Pyrococcus horikoshii OT3

Summary

Alias: Pyrococcus OT3, Pyrococcus horikoshii OT-3, Pyrococcus horikoshii str. OT3, Pyrococcus shinkaii OT3, Pyrococcus sp. OT3

Top Publications

  1. Chon H, Matsumura H, Koga Y, Takano K, Kanaya S. Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution. Proteins. 2005;61:685-8 pubmed
  2. Naganuma T, Nomura N, Yao M, Mochizuki M, Uchiumi T, Tanaka I. Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes. J Biol Chem. 2010;285:4747-56 pubmed publisher
    ..Together with the mutational experiments we infer that the functional significance of multiple copies of P1 is in creating a factor pool within a limited space near the stalk base of the ribosome. ..
  3. Englert M, Xia S, Okada C, Nakamura A, Tanavde V, Yao M, et al. Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH. Proc Natl Acad Sci U S A. 2012;109:15235-40 pubmed
  4. Desai K, Bingman C, Phillips G, Raines R. Structures of the noncanonical RNA ligase RtcB reveal the mechanism of histidine guanylylation. Biochemistry. 2013;52:2518-25 pubmed publisher
  5. Nomura T, Nakano K, Maki Y, Naganuma T, Nakashima T, Tanaka I, et al. In vitro reconstitution of the GTPase-associated centre of the archaebacterial ribosome: the functional features observed in a hybrid form with Escherichia coli 50S subunits. Biochem J. 2006;396:565-71 pubmed
    ..The results suggest that the archaebacterial proteins, including the Ph-L12 homodimer, are functionally accessible to eukaryotic translation factors. ..
  6. Yernool D, Boudker O, Jin Y, Gouaux E. Structure of a glutamate transporter homologue from Pyrococcus horikoshii. Nature. 2004;431:811-8 pubmed
    ..We propose that transport of glutamate is achieved by movements of the hairpins that allow alternating access to either side of the membrane...
  7. Sakuraba H, Tsuge H, Yoneda K, Katunuma N, Ohshima T. Crystal structure of the NAD biosynthetic enzyme quinolinate synthase. J Biol Chem. 2005;280:26645-8 pubmed
    ..The model of the catalytic state during the first condensation step of the quinolinate synthase reaction indicates that the elimination of inorganic phosphate from dihydroxyacetone phosphate may precede the condensation reaction...
  8. Boudker O, Ryan R, Yernool D, Shimamoto K, Gouaux E. Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature. 2007;445:387-93 pubmed
  9. Yokoyama K, Ishijima S, Koike H, Kurihara C, Shimowasa A, Kabasawa M, et al. Feast/famine regulation by transcription factor FL11 for the survival of the hyperthermophilic archaeon Pyrococcus OT3. Structure. 2007;15:1542-54 pubmed publisher
    Transcriptional repressor FL11 from the hyperthermophilic archaeon, Pyrococcus OT3, was crystallized in its dimer form in complex with a DNA duplex, TGAAAWWWTTTCA...

More Information

Publications135 found, 100 shown here

  1. Yokoyama H, Matsui I. A novel thermostable membrane protease forming an operon with a stomatin homolog from the hyperthermophilic archaebacterium Pyrococcus horikoshii. J Biol Chem. 2005;280:6588-94 pubmed
    ..From this result and the probability of an operon, PH1510 probably functions in cooperation with PH1511. It is hypothesized that the cleavage of the stomatin-homolog PH1511 by the PH1510 protease causes an ion channel to open. ..
  2. Harris D, Ward D, Feasel J, Lancaster K, Murphy R, Mallet T, et al. Discovery and characterization of a Coenzyme A disulfide reductase from Pyrococcus horikoshii. Implications for this disulfide metabolism of anaerobic hyperthermophiles. FEBS J. 2005;272:1189-200 pubmed publisher
    ..P. furiosus cells were assayed for small molecular mass thiols and found to contain 0.64 micromol CoA.g dry weight(-1) (corresponding to 210 microM CoA in the cell) consistent with CoA acting as a pool of disulfide reducing equivalents...
  3. Lokanath N, Matsuura Y, Kuroishi C, Takahashi N, Kunishima N. Dimeric core structure of modular stator subunit E of archaeal H+ -ATPase. J Mol Biol. 2007;366:933-44 pubmed publisher
    ..Here we report the first crystal structure of subunit E of A-ATPase from Pyrococcus horikoshii OT3 at 1.85 A resolution. The protomer structure of subunit E represents a novel fold...
  4. Yoon J, Park C, Lee H, Suh S. Overexpression, crystallization and preliminary X-ray crystallographic analysis of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012;68:440-2 pubmed publisher
    ..30, b = 178.56, c = 109.23 Å, ? = 102.97°. The asymmetric unit contained six monomers, with a corresponding V(M) of 2.54 Å(3) Da(-1) and a solvent content of 51.5% by volume. ..
  5. Dur M, Rosenbaum E, Larabi A, Gabel F, Vellieux F, Franzetti B. The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea. Mol Microbiol. 2009;72:26-40 pubmed publisher
    ..In conclusion, PhTETs are complementary peptide destruction machines that may play an important role in the metabolism of P. horikoshii...
  6. Desai K, Cheng C, Bingman C, Phillips G, Raines R. A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation. Nucleic Acids Res. 2014;42:3931-42 pubmed publisher
    ..Substitution of the Archease metal-binding residues drastically reduced Archease-dependent activation of RtcB. Thus, evolution has sought to co-express archease and rtcB by creating a tRNA splicing operon. ..
  7. Berrisford J, Hounslow A, Akerboom J, Hagen W, Brouns S, van der Oost J, et al. Evidence supporting a cis-enediol-based mechanism for Pyrococcus furiosus phosphoglucose isomerase. J Mol Biol. 2006;358:1353-66 pubmed
  8. Lokanath N, Yamamoto H, Matsunaga E, Sugahara M, Kunishima N. Purification, crystallization and initial X-ray crystallographic analysis of the putative GTPase PH0525 from Pyrococcus horikoshii OT3. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:892-4 pubmed
    ..The putative GTPase PH0525 from Pyrococcus horikoshii OT3 has been overexpressed in Escherichia coli and purified...
  9. Terada A, Honda T, Fukuhara H, Hada K, Kimura M. Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3. J Biochem. 2006;140:293-8 pubmed publisher
    ..five proteins (PhoPop5, PhoRpp38, PhoRpp21, PhoRpp29, and PhoRpp30) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 reconstituted RNase P activity that exhibits enzymatic properties like those of the authentic enzyme...
  10. Manjunath K, Kanaujia S, Kanagaraj S, Jeyakanthan J, Sekar K. Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: insights into thermal stability. Int J Biol Macromol. 2013;53:7-19 pubmed publisher
    ..synthetase (SAICAR synthetase) from a hyperthermophilic organism Pyrococcus horikoshii OT3 was determined in two space groups H3 (Type-1: Resolution 2.35Å) and in C222(1) (Type-2: Resolution 1...
  11. Liu B, Ni J, Shen Y. [Cloning, expression and biochemical characterization of a novel diacetylchitobiose deacetylase from the hyperthermophilic archaeon Pyrococcus horikoshii]. Wei Sheng Wu Xue Bao. 2006;46:255-8 pubmed
    ..By reaction together with Exo-beta-D-Glucosaminidase in P. horikoshii, Dacph probably plays a key role in the new chitin degradation pathway in hyperthermophilic archaea (the genera Thermococcus and Pyrococcus). ..
  12. Goda S, Sakuraba H, Kawarabayasi Y, Ohshima T. The first archaeal agmatinase from anaerobic hyperthermophilic archaeon Pyrococcus horikoshii: cloning, expression, and characterization. Biochim Biophys Acta. 2005;1748:110-5 pubmed
    ..Phylogenic analysis revealed that the agmatinase from P. horikoshii does not belong to any clusters of enzymes found in bacteria and eukarya. This is the first description of the presence of archaeal agmatinase and its characteristics. ..
  13. Lokanath N, Kunishima N. Purification, crystallization and preliminary X-ray crystallographic analysis of the archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:788-90 pubmed
    ..The archaeal phosphoglycerate mutase PH0037 from Pyrococcus horikoshii OT3 has been overexpressed in Escherichia coli and purified...
  14. Sakai N, Yao M, Itou H, Watanabe N, Yumoto F, Tanokura M, et al. The three-dimensional structure of septum site-determining protein MinD from Pyrococcus horikoshii OT3 in complex with Mg-ADP. Structure. 2001;9:817-26 pubmed
    ..The three-dimensional structure of the MinD-2 from Pyrococcus horikoshii OT3 (PH0612) has been determined at 2.3 A resolution by X-ray crystallography using the Se-Met MAD method...
  15. Gao Y, Yao M, Yong Z, Tanaka I. Crystal structure of the putative RNA methyltransferase PH1948 from Pyrococcus horikoshii, in complex with the copurified S-adenosyl-L-homocysteine. Proteins. 2005;61:1141-5 pubmed publisher
  16. Jeyakanthan J, Rangarajan S, Mridula P, Kanaujia S, Shiro Y, Kuramitsu S, et al. Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii. Acta Crystallogr D Biol Crystallogr. 2008;64:1012-9 pubmed publisher
    ..pi interactions to fulfill its functions. This study may shed light on the catalytic mechanism of the enzyme and throw open new questions on the mechanism of product removal in carbonic anhydrases. ..
  17. Yokoyama H, Fujii S, Matsui I. Crystal structure of a core domain of stomatin from Pyrococcus horikoshii Illustrates a novel trimeric and coiled-coil fold. J Mol Biol. 2008;376:868-78 pubmed publisher
    ..According to chemical cross-linking experiments, PhSto(CD) would be able to assemble into an oligomeric form. The coiled-coil fold observed in the crystal probably contributes to self-association...
  18. Tanimoto K, Higashi N, Nishioka M, Ishikawa K, Taya M. Characterization of thermostable aminoacylase from hyperthermophilic archaeon Pyrococcus horikoshii. FEBS J. 2008;275:1140-9 pubmed publisher
    ..Other residues, His198 and Arg260, were also found to be involved in the catalytic reaction, suggesting that PhoACY obeys a similar reaction mechanism to that proposed for mammalian aminoacylases. ..
  19. Schoehn G, Vellieux F, Asunci n Dur M, Receveur Br chot V, Fabry C, Ruigrok R, et al. An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron. J Biol Chem. 2006;281:36327-37 pubmed publisher
    ..PhTET1 assembles into two different quaternary structures because of quasi-equivalent contacts that previously have only been identified in viral capsids...
  20. Kim H, Ishikawa K. Structure of hyperthermophilic endocellulase from Pyrococcus horikoshii. Proteins. 2010;78:496-500 pubmed publisher
  21. Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O. Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc Natl Acad Sci U S A. 2009;106:15616-21 pubmed publisher
    ..Our findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the "acp" group, and not the methyl group, from AdoMet to the nucleobase...
  22. Sugahara M, Murai S, Sugahara M, Kunishima N. Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007;63:56-8 pubmed
    The putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3 has been overexpressed and purified...
  23. Goto Ito S, Ishii R, Ito T, Shibata R, Fusatomi E, Sekine S, et al. Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis. Acta Crystallogr D Biol Crystallogr. 2007;63:1059-68 pubmed publisher
    ..On the basis of the surface properties, a docking model of P. horikoshii TYW1, the tRNA, the FeS clusters and the AdoMet molecule was constructed, with the nucleoside at position 37 of tRNA flipped out from the canonical tRNA structure...
  24. Yamada K, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, et al. Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids. Acta Crystallogr D Struct Biol. 2017;73:757-766 pubmed publisher
    ..a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP)...
  25. Sokabe M, Okada A, Yao M, Nakashima T, Tanaka I. Molecular basis of alanine discrimination in editing site. Proc Natl Acad Sci U S A. 2005;102:11669-74 pubmed publisher
    ..These observations strongly suggested conservation of the chemical discrimination among trans- and cis-editing of tRNA(Ala)...
  26. DeDecker B, O Brien R, Fleming P, Geiger J, Jackson S, Sigler P. The crystal structure of a hyperthermophilic archaeal TATA-box binding protein. J Mol Biol. 1996;264:1072-84 pubmed publisher
    ..The total reliance on a hydrophobic interface with DNA may explain the enhanced affinity of PwTBP for its DNA promoter at higher temperatures and increased salt concentration...
  27. Hosaka H, Yao M, Kimura M, Tanaka I. The structure of the archaebacterial ribosomal protein S7 and its possible interaction with 16S rRNA. J Biochem. 2001;130:695-701 pubmed
    ..Some of the inserted chains might pass through gaps formed by helices of the 16S rRNA. ..
  28. Matsui E, Musti K, Abe J, Yamasaki K, Matsui I, Harata K. Molecular structure and novel DNA binding sites located in loops of flap endonuclease-1 from Pyrococcus horikoshii. J Biol Chem. 2002;277:37840-7 pubmed
    ..For the exo-activity, all four sites were needed, but Arg(118)-Lys(119) was dominant. The major binding sites for both the nick substrate and double-stranded DNA might be the same. ..
  29. Miyazono K, Sawano Y, Tanokura M. Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3. Proteins. 2005;61:196-205 pubmed
    To elucidate the structural basis for the high stability of acylphosphatase (AcP) from Pyrococcus horikoshii OT3, we determined its crystal structure at 1.72 A resolution. P...
  30. Menyhárd D, Kiss Szemán A, Tichy Rács É, Hornung B, Rádi K, Szeltner Z, et al. A self-compartmentalizing hexamer serine protease from Pyrococcus horikoshii: substrate selection achieved through multimerization. J Biol Chem. 2013;288:17884-94 pubmed publisher
    ..We propose that self-assembly within the family results in characteristically different substrate selection mechanisms coupled to different multimerization states. ..
  31. Bouyoub A, Barbier G, Forterre P, Labedan B. The adenylosuccinate synthetase from the hyperthermophilic archaeon Pyrococcus species displays unusual structural features. J Mol Biol. 1996;261:144-54 pubmed
    ..Reconstruction of phylogenetic trees showed that the archaeal gene is equally distantly related to both eukaryotes and bacteria, independently of the numerous substitutions observed at critical positions. ..
  32. Yokoyama H, Hamamatsu S, Fujii S, Matsui I. Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin. J Synchrotron Radiat. 2008;15:254-7 pubmed publisher
    ..The L2 loop, which is disordered in the wild-type structure, is significantly kinked at around A-138 in the K138A mutant. Thus Lys138 probably has an important role on the conformation of L2. ..
  33. Kitao T, Kuroishi C, Tahirov T. Crystallization and preliminary crystallographic analysis of the nickel-responsive regulator NikR from Pyrococcus horikoshii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:43-5 pubmed
    The nickel-responsive repressor from Pyrococcus horikoshii OT3 (PhNikR) has been crystallized in the apo form (PhNikR-apo) and two nickel-bound forms (PhNikR-Ni-1 and PhNikR-Ni-2)...
  34. Sindhikara D, Roitberg A, Merz K. Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations. Biochemistry. 2009;48:12024-33 pubmed publisher
    ..Mutation of key regions of P. horikoshii and analogous regions in both E. coli and H. pylori are suggested that might inhibit DNA-binding activity while not affecting nickel-binding...
  35. Yokoyama H, Kobayashi D, Takizawa N, Fujii S, Matsui I. Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease. J Synchrotron Radiat. 2013;20:933-7 pubmed publisher
    ..The N-terminal half of the peptide binds to 1510-N more tightly than the C-terminal half of the peptide. The flexible L2 loops of 1510-N cover the peptide, and are involved in the protease activity. ..
  36. Du X, Wang W, Kim R, Yakota H, Nguyen H, Kim S. Crystal structure and mechanism of catalysis of a pyrazinamidase from Pyrococcus horikoshii. Biochemistry. 2001;40:14166-72 pubmed
    ..Because of extensive homology between PH999 and PZAase of M. tuberculosis (37% sequence identity), the structure of PH999 provides a structural basis for understanding PZA-resistance by M. tuberculosis harboring PZAase mutations...
  37. Li T, Ji X, Sun F, Gao R, Cao S, Feng Y, et al. Crystallization and preliminary X-ray analysis of recombinant histone HPhA from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Acta Crystallogr D Biol Crystallogr. 2002;58:870-1 pubmed
    Recombinant archaeal histone from the hyperthermophile Pyrococcus horikoshii OT3 (HPhA) was crystallized by the hanging-drop vapour-diffusion method. Crystals grew at 291 K in 200 mM (NH(4))(2)SO(4), 100 mM sodium acetate buffer pH 4...
  38. Dabrowski S, Kiaer Ahring B. Cloning, expression, and purification of the His6-tagged hyper-thermostable dUTPase from Pyrococcus woesei in Escherichia coli: application in PCR. Protein Expr Purif. 2003;31:72-8 pubmed
    ..We observed that the thermostable His(6)-tagged Pwo dUTPase used for the polymerase chain reaction with P. woesei DNA polymerase improves the efficiency of PCR and it allows for amplification of longer targets...
  39. Yao M, Yasutake Y, Morita H, Tanaka I. Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution. Acta Crystallogr D Biol Crystallogr. 2005;61:294-301 pubmed
    ..The flexible loop of the type II enzyme is considered to serve as a mobile gate to the active site. Therefore, the loop stabilization observed in the PhA structure may cause limitation of the access of the substrate to the active site. ..
  40. Ohtaki A, Nakano Y, Iizuka R, Arakawa T, Yamada K, Odaka M, et al. Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism. Proteins. 2008;70:1167-74 pubmed
    b>Pyrococcus horikoshii OT3 aspartate racemase (PhAspR) catalyzes the interconversion between L- and D-aspartate...
  41. Sugahara M, Asada Y, Morikawa Y, Kageyama Y, Kunishima N. Nucleant-mediated protein crystallization with the application of microporous synthetic zeolites. Acta Crystallogr D Biol Crystallogr. 2008;64:686-95 pubmed publisher
    ..The hetero-epitaxic growth of the zeolite-mediated crystals was confirmed by a crystal-packing analysis which revealed a layer-like structure in the crystal lattice...
  42. Ito K, Honda T, Suzuki T, Miyoshi T, Murakami R, Yao M, et al. Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1α. Nucleic Acids Res. 2014;42:14042-52 pubmed publisher
    ..Furthermore, phylogenetic perspectives and functional analyses suggested that the eukaryotic stalk protein also interacts directly with domains 1 and 3 of eEF1α, in a manner similar to the interaction of archaeal aP1 with aEF1α. ..
  43. Du X, Choi I, Kim R, Wang W, Jancarik J, Yokota H, et al. Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-A resolution. Proc Natl Acad Sci U S A. 2000;97:14079-84 pubmed publisher
    ..In the crystal, PH1704 forms a hexameric ring structure, and the active sites are formed at the interfaces between three pairs of monomers...
  44. Ura H, Harata K, Matsui I, Kuramitsu S. Temperature dependence of the enzyme-substrate recognition mechanism. J Biochem. 2001;129:173-8 pubmed
    ..This rule seems to be applicable to many other enzymes already reported. ..
  45. Koike H, Ishijima S, Clowney L, Suzuki M. The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription. Proc Natl Acad Sci U S A. 2004;101:2840-5 pubmed publisher
    ..These considerations lead us to propose a possible mechanism for regulating a number of genes by varying assembly forms and by combining different FFRPs into these assemblies, responding to environmental changes...
  46. Shen Y, Tang X, Matsui E, Matsui I. Subunit interaction and regulation of activity through terminal domains of the family D DNA polymerase from Pyrococcus horikoshii. Biochem Soc Trans. 2004;32:245-9 pubmed
    ..horikoshii probably forms a heterotetrameric structure in solution. Based on these results, a model regarding the subunit interaction and regulation of activity of PolDPho is proposed...
  47. Ishijima J, Uchida Y, Kuroishi C, Tuzuki C, Takahashi N, Okazaki N, et al. Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution. Proteins. 2006;62:1133-7 pubmed publisher
  48. Okada U, Sakai N, Yao M, Watanabe N, Tanaka I. Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3. Proteins. 2006;63:1084-6 pubmed
  49. Kita A, Tasaki S, Yohda M, Miki K. Crystal structure of PH1733, an aspartate racemase homologue, from Pyrococcus horikoshii OT3. Proteins. 2009;74:240-4 pubmed publisher
  50. Ishikawa K, Matsui I, Payan F, Cambillau C, Ishida H, Kawarabayasi Y, et al. A hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii characterization and three-dimensional structure. Structure. 2002;10:877-86 pubmed
    ..The 3D structures and the characterization of different mutants indicate a direct or indirect catalytic role for the residues E107, D85, and K98. ..
  51. Li T, Sun F, Ji X, Feng Y, Rao Z. Structure based hyperthermostability of archaeal histone HPhA from Pyrococcus horikoshii. J Mol Biol. 2003;325:1031-7 pubmed
    ..We also observe a unique network of tyrosine residues located at the crossover point of the two HPhA monomers, which locks them together and stabilizes the dimer. These factors together account for the increased thermal stability...
  52. Ito N, Nureki O, Shirouzu M, Yokoyama S, Hanaoka F. Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Genes Cells. 2003;8:913-23 pubmed
    ..Based on the complex structure, we constructed a model between the DNA primase and a primer/template DNA for the primer synthesis. This model facilitates the comprehension of the reported features of DNA primase...
  53. Kashima Y, Mori K, Fukada H, Ishikawa K. Analysis of the function of a hyperthermophilic endoglucanase from Pyrococcus horikoshii that hydrolyzes crystalline cellulose. Extremophiles. 2005;9:37-43 pubmed
    ..furiosus was added to the C-terminal region. ..
  54. Fukunaga R, Yokoyama S. Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii. Acta Crystallogr D Biol Crystallogr. 2004;60:1916-8 pubmed
    ..7%. A data set diffracting to 2.2 A resolution was collected from a single crystal at 100 K. Selenomethionine-substituted protein crystals were prepared in order to solve the structure by the SAD phasing method. ..
  55. Takagi H, Kakuta Y, Okada T, Yao M, Tanaka I, Kimura M. Crystal structure of archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects. Nat Struct Mol Biol. 2005;12:327-31 pubmed publisher
    ..The hyperthermophilic archaeon Pyrococcus horikoshii OT3 has the archaeal homologs aRelE and aRelB...
  56. Inagaki E, Sakamoto K, Obayashi N, Terada T, Shirouzu M, Bessho Y, et al. Expression, purification, crystallization and preliminary X-ray diffraction analysis of galactokinase from Pyrococcus horikoshii. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:169-71 pubmed
    ..57 A, beta = 109.8 degrees. The ternary complex form was isomorphous with the apo form, except for the length of the a axis. The galactokinase activity of the enzyme was confirmed and the kinetic parameters at 323 K were determined. ..
  57. Kurimoto E, Nishi Y, Yamaguchi Y, Zako T, Iizuka R, Ide N, et al. Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy. Proteins. 2008;70:1257-63 pubmed
    ..1 mda. ..
  58. Rowlands T, Baumann P, Jackson S. The TATA-binding protein: a general transcription factor in eukaryotes and archaebacteria. Science. 1994;264:1326-9 pubmed
    ..This suggests that TBP's role in transcription was established before the archaebacterial and eukaryotic lineages diverged and that the transcription systems of archaebacteria and eukaryotes are fundamentally homologous...
  59. Kim H, Kashima Y, Ishikawa K, Yamano N. Purification and characterization of the first archaeal glutamate decarboxylase from Pyrococcus horikoshii. Biosci Biotechnol Biochem. 2009;73:224-7 pubmed
    ..Its biochemical properties were different from those reported for other GADs. The enzyme had broad substrate specificity, and its optimum pH and temperature were pH 8.0 and > 97 degrees C. ..
  60. Zhang Y, Zhu X, Torelli A, Lee M, Dzikovski B, Koralewski R, et al. Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme. Nature. 2010;465:891-6 pubmed publisher
    ..Our results suggest that P. horikoshii Dph2 represents a previously unknown, SAM-dependent, [4Fe-4S]-containing enzyme that catalyses unprecedented chemistry...
  61. Kang H, Kubota K, Miyazono K, Tanokura M. Expression, purification, crystallization and preliminary X-ray analysis of the KaiC-like protein PH0187 from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:144-6 pubmed publisher
    ..8) and diffracted X-rays to 2.75?Å resolution. The crystal of PH0187 belonged to space group P6(3)22, with unit-cell parameters a=b=239.1, c=106.5?Å. The crystal contained four PH0187 molecules in the asymmetric unit. ..
  62. Kim H, Ishikawa K. Functional analysis of hyperthermophilic endocellulase from Pyrococcus horikoshii by crystallographic snapshots. Biochem J. 2011;437:223-30 pubmed publisher
  63. Creti R, Citarella F, Tiboni O, Sanangelantoni A, Palm P, Cammarano P. Nucleotide sequence of a DNA region comprising the gene for elongation factor 1 alpha (EF-1 alpha) from the ultrathermophilic archaeote Pyrococcus woesei: phylogenetic implications. J Mol Evol. 1991;33:332-42 pubmed
    ..A closer relation of Pyrococcus to Euryarchaeota than to Crenarchaeota was also inferred from sequence analysis of S10 ribosomal proteins. ..
  64. Creti R, Londei P, Cammarano P. Complete nucleotide sequence of an archaeal (Pyrococcus woesei) gene encoding a homolog of eukaryotic transcription factor IIB (TFIIB). Nucleic Acids Res. 1993;21:2942 pubmed
  65. Franzetti B, Schoehn G, Hernandez J, Jaquinod M, Ruigrok R, Zaccai G. Tetrahedral aminopeptidase: a novel large protease complex from archaea. EMBO J. 2002;21:2132-8 pubmed publisher
    ..This architecture is different from that of all the proteolytic complexes described to date that are made up by rings or barrels with a single central channel and only two openings...
  66. Kakuta Y, Tahara M, Maetani S, Yao M, Tanaka I, Kimura M. Crystal structure of the regulatory subunit of archaeal initiation factor 2B (aIF2B) from hyperthermophilic archaeon Pyrococcus horikoshii OT3: a proposed structure of the regulatory subcomplex of eukaryotic IF2B. Biochem Biophys Res Commun. 2004;319:725-32 pubmed
    ..structure of an archaeal regulatory subunit (aIF2Balpha) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 determined by X-ray crystallography at 2.2A resolution...
  67. Numata T, Ishimatsu I, Kakuta Y, Tanaka I, Kimura M. Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29. RNA. 2004;10:1423-32 pubmed publisher
    ..structure of an archaeal RNase P protein, Ph1771p (residues 36-127) from hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by X-ray crystallography...
  68. Liu B, Hong Y, Wu L, Li Z, Ni J, Sheng D, et al. A unique highly thermostable 2-phosphoglycerate forming glycerate kinase from the hyperthermophilic archaeon Pyrococcus horikoshii: gene cloning, expression and characterization. Extremophiles. 2007;11:733-9 pubmed
    ..The enzyme was highly thermostable with almost no loss of activity at 90 degrees C for 12 h. Based on sequence alignment and structural comparison it was assigned to group I of the trichotomy of GKs. ..
  69. Gao Y, Yao M, Tanaka I. Structure of protein PH0536 from Pyrococcus horikoshii at 1.7 A resolution reveals a novel assembly of an oligonucleotide/oligosaccharide-binding fold and an alpha-helical bundle. Proteins. 2008;71:503-8 pubmed publisher
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    ..It is possible that these open reading frames are the products of gene duplication and that they are the early forms of an electron transfer domain in archaea which may have later contributed to many electron transfer enzymes. ..
  71. Soriano E, Zhang Y, Colabroy K, Sanders J, Settembre E, Dorrestein P, et al. Active-site models for complexes of quinolinate synthase with substrates and intermediates. Acta Crystallogr D Biol Crystallogr. 2013;69:1685-96 pubmed publisher
    ..2005), J. Biol. Chem. 280, 26645-26648]. The domain arrangement in P. furiosus QS may be related to protection of cysteine side chains, which are required to chelate the [4Fe-4S] cluster, prior to cluster assembly. ..
  72. Okada K, Angkawidjaja C, Koga Y, Takano K, Kanaya S. Characteristic features of kynurenine aminotransferase allosterically regulated by (alpha)-ketoglutarate in cooperation with kynurenine. PLoS ONE. 2012;7:e40307 pubmed publisher
    Kynurenine aminotransferase from Pyrococcus horikoshii OT3 (PhKAT), which is a homodimeric protein, catalyzes the conversion of kynurenine (KYN) to kynurenic acid (KYNA)...
  73. Empadinhas N, Marugg J, Borges N, Santos H, da Costa M. Pathway for the synthesis of mannosylglycerate in the hyperthermophilic archaeon Pyrococcus horikoshii. Biochemical and genetic characterization of key enzymes. J Biol Chem. 2001;276:43580-8 pubmed publisher
    ..2 and 6.4. This is the first report of the characterization of MPG synthase and MPG phosphatase and the elucidation of a pathway for the synthesis of mannosylglycerate in an archaeon...
  74. Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, S ll D, et al. Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat Struct Biol. 2002;9:257-62 pubmed publisher
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    ..determined the three-dimensional structure of aspartate racemase from the hyperthermophilic archaeum Pyrococcus horikoshii OT3 at 1.9 A resolution by X-ray crystallography and refined it to a crystallographic R factor of 19...
  76. Sokabe M, Kawamura T, Sakai N, Yao M, Watanabe N, Tanaka I. The X-ray crystal structure of pyrrolidone-carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii. J Struct Funct Genomics. 2002;2:145-54 pubmed
    ..The result suggests that the thermostability of PhoPCP may be obtained by the accumulation of many weak factors...
  77. Tajika Y, Sakai N, Tanaka Y, Yao M, Watanabe N, Tanaka I. Crystal structure of conserved protein PH1136 from Pyrococcus horikoshii. Proteins. 2004;55:210-3 pubmed publisher
  78. Cheung Y, Allen M, Bycroft M, Wong K. Crystallization and preliminary crystallographic analysis of an acylphosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii. Acta Crystallogr D Biol Crystallogr. 2004;60:1308-10 pubmed publisher
    ..9 A Da(-1) and a solvent content of 68.6%. A data set diffracting to 1.6 A resolution was collected from a single crystal at 100 K...
  79. Akiba T, Nishio M, Matsui I, Harata K. X-ray structure of a membrane-bound beta-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii. Proteins. 2004;57:422-31 pubmed publisher
    ..The enzyme could thus adhere to the membrane in the proximity of its glycolipid substrate...
  80. Cheung Y, Lam S, Chu W, Allen M, Bycroft M, Wong K. Crystal structure of a hyperthermophilic archaeal acylphosphatase from Pyrococcus horikoshii--structural insights into enzymatic catalysis, thermostability, and dimerization. Biochemistry. 2005;44:4601-11 pubmed publisher
    ..New insights into catalysis were gained by docking acetyl phosphate to the active site of PhAcP...
  81. Okada C, Maegawa Y, Yao M, Tanaka I. Crystal structure of an RtcB homolog protein (PH1602-extein protein) from Pyrococcus horikoshii reveals a novel fold. Proteins. 2006;63:1119-22 pubmed publisher
  82. Yokoyama H, Matsui E, Akiba T, Harata K, Matsui I. Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii. J Mol Biol. 2006;358:1152-64 pubmed publisher
    ..These findings suggest that the binding of the substrate to the catalytic site of 1510-N induces conformational changes in a region that includes loop L2 so that Lys138 approaches the catalytic Ser97...
  83. Ito N, Matsui I, Matsui E. Molecular basis for the subunit assembly of the primase from an archaeon Pyrococcus horikoshii. FEBS J. 2007;274:1340-51 pubmed publisher
    ..These findings and a structural comparison with a previously reported PriL(NTD)-PriS complex suggest that the presented alternative conformations of the twisted-strand domain facilitate the heterodimer assembly...
  84. Kuratani M, Bessho Y, Nishimoto M, Grosjean H, Yokoyama S. Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA. J Mol Biol. 2008;375:1064-75 pubmed publisher
    ..However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate...
  85. Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N. Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate. J Biol Chem. 2008;283:14739-50 pubmed publisher
    ..The existence of formation and product stages before and after the reaction stage would be favorable to ensure both the reaction efficiency and the extreme substrate specificity of the biotinylation reaction...
  86. Sokabe M, Ose T, Nakamura A, Tokunaga K, Nureki O, Yao M, et al. The structure of alanyl-tRNA synthetase with editing domain. Proc Natl Acad Sci U S A. 2009;106:11028-33 pubmed publisher
    ..As Asn-194 in eubacterial AlaRS important for Ser misactivation is replaced by Thr-213 in archaeal AlaRS, a different Ser accommodation mechanism is proposed...
  87. Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, et al. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat Chem Biol. 2010;6:277-82 pubmed publisher
    ..Although agm(2)C is chemically similar to lysidine, TiaS constitutes a distinct class of enzyme from tRNA(Ile)-lysidine synthetase (TilS), suggesting that the decoding systems evolved convergently across domains...
  88. Sandman K, Perler F, Reeve J. Histone-encoding genes from Pyrococcus: evidence for members of the HMf family of archaeal histones in a non-methanogenic Archaeon. Gene. 1994;150:207-8 pubmed
    ..60% identical to the histones HMf and HMt, characterized from methanogenic Archaea. These archaeal histones also contain the amino-acid sequences, conserved in eukaryotic H4 histones, that are thought to interact directly with DNA...
  89. Bobik T, Rasche M. Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome. J Biol Chem. 2001;276:37194-8 pubmed publisher
    ..Importantly, such analyses are rapid and may be generally applicable for the identification of human genes that lack homologues of known function or that have been misidentified on the basis of sequence similarity searches...
  90. Tsuge H, Sakuraba H, Kobe T, Kujime A, Katunuma N, Ohshima T. Crystal structure of the ADP-dependent glucokinase from Pyrococcus horikoshii at 2.0-A resolution: a large conformational change in ADP-dependent glucokinase. Protein Sci. 2002;11:2456-63 pubmed publisher
    ..The ADP-binding loop (430-439) was disordered in the apo form. It is suggested that a large conformational change takes place during the enzymatic reaction...
  91. Kouzuma Y, Mizoguchi M, Takagi H, Fukuhara H, Tsukamoto M, Numata T, et al. Reconstitution of archaeal ribonuclease P from RNA and four protein components. Biochem Biophys Res Commun. 2003;306:666-73 pubmed
    ..A homology search of the hyperthermophilic archaeon Pyrococcus horikoshii OT3 genome database revealed that the four genes, PH1481, PH1601, PH1771, and PH1877, have a significant ..
  92. Umetsu M, Tsumoto K, Ashish K, Nitta S, Tanaka Y, Adschiri T, et al. Structural characteristics and refolding of in vivo aggregated hyperthermophilic archaeon proteins. FEBS Lett. 2004;557:49-56 pubmed
    ..to provide the secondary structural characteristics of the proteins from hyperthermophilic archaeon Pyrococcus horikoshii OT3 (hyperthermophilic proteins) in inclusion bodies...