sci U S A. 2015;112:7701-6 pubmed publisher
  25. Greenough L, Kelman Z, Gardner A. The roles of family B and D DNA polymerases in Thermococcus species 9°N Okazaki fragment maturation. J Biol Chem. 2015;290:12514-22 pubmed publisher
    ..The similarities to both bacterial and eukaryotic systems and evolutionary implications of archaeal Okazaki fragment maturation are discussed. ..
  26. Fujiwara S, Yamanaka A, Hirooka K, Kobayashi A, Imanaka T, Fukusaki E. Temperature-dependent modulation of farnesyl diphosphate/geranylgeranyl diphosphate synthase from hyperthermophilic archaea. Biochem Biophys Res Commun. 2004;325:1066-74 pubmed
    ..Mutation study indicated that the aromatic side chain of Tyr-81 acts as a steric hindrance to terminate the chain elongation and defines the final product length. ..
  27. Castrec B, Laurent S, Henneke G, Flament D, Raffin J. The glycine-rich motif of Pyrococcus abyssi DNA polymerase D is critical for protein stability. J Mol Biol. 2010;396:840-8 pubmed publisher
    ..These studies suggest that the (G)-PYF box motif mediates intersubunit interactions and that it may be crucial for the thermostability of PabPol D...
  28. Nisar M, Rashid N, Bashir Q, Gardner Q, Shafiq M, Akhtar M. TK1299, a highly thermostable NAD(P)H oxidase from Thermococcus kodakaraensis exhibiting higher enzymatic activity with NADPH. J Biosci Bioeng. 2013;116:39-44 pubmed publisher
    ..To our knowledge this is the most thermostable and unique NAD(P)H oxidase displaying higher enzyme activity with NADPH. ..
  29. Perveen S, Rashid N, Tang X, Imanaka T, Papageorgiou A. Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure. FEBS Open Bio. 2017;7:1217-1230 pubmed publisher
    ..Based on the TkTrpD-Zn2+ structure, it is suggested that the formation of a new dimer may be responsible for the higher enzyme activity of TkTrpD in the presence of Zn2+ ions. ..
  30. Iida T, Kanai S, Inatomi K, Kamagata Y, Maruyama T. Alpha- and beta-subunits of a V-type membrane ATPase in a hyperthermophilic sulfur-dependent archaeum, Thermococcus sp. KI. Biochim Biophys Acta. 1997;1329:12-7 pubmed
    ..coli F-type ATPase, respectively. Phylogenetic analysis revealed that Thermococcus ATPase was closely related to that of Thermus, and those of Methanosarcina and Halobacterium. ..
  31. Fukushima E, Shinka Y, Fukui T, Atomi H, Imanaka T. Methionine sulfoxide reductase from the hyperthermophilic archaeon Thermococcus kodakaraensis, an enzyme designed to function at suboptimal growth temperatures. J Bacteriol. 2007;189:7134-44 pubmed
    ..kodakaraensis is exceptional among the hyperthermophiles, the enzyme may represent a novel strategy for this organism to deal with low-temperature environments in which the dissolved oxygen concentrations increase. ..
  32. Okada K, Hidese R, Fukuda W, Niitsu M, Takao K, Horai Y, et al. Identification of a novel aminopropyltransferase involved in the synthesis of branched-chain polyamines in hyperthermophiles. J Bacteriol. 2014;196:1866-76 pubmed publisher
    ..These findings indicate that BpsA is a novel aminopropyltransferase essential for the synthesis of branched-chain polyamines, enabling thermophiles to grow in high-temperature environments. ..
  33. Auer J, Spicker G, Bock A. Nucleotide sequence of the gene for elongation factor EF-1 alpha from the extreme thermophilic archaebacterium Thermococcus celer. Nucleic Acids Res. 1990;18:3989 pubmed
  34. Koga Y, Katsumi R, You D, Matsumura H, Takano K, Kanaya S. Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form. FEBS J. 2008;275:2632-43 pubmed publisher
    ..These results suggest that the ion pairs in the alpha16 helix contribute to the stabilization of Tk-GK in a cooperative manner. ..
  35. Nagahisa K, Ezaki S, Fujiwara S, Imanaka T, Takagi M. Sequence and transcriptional studies of five clustered flagellin genes from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. FEMS Microbiol Lett. 1999;178:183-90 pubmed
    ..kodakaraensis KOD1 revealed that four major transcripts (0.98, 3.7, 5.4 and 9.2 kb) initiating from immediately upstream of flaB1 encode different combinations of five flagellins...
  36. Shomura Y, Yoshida T, Maruyama T, Yohda M, Miki K. Crystallization and preliminary X-ray characterization of archaeal group II chaperonin alpha-subunit from Thermococcus strain KS-1. Acta Crystallogr D Biol Crystallogr. 2002;58:1830-2 pubmed
    ..8, c = 182.4 A. This form only diffracts X-rays to 6 A resolution. Diffraction data collected from the former crystal enabled initial successful phases to be obtained by the molecular-replacement method. ..
  37. Sato T, Atomi H, Imanaka T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science. 2007;315:1003-6 pubmed publisher
    ..Archaea with type III RuBisCOs all harbor both DeoA and the corresponding E2b2 homologs. In this pathway, adenine was released from AMP and the phosphoribose moiety entered central-carbon metabolism...
  38. Akahane S, Kamata H, Yagisawa H, Hirata H. A novel neutral amino acid transporter from the hyperthermophilic archaeon Thermococcus sp. KS-1. J Biochem. 2003;133:173-80 pubmed
    ..To our knowledge, this is the first report on the cloning of a gene of an amino acid transporter from a hyperthermophilic archaeon...
  39. Rohman M, Koga Y, Takano K, Chon H, Crouch R, Kanaya S. Effect of the disease-causing mutations identified in human ribonuclease (RNase) H2 on the activities and stabilities of yeast RNase H2 and archaeal RNase HII. FEBS J. 2008;275:4836-49 pubmed publisher
    ..These results indicate that Gly10 is required to make the protein fully active and stable...
  40. Chohan S, Rashid N. TK1656, a thermostable l-asparaginase from Thermococcus kodakaraensis, exhibiting highest ever reported enzyme activity. J Biosci Bioeng. 2013;116:438-43 pubmed publisher
  41. Nishitani Y, Aono R, Nakamura A, Sato T, Atomi H, Imanaka T, et al. Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. J Mol Biol. 2013;425:2709-21 pubmed publisher
    ..Our findings unveil a unique archaeal nucleotide phosphorylase that is distinct in both function and structure from previously known members of the nucleoside phosphorylase II family. ..
  42. Suematsu K, Ueda T, Nakashima T, Kakuta Y, Kimura M. On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis. Biosci Biotechnol Biochem. 2015;79:952-9 pubmed publisher
    ..This finding demonstrates that RNase P proteins in T. kodakarensis and P. horikoshii are interchangeable and that their three-dimensional structures are highly conserved. ..
  43. Imanaka H, Yamadzumi D, Yanagita K, Ishida N, Nakanishi K, Imamura K. The use of a proteinaceous "cushion" with a polystyrene-binding peptide tag to control the orientation and function of a target peptide adsorbed to a hydrophilic polystyrene surface. Biotechnol Prog. 2016;32:527-34 pubmed publisher
    ..Accordingly, the use of a proteinaceous cushion appears to be promising for the immobilization of functional biomolecules on a solid surface. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:527-534, 2016. ..
  44. Hashimoto H, Inoue T, Nishioka M, Fujiwara S, Takagi M, Imanaka T, et al. Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase. J Mol Biol. 1999;292:707-16 pubmed publisher
    ..Furthermore, structural features of helix cappings, intra and inter-helix ion-pairs are found around the active-site structure in Pk-MGMT...
  45. Maeda N, Kitano K, Fukui T, Ezaki S, Atomi H, Miki K, et al. Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure. J Mol Biol. 1999;293:57-66 pubmed publisher
    ..This is the first report of a decameric assembly of Rubisco, which is thought to belong to neither type I nor type II Rubiscos...
  46. Ronimus R, de Heus E, Morgan H. Sequencing, expression, characterisation and phylogeny of the ADP-dependent phosphofructokinase from the hyperthermophilic, euryarchaeal Thermococcus zilligii. Biochim Biophys Acta. 2001;1517:384-91 pubmed
    ..coli ATP-PFK (E.C. 2.7.1.11) and its associated ATP- and pyrophosphate-dependent PFKs (EC.2.7.1.90), the PFKB family (E. coli PFK 2 encoded by the pfkB gene and its homologues) and the ADP-PFKs of the Euryarchaeota reported here. ..
  47. Jeon S, Fujiwara S, Takagi M, Tanaka T, Imanaka T. Tk-PTP, protein tyrosine/serine phosphatase from hyperthermophilic archaeon Thermococcus kodakaraensis KOD1: enzymatic characteristics and identification of its substrate proteins. Biochem Biophys Res Commun. 2002;295:508-14 pubmed
    The Tk-ptp gene encoding a protein tyrosine phosphatase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 was cloned and biochemical characteristics of the recombinant protein (Tk-PTP) were examined...
  48. Arai T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K. Crystallization and preliminary X-ray crystallographic study of [NiFe]-hydrogenase maturation factor HypE from Thermococcus kodakaraensis KOD1. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007;63:765-7 pubmed
    ..Here, the crystallization and preliminary crystallographic analysis of HypE from Thermococcus kodakaraensis KOD1 are reported. Crystals of HypE (338 amino acids, 35...
  49. Qian X, Jeon C, Yoon H, Agarwal K, Weiss M. Structure of a new nucleic-acid-binding motif in eukaryotic transcriptional elongation factor TFIIS. Nature. 1993;365:277-9 pubmed publisher
    ..This new structure, designated the Zn ribbon, extends the repertoire of Zn-mediated peptide architectures and highlights the growing recognition of the beta-sheet as a motif of nucleic-acid recognition...
  50. Izumi M, Fujiwara S, Takagi M, Kanaya S, Imanaka T. Isolation and characterization of a second subunit of molecular chaperonin from Pyrococcus kodakaraensis KOD1: analysis of an ATPase-deficient mutant enzyme. Appl Environ Microbiol. 1999;65:1801-5 pubmed
    ..These results implied that both CpkA and CpkB could assist protein folding for nascent protein in E. coli without requiring energy from ATP hydrolysis...
  51. Rashid N, Cornista J, Ezaki S, Fukui T, Atomi H, Imanaka T. Characterization of an archaeal cyclodextrin glucanotransferase with a novel C-terminal domain. J Bacteriol. 2002;184:777-84 pubmed
    A gene encoding a cyclodextrin glucanotransferase (CGTase) from Thermococcus kodakaraensis KOD1 (CGT(Tk)) was identified and characterized...
  52. Tumbula Hansen D, Feng L, Toogood H, Stetter K, S ll D. Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms. J Biol Chem. 2002;277:37184-90 pubmed publisher
    ..The high sequence identity, up to 60% between discriminating and nondiscriminating archaeal AspRSs, suggests that few mutational steps may be necessary to convert the tRNA-discriminating ability of a tRNA synthetase...
  53. Hirata A, Kanai T, Santangelo T, Tajiri M, Manabe K, Reeve J, et al. Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive. Mol Microbiol. 2008;70:623-33 pubmed publisher
  54. Bashir Q, Rashid N, Jamil F, Imanaka T, Akhtar M. Highly thermostable L-threonine dehydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis. J Biochem. 2009;146:95-102 pubmed publisher
    ..This is the most thermostable threonine dehydrogenase exhibiting optimal activity at the highest pH (12) reported to date. This is the first report on the characterization of a TDH from genus Thermococcus...
  55. Han T, Zeng F, Li Z, Liu L, Wei M, Guan Q, et al. Biochemical characterization of a recombinant pullulanase from Thermococcus kodakarensis KOD1. Lett Appl Microbiol. 2013;57:336-43 pubmed publisher
    ..hydrolase 13 family pullulanase gene (Tk0977) was cloned from a thermophilic anaerobic archaeon Thermococcus kodakarensis KOD1 (Pul-Tk). Pul-Tk encodes a protein of 765 amino acids including a putative 22-residue signal peptide...
  56. Tominaga T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K. Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation. Proc Natl Acad Sci U S A. 2013;110:20485-90 pubmed publisher
    ..These observations suggest that the dehydration of thiocarboxamide into thiocyanate is catalyzed by a two-step deprotonation process, in which Lys134 and Glu272 function as the first and second bases, respectively...
  57. Perveen S, Rashid N, Papageorgiou A. Crystal structure of a phosphoribosyl anthranilate isomerase from the hyperthermophilic archaeon Thermococcus kodakaraensis. Acta Crystallogr F Struct Biol Commun. 2016;72:804-812 pubmed
    ..Potential factors for the thermostability of TkTrpF were attributed to an increase in helical structure, an increased number of charged residues and an increase in the number of salt bridges. ..
  58. Nishioka M, Fujiwara S, Takagi M, Imanaka T. Characterization of two intein homing endonucleases encoded in the DNA polymerase gene of Pyrococcus kodakaraensis strain KOD1. Nucleic Acids Res. 1998;26:4409-12 pubmed
    ..kodakaraensis KOD1 was used as substrate. Therefore, it is suggested that these endonucleases are switching endonucleases whose function lies in the rearrangement of chromosomal DNA...
  59. Haruki M, Hayashi K, Kochi T, Muroya A, Koga Y, Morikawa M, et al. Gene cloning and characterization of recombinant RNase HII from a hyperthermophilic archaeon. J Bacteriol. 1998;180:6207-14 pubmed
    ..In addition, these enzymes cleave oligomeric substrates in a similar manner. These results suggest that RNase HIIPk and E. coli RNases HI and HII are structurally and functionally related to one another...
  60. Ezaki S, Maeda N, Kishimoto T, Atomi H, Imanaka T. Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1. J Biol Chem. 1999;274:5078-82 pubmed
    ..kodakaraensis KOD1. Furthermore, Western blot analysis with cell-free extract of P. kodakaraensis KOD1 clearly indicated the presence of Pk-Rubisco in the native host cells...
  61. Hashimoto H, Nishioka M, Inoue T, Fujiwara S, Takagi M, Imanaka T, et al. Crystallization and preliminary X-ray crystallographic analysis of archaeal O6-methylguanine-DNA methyltransferase. Acta Crystallogr D Biol Crystallogr. 1998;54:1395-6 pubmed
    ..3 A3 Da-1 and a solvent content of 48% by volume. A full set of X-ray diffraction data was collected to 2.0 A Bragg spacings from the native crystal...
  62. Chen Y, Bycroft M, Wong K. Crystal structure of ribosomal protein L30e from the extreme thermophile Thermococcus celer: thermal stability and RNA binding. Biochemistry. 2003;42:2857-65 pubmed publisher
    ..By comparing it with the yeast homologue, we also identified the residues that are responsible for RNA binding and built a model to illustrate how L30e binds to an RNA kink turn motif...
  63. Yamamoto T, Matsuda T, Inoue T, Matsumura H, Morikawa M, Kanaya S, et al. Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA. Protein Sci. 2006;15:152-61 pubmed publisher
  64. Rodrigues M, Borges N, Henriques M, Lamosa P, Ventura R, Fernandes C, et al. Bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper)thermophiles. J Bacteriol. 2007;189:5405-12 pubmed publisher
    ..The use of the designation di-myo-inositol-1,3'-phosphate is recommended to facilitate tracing individual carbon atoms through metabolic pathways...
  65. Mukaiyama A, Koga Y, Takano K, Kanaya S. Osmolyte effect on the stability and folding of a hyperthermophilic protein. Proteins. 2008;71:110-8 pubmed publisher
    ..Our results also imply that the basic protein folding principle is not dependent on protein stability and evolution...
  66. Kobori H, Ogino M, Orita I, Nakamura S, Imanaka T, Fukui T. Characterization of NADH oxidase/NADPH polysulfide oxidoreductase and its unexpected participation in oxygen sensitivity in an anaerobic hyperthermophilic archaeon. J Bacteriol. 2010;192:5192-202 pubmed publisher
    ..kodakarensis in the absence of sulfur...
  67. Guldan H, Matysik F, Bocola M, Sterner R, Babinger P. Functional assignment of an enzyme that catalyzes the synthesis of an archaea-type ether lipid in bacteria. Angew Chem Int Ed Engl. 2011;50:8188-91 pubmed publisher
    ..The product becomes dephosphorylated and acetylated in vivo...
  68. Matsuda T, Morikawa M, Haruki M, Higashibata H, Imanaka T, Kanaya S. Isolation of TBP-interacting protein (TIP) from a hyperthermophilic archaeon that inhibits the binding of TBP to TATA-DNA. FEBS Lett. 1999;457:38-42 pubmed
    ..24-1.46 microM. A gel mobility shift assay indicated that Pk-TIP inhibited the interaction between Pk-TBP and a TATA-DNA. Pk-TIP may be one of the archaeal factors which negatively regulate transcription...
  69. Jeon S, Fujiwara S, Takagi M, Imanaka T. Pk-cdcA encodes a CDC48/VCP homolog in the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1: transcriptional and enzymatic characterization. Mol Gen Genet. 1999;262:559-67 pubmed
    ..Equal levels of Pk-CdcA expression were observed during exponential and stationary phases. Growth phase-specific fragmentation of Pk-CdcA was found in stationary-phase cells...
  70. Kannan Y, Koga Y, Inoue Y, Haruki M, Takagi M, Imanaka T, et al. Active subtilisin-like protease from a hyperthermophilic archaeon in a form with a putative prosequence. Appl Environ Microbiol. 2001;67:2445-52 pubmed publisher
    ..kodakaraensis subtilisin was cloned from a hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. T...
  71. Maeda N, Kanai T, Atomi H, Imanaka T. The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability. J Biol Chem. 2002;277:31656-62 pubmed publisher
    ..ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) from the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. Here we have carried out biochemical studies to identify the necessities and/or advantages of this ..
  72. Feng L, Tumbula Hansen D, Toogood H, Soll D. Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. Proc Natl Acad Sci U S A. 2003;100:5676-81 pubmed publisher
    ..kodakaraensis AspRS with the anticodon nucleotide C36 of tRNA(Asp). Thus, a switch between D-AspRS and ND-AspRS enzymes could have evolved with only limited amino acid changes...
  73. Shiraki K, Tsuji M, Hashimoto Y, Fujimoto K, Fujiwara S, Takagi M, et al. Genetic, enzymatic, and structural analyses of phenylalanyl-tRNA synthetase from Thermococcus kodakaraensis KOD1. J Biochem. 2003;134:567-74 pubmed
    Phenylalanyl-tRNA synthetase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-PheRS) was cloned...
  74. Sato T, Imanaka H, Rashid N, Fukui T, Atomi H, Imanaka T. Genetic evidence identifying the true gluconeogenic fructose-1,6-bisphosphatase in Thermococcus kodakaraensis and other hyperthermophiles. J Bacteriol. 2004;186:5799-807 pubmed publisher
    ..and IMPase activities and a structurally novel FBPase (FbpTk) from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 have been proposed as the "missing" FBPase. For this study, using T...
  75. Fukuda W, Ismail Y, Fukui T, Atomi H, Imanaka T. Characterization of an archaeal malic enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Archaea. 2005;1:293-301 pubmed
    ..homolog of malic enzyme identified in the genome of a heterotrophic, hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-Mae)...
  76. Pulido M, Tanaka S, Sringiew C, You D, Matsumura H, Koga Y, et al. Requirement of left-handed glycine residue for high stability of the Tk-subtilisin propeptide as revealed by mutational and crystallographic analyses. J Mol Biol. 2007;374:1359-73 pubmed publisher
    ..Stabilization of this fold leads to strong binding of Tk-propeptide to Tk-subtilisin, high resistance of Tk-propeptide to proteolytic degradation, and slow maturation of Pro-Tk-subtilisin...
  77. Kanai T, Takedomi S, Fujiwara S, Atomi H, Imanaka T. Identification of the Phr-dependent heat shock regulon in the hyperthermophilic archaeon, Thermococcus kodakaraensis. J Biochem. 2010;147:361-70 pubmed publisher
    ..kodakaraensis...
  78. Maruyama H, Shin M, Oda T, Matsumi R, Ohniwa R, Itoh T, et al. Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis. Mol Biol Cell. 2011;22:386-98 pubmed publisher
    ..These results show that the archaeal chromosome is organized into heterogeneous structures and that TK0471/TrmBL2 acts as a general chromosomal protein as well as a global transcriptional repressor...
  79. Fujikane R, Ishino S, Ishino Y, Forterre P. Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis. Genes Genet Syst. 2010;85:243-57 pubmed
  80. Awano T, Wilming A, Tomita H, Yokooji Y, Fukui T, Imanaka T, et al. Characterization of two members among the five ADP-forming acyl coenzyme A (Acyl-CoA) synthetases reveals the presence of a 2-(Imidazol-4-yl)acetyl-CoA synthetase in Thermococcus kodakarensis. J Bacteriol. 2014;196:140-7 pubmed publisher
    ..The results presented here, together with those of previous studies, have clarified the substrate specificities of all five known NDP-forming acyl-CoA synthetase proteins in the Thermococcales...
  81. Kaine B, Mehr I, Woese C. The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription. Proc Natl Acad Sci U S A. 1994;91:3854-6 pubmed
    ..6). Homology is also seen with the eukaryotic transcription factor TFIIS, but it involves only the terminal 45 amino acids of the archaeal proteins. Evolutionary implications of these homologies are discussed...
  82. Charron C, Roy H, Blaise M, Gieg R, Kern D. Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. EMBO J. 2003;22:1632-43 pubmed publisher
    ..Its particular status is demonstrated by a loop-exchange experiment that renders the Pyrococcus AspRS non-discriminating...
  83. Kempenaers M, Roovers M, Oudjama Y, Tkaczuk K, Bujnicki J, Droogmans L. New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. Nucleic Acids Res. 2010;38:6533-43 pubmed publisher
    ..This is to our knowledge the first example of a tRNA methyltransferase with a broadened nucleoside recognition capability. The evolution of tRNA methyltransferases methylating the N(1) atom of a purine residue is discussed...
  84. Klenk H, Schwass V, Zillig W. Nucleotide sequence of the genes encoding the L30, S12 and S7 equivalent ribosomal proteins from the archaeum Thermococcus celer. Nucleic Acids Res. 1991;19:6047 pubmed
  85. Siddiqui M, Fujiwara S, Imanaka T. Indolepyruvate ferredoxin oxidoreductase from Pyrococcus sp. KOD1 possesses a mosaic structure showing features of various oxidoreductases. Mol Gen Genet. 1997;254:433-9 pubmed
    ..The optimal temperature for activity of recombinant IOR was 70 degrees C and the half-life of this enzyme in the presence of air was 15 min at 25 degrees C. ..
  86. Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry J, Moras D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 1998;17:5227-37 pubmed publisher
    ..An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaeal and eukaryotic AspRSs, but absent from the eubacterial enzymes...
  87. Henneke G, Raffin J, Ferrari E, Jónsson Z, Dietrich J, Hubscher U. The PCNA from Thermococcus fumicolans functionally interacts with DNA polymerase delta. Biochem Biophys Res Commun. 2000;276:600-6 pubmed
    ..Our data suggest that PCNA has been functionally conserved not only within eukaryotes but also from hyperthermophilic euryarchaeotes to mammals. ..
  88. Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, et al. Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. J Mol Biol. 2001;306:469-77 pubmed publisher
    ..The stabilization of the melted DNA structure at the forked-point may be correlated with the high PCR performance of KOD DNA polymerase, which is due to low error rate, high elongation rate and processivity...
  89. Wong K, Lee C, Chan S, Leung T, Chen Y, Bycroft M. Solution structure and thermal stability of ribosomal protein L30e from hyperthermophilic archaeon Thermococcus celer. Protein Sci. 2003;12:1483-95 pubmed publisher
    ..2 degrees C at 0.5 M NaCl. This salt-dependency of melting temperatures strongly suggests that electrostatic interactions contribute to the thermostability of T. celer L30e...
  90. Atomi H, Matsumi R, Imanaka T. Reverse gyrase is not a prerequisite for hyperthermophilic life. J Bacteriol. 2004;186:4829-33 pubmed publisher
    We disrupted the reverse gyrase gene from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. An apparent positive supercoiling activity that was observed in the host strain was not found in the disruptant strain...
  91. Siddiqui M, Yamanaka A, Hirooka K, Bamaba T, Kobayashi A, Imanaka T, et al. Enzymatic and structural characterization of type II isopentenyl diphosphate isomerase from hyperthermophilic archaeon Thermococcus kodakaraensis. Biochem Biophys Res Commun. 2005;331:1127-36 pubmed publisher
    ..This speculation was supported by the result of the circular dichroism analysis that showed the shift of the alpha-helical content occurred at 80 degrees C...
  92. Imanaka H, Yamatsu A, Fukui T, Atomi H, Imanaka T. Phosphoenolpyruvate synthase plays an essential role for glycolysis in the modified Embden-Meyerhof pathway in Thermococcus kodakarensis. Mol Microbiol. 2006;61:898-909 pubmed publisher
    ..kodakarensis. The physiological roles of the two enzymes under various growth conditions are discussed...