Pyrococcus abyssi GE5

Summary

Alias: Pyrococcus abyssi Orsay, Pyrococcus abyssi str. GE5, Pyrococcus abyssi str. Orsay, Pyrococcus abyssi strain GE5

Top Publications

  1. Charron C, Manival X, Charpentier B, Branlant C, Aubry A. Purification, crystallization and preliminary X-ray diffraction data of L7Ae sRNP core protein from Pyrococcus abyssii. Acta Crystallogr D Biol Crystallogr. 2004;60:122-4 pubmed
    ..7, b = 112.9, c = 34.8 A. There are two monomers of MW 14 200 Da per asymmetric unit and the packing density V(M) is 2.45 A(3) Da(-1). A molecular-replacement analysis gave solutions for the rotation and translation functions. ..
  2. Perrochia L, Crozat E, Hecker A, Zhang W, Bareille J, Collinet B, et al. In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res. 2013;41:1953-64 pubmed publisher
    ..These findings shed light on the reaction mechanism of t(6)A synthesis and evolution of molecular systems that promote translation fidelity in present-day cells...
  3. Cortez D, Quevillon Cheruel S, Gribaldo S, Desnoues N, Sezonov G, Forterre P, et al. Evidence for a Xer/dif system for chromosome resolution in archaea. PLoS Genet. 2010;6:e1001166 pubmed publisher
    ..Whereas Archaea and Bacteria use a completely different set of proteins for chromosome replication, our data strongly suggest that XerA is most likely used for chromosome resolution in Archaea...
  4. Urbonavicius J, Auxilien S, Walbott H, Trachana K, Golinelli Pimpaneau B, Brochier Armanet C, et al. Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer. Mol Microbiol. 2008;67:323-35 pubmed
    ..This functional shift probably occurred in an ancestor of all Thermococcales. This study also provides new evidence in favour of a close relationship between Thermococcales and Nanoarchaea...
  5. Roovers M, Wouters J, Bujnicki J, Tricot C, Stalon V, Grosjean H, et al. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 2004;32:465-76 pubmed
    ..The origin and evolution of m(1)A MTases is discussed in the context of different hypotheses of the tree of life...
  6. Hecker A, Leulliot N, Gadelle D, Graille M, Justome A, Dorlet P, et al. An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro. Nucleic Acids Res. 2007;35:6042-51 pubmed
    ..Kae1 is thus a novel and atypical universal DNA interacting protein whose importance could rival those of RecA (RadA/Rad51) in the maintenance of genome integrity in all living cells...
  7. Auxilien S, El Khadali F, Rasmussen A, Douthwaite S, Grosjean H. Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase. J Biol Chem. 2007;282:18711-21 pubmed
    ..This P. abyssi system possibly reflects the general function of archeases in preventing protein aggregation and modulating the function of their accompanying proteins...
  8. Ferri Fioni M, Fromant M, Bouin A, Aubard C, Lazennec C, Plateau P, et al. Identification in archaea of a novel D-Tyr-tRNATyr deacylase. J Biol Chem. 2006;281:27575-85 pubmed publisher
    ..Taken together, these observations suggest evolutionary links between the various hydrolases in charge of the recycling of metabolically inactive tRNAs during translation...
  9. 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...

More Information

Publications93

  1. DiRuggiero J, Robb F, Jagus R, Klump H, Borges K, Kessel M, et al. Characterization, cloning, and in vitro expression of the extremely thermostable glutamate dehydrogenase from the hyperthermophilic Archaeon, ES4. J Biol Chem. 1993;268:17767-74 pubmed
    ..difficile, and other Archaea. The gdhA gene of ES4 was expressed in vitro in a rabbit reticulocyte cell-free lysate, thus providing a system for structural studies of the mechanisms of thermostability in hyper-thermophilic proteins. ..
  2. Dwivedi S, Kruparani S, Sankaranarayanan R. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria. Acta Crystallogr D Biol Crystallogr. 2004;60:1662-4 pubmed
    ..The crystals belong to the trigonal space group P3(1(2))21, with one molecule in the asymmetric unit. ..
  3. Henneke G, Gueguen Y, Flament D, Azam P, Querellou J, Dietrich J, et al. Replication factor C from the hyperthermophilic archaeon Pyrococcus abyssi does not need ATP hydrolysis for clamp-loading and contains a functionally conserved RFC PCNA-binding domain. J Mol Biol. 2002;323:795-810 pubmed
    ..In addition, ATP hydrolysis was not required either for DNA polymerase stimulation or PCNA-loading in vitro. ..
  4. Hussain T, Kruparani S, Pal B, Dock Bregeon A, Dwivedi S, Shekar M, et al. Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea. EMBO J. 2006;25:4152-62 pubmed publisher
  5. 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. ..
  6. Purcarea C, Herve G, Cunin R, Evans D. Cloning, expression, and structure analysis of carbamate kinase-like carbamoyl phosphate synthetase from Pyrococcus abyssi. Extremophiles. 2001;5:229-39 pubmed
    ..In contrast, P. abyssi CPSase has intrinsic bicarbonate-dependent ATPase activity, suggesting that the enzyme can catalyze the phosphorylation of the isosteric substrates carbamate and bicarbonate. ..
  7. Kohlhoff M, Dahm A, Hensel R. Tetrameric triosephosphate isomerase from hyperthermophilic Archaea. FEBS Lett. 1996;383:245-50 pubmed
  8. 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. ..
  9. Urbonavicius J, Rutkienė R, Lopato A, Tauraite D, Stankeviciute J, Aučynaitė A, et al. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. RNA. 2016;22:1871-1883 pubmed
    ..We thus suggest renaming such aTrm5a methyltransferases as Taw21 to distinguish between monofunctional and bifunctional aTrm5a enzymes. ..
  10. Matsunaga F, Glatigny A, Mucchielli Giorgi M, Agier N, Delacroix H, Marisa L, et al. Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp. Nucleic Acids Res. 2007;35:3214-22 pubmed publisher
    ..Our ChIP-chip analysis also revealed that Mcm alters the binding specificity to the oriC region according to the growth phase, consistent with its role as a licensing factor...
  11. Creti R, Ceccarelli E, Bocchetta M, Sanangelantoni A, Tiboni O, Palm P, et al. Evolution of translational elongation factor (EF) sequences: reliability of global phylogenies inferred from EF-1 alpha(Tu) and EF-2(G) proteins. Proc Natl Acad Sci U S A. 1994;91:3255-9 pubmed
    ..In no case, however, do any of the tree topologies inferred from EF-1 alpha(Tu) sequence analyses receive significant bootstrap support. ..
  12. Mueller P, Egorova K, Vorgias C, Boutou E, Trauthwein H, Verseck S, et al. Cloning, overexpression, and characterization of a thermoactive nitrilase from the hyperthermophilic archaeon Pyrococcus abyssi. Protein Expr Purif. 2006;47:672-81 pubmed publisher
    ..The nitrilase hydrolyzes preferentially aliphatic substrates and the best substrate is malononitrile with a K(m) value of 3.47 mM...
  13. Lucas S, Toffin L, Zivanovic Y, Charlier D, Moussard H, Forterre P, et al. Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microbiol. 2002;68:5528-36 pubmed
    ..Vector pYS2 proved to be very stable and was maintained at high copy number under selective conditions in both Escherichia coli and P. abyssi...
  14. Dwivedi S, Kruparani S, Sankaranarayanan R. A D-amino acid editing module coupled to the translational apparatus in archaea. Nat Struct Mol Biol. 2005;12:556-7 pubmed publisher
    ..These results together indicate the presence of these deacylases in all three kingdoms of life. This underlines an important role they may have played in enforcing homochirality during translation...
  15. 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
  16. Brooks M, Meslet Cladi re L, Graille M, Kuhn J, Blondeau K, Myllykallio H, et al. The structure of an archaeal homodimeric ligase which has RNA circularization activity. Protein Sci. 2008;17:1336-45 pubmed publisher
    ..Additionally, we show that the protein is indeed capable of circularizing RNA molecules in an ATP-dependent reaction. These structural and biochemical results provide an insight into the potential physiological roles of Pab1020...
  17. 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. ..
  18. Walbott H, Leulliot N, Grosjean H, Golinelli Pimpaneau B. The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity. Nucleic Acids Res. 2008;36:4929-40 pubmed publisher
    ..We also predict that a large TPsiC loop conformational change has to occur for the flipping of the target uridine into the (Pab)TrmU54 active site during catalysis...
  19. Serre M, El Arnaout T, Brooks M, Durand D, Lisboa J, Lazar N, et al. The carboxy-terminal ?N helix of the archaeal XerA tyrosine recombinase is a molecular switch to control site-specific recombination. PLoS ONE. 2013;8:e63010 pubmed publisher
  20. 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. ..
  21. Purcarea C, Herv G, Ladjimi M, Cunin R. Aspartate transcarbamylase from the deep-sea hyperthermophilic archaeon Pyrococcus abyssi: genetic organization, structure, and expression in Escherichia coli. J Bacteriol. 1997;179:4143-57 pubmed
    ..abyssi cells this enzyme is further stabilized through its association with other cellular components...
  22. Wydau S, Ferri Fioni M, Blanquet S, Plateau P. GEK1, a gene product of Arabidopsis thaliana involved in ethanol tolerance, is a D-aminoacyl-tRNA deacylase. Nucleic Acids Res. 2007;35:930-8 pubmed publisher
    ..coli for the absence of endogeneous d-Tyr- tRNA(Tyr) deacylase. Possible connections between exposure of plants to ethanol/acetaldehyde and misaminoacylation of tRNA by d-amino acids are considered...
  23. Watrin L, Lucas S, Purcarea C, Legrain C, Prieur D. Isolation and characterization of pyrimidine auxotrophs, and molecular cloning of the pyrE gene from the hyperthermophilic archaeon Pyrococcus abyssi. Mol Gen Genet. 1999;262:378-81 pubmed
    ..The pyrE gene of wild-type P. abyssi and one of its mutant derivatives were cloned and sequenced. This pyrE gene could serve as selectable marker for the development of gene manipulation systems in archaeal hyperthermophiles. ..
  24. Loc h J, Blaud M, Réty S, Lebaron S, Deschamps P, Bareille J, et al. RNA mimicry by the fap7 adenylate kinase in ribosome biogenesis. PLoS Biol. 2014;12:e1001860 pubmed publisher
    ..Incorporation of Rps14 by Fap7 leads to a structural rearrangement of the platform domain necessary for the pre-rRNA to acquire a cleavage competent conformation. ..
  25. Manival X, Charron C, Fourmann J, Godard F, Charpentier B, Branlant C. Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity. Nucleic Acids Res. 2006;34:826-39 pubmed publisher
    ..By gel filtration assay, we showed that aNOP10 can dimerize in solution. As both residues Y41 and L48 were needed for dimerization, the dimerization likely takes place by interaction of parallel alpha-helices...
  26. Hecker A, Graille M, Madec E, Gadelle D, Le Cam E, van Tilbergh H, et al. The universal Kae1 protein and the associated Bud32 kinase (PRPK), a mysterious protein couple probably essential for genome maintenance in Archaea and Eukarya. Biochem Soc Trans. 2009;37:29-35 pubmed publisher
    ..Understanding the precise biochemical function and biological role of these two proteins (which are probably essential for genome maintenance) remains a major challenge...
  27. Renalier M, Joseph N, Gaspin C, Thebault P, Mougin A. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. RNA. 2005;11:1051-63 pubmed publisher
    ..In this archaea, the C56 2'-O-methylation is provided by a C/D sRNP. Our work is the first demonstration that, within the same kingdom, two different mechanisms are used to modify the same nucleoside in tRNAs...
  28. Ren B, K hn J, Meslet Cladiere L, Briffotaux J, Norais C, Lavigne R, et al. Structure and function of a novel endonuclease acting on branched DNA substrates. EMBO J. 2009;28:2479-89 pubmed publisher
    ..Altogether, our data suggest that NucS proteins constitute a new family of structure-specific DNA endonucleases that are widely distributed in archaea and in bacteria, including Mycobacterium tuberculosis...
  29. Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, et al. Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res. 2007;35:1908-18 pubmed publisher
    ..These results demonstrate the value of genome comparison and the wheat-germ-based system in finding a novel DNA-binding motif in mobile DNases and, in general, a novel protein fold in horizontally transferred genes...
  30. Du Z, Liu J, Albracht C, Hsu A, Chen W, Marieni M, et al. Structural and mutational studies of a hyperthermophilic intein from DNA polymerase II of Pyrococcus abyssi. J Biol Chem. 2011;286:38638-48 pubmed publisher
    ..NMR spin relaxation indicates that the Pab PolII intein is significantly more rigid than mesophilic inteins, which may contribute to the higher optimal temperature for protein splicing...
  31. Guelorget A, Roovers M, Gu rineau V, Barbey C, Li X, Golinelli Pimpaneau B. Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res. 2010;38:6206-18 pubmed publisher
    ..When A59 is absent in tRNA(Asp), only A57 is modified. Identification of the methylated positions in tRNAAsp by mass spectrometry confirms that (Pab)TrmI methylates the first adenine of an AA sequence...
  32. Gras S, Chaumont V, Fernandez B, Carpentier P, Charrier Savournin F, Schmitt S, et al. Structural insights into a new homodimeric self-activated GTPase family. EMBO Rep. 2007;8:569-75 pubmed publisher
    ..Owing to this unique functional feature, we propose to call this family as GPN-loop GTPase...
  33. Horcajada C, Guinovart J, Fita I, Ferrer J. Crystal structure of an archaeal glycogen synthase: insights into oligomerization and substrate binding of eukaryotic glycogen synthases. J Biol Chem. 2006;281:2923-31 pubmed publisher
  34. Meslet Cladi re L, Norais C, Kuhn J, Briffotaux J, Sloostra J, Ferrari E, et al. A novel proteomic approach identifies new interaction partners for proliferating cell nuclear antigen. J Mol Biol. 2007;372:1137-48 pubmed publisher
    ..Furthermore we show that PIP-peptides interact with PCNA largely in a sequence independent manner. Our experimental approach also identified many so far unidentified PCNA interacting peptides in a number of human proteins...
  35. Gregory L, Aguissa Tour A, Pinaud N, Legrand P, Gleizes P, Fribourg S. Molecular basis of Diamond-Blackfan anemia: structure and function analysis of RPS19. Nucleic Acids Res. 2007;35:5913-21 pubmed publisher
    ..This data indicate that missense mutations in DBA primarily affect the capacity of the protein to be incorporated into pre-ribosomes, thus blocking maturation of the pre-40S particles...
  36. Van Boxstael S, Cunin R, Khan S, Maes D. Aspartate transcarbamylase from the hyperthermophilic archaeon Pyrococcus abyssi: thermostability and 1.8A resolution crystal structure of the catalytic subunit complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate. J Mol Biol. 2003;326:203-16 pubmed
    ..Other known thermostabilizing devices such as increased packing density or reduction of cavity volumes do not appear to contribute to the high thermostability of the P.abyssi enzyme...
  37. Navarro M, Oliveira C, Zanchin N, Guimar es B. Insights into the mechanism of progressive RNA degradation by the archaeal exosome. J Biol Chem. 2008;283:14120-31 pubmed publisher
    ..Finally, comparisons between the archaeal and human exosome structures provide a possible explanation for the eukaryotic exosome inability to catalyze phosphate-dependent RNA degradation...
  38. Thore S, Mayer C, Sauter C, Weeks S, Suck D. Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya. J Biol Chem. 2003;278:1239-47 pubmed publisher
    ..RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions...
  39. Crepin T, Schmitt E, Blanquet S, Mechulam Y. Structure and function of the C-terminal domain of methionyl-tRNA synthetase. Biochemistry. 2002;41:13003-11 pubmed
    ..Comparison of the resulting mutants to native and C-truncated MetRS shows that the presence of the appended C-domain improves tRNA(Met) binding affinity. However, dimer formation is required to evidence the gain in affinity...
  40. Le Breton M, Henneke G, Norais C, Flament D, Myllykallio H, Querellou J, et al. The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair?. J Mol Biol. 2007;374:1172-85 pubmed publisher
    ..Our results are in favor of a multifunctional archaeal primase involved in priming and repair...
  41. B nisch H, Schmidt C, Bianco P, Ladenstein R. Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S. Acta Crystallogr D Biol Crystallogr. 2005;61:990-1004 pubmed publisher
  42. Gras S, Fernandez B, Chaumont V, Carpentier P, Armengaud J, Housset D. Expression, purification, crystallization and preliminary crystallographic analysis of the PAB0955 gene product. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:208-11 pubmed publisher
    ..Crystals have been obtained either without nucleotide or in the presence of GDP or GTPgammaS. Preliminary X-ray crystallographic data up to 2.08 A resolution have been collected from these crystals...
  43. Coltri P, Guimar es B, Granato D, Luz J, Teixeira E, Oliveira C, et al. Structural insights into the interaction of the Nip7 PUA domain with polyuridine RNA. Biochemistry. 2007;46:14177-87 pubmed publisher
    ..This work provides experimental verification that the PUA domain mediates Nip7 interaction with RNA and reveals that the preference for interaction with polyuridine sequences is conserved in Archaea and eukaryotic Nip7 proteins...
  44. Creze C, Ligabue A, Laurent S, Lestini R, Laptenok S, Khun J, et al. Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels. J Biol Chem. 2012;287:15648-60 pubmed publisher
  45. Crepin T, Schmitt E, Blanquet S, Mechulam Y. Three-dimensional structure of methionyl-tRNA synthetase from Pyrococcus abyssi. Biochemistry. 2004;43:2635-44 pubmed publisher
    ..Moreover, association of tRNA(Met) to the core enzyme is enhanced in the presence of the C-domain. Together, these experiments suggest positive control in trans by the C-domain on recognition of tRNA by the core moiety of MetRS...
  46. Auxilien S, Rasmussen A, Rose S, Brochier Armanet C, Husson C, Fourmy D, et al. Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases. RNA. 2011;17:45-53 pubmed publisher
    ..abyssi 23S rRNA. The findings indicate that PAB0719 and PAB0760 originated as RlmD-type m(5)U methyltransferases and underwent changes in target specificity after their acquisition by a Thermococcales ancestor from a bacterial source...
  47. Charron C, Manival X, Cl ry A, Senty S gault V, Charpentier B, Marmier Gourrier N, et al. The archaeal sRNA binding protein L7Ae has a 3D structure very similar to that of its eukaryal counterpart while having a broader RNA-binding specificity. J Mol Biol. 2004;342:757-73 pubmed publisher
    ..The Glu43-Lys46 ion pair of protein L7Ae belongs to a complex network of ion pairs that may participate to protein thermostability...
  48. 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...
  49. Schmitt E, Blanquet S, Mechulam Y. The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors. EMBO J. 2002;21:1821-32 pubmed publisher
    ..Implications for the mechanism of translation initiation in both eukarya and archaea are discussed. In particular, positioning of the initiator tRNA in the ribosomal A site during the search for the initiation codon is envisaged...
  50. Armengaud J, Fernandez B, Chaumont V, Rollin Genetet F, Finet S, Marchetti C, et al. Identification, purification, and characterization of an eukaryotic-like phosphopantetheine adenylyltransferase (coenzyme A biosynthetic pathway) in the hyperthermophilic archaeon Pyrococcus abyssi. J Biol Chem. 2003;278:31078-87 pubmed publisher
    ..The existence of operational proteins highly conserved between Archaea and Eukarya involved in a central metabolic pathway challenge evolutionary scenarios in which eukaryal operational proteins are strictly of bacterial origin...
  51. Erauso G, Marsin S, Benbouzid Rollet N, Baucher M, Barbeyron T, Zivanovic Y, et al. Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J Bacteriol. 1996;178:3232-7 pubmed
    The plasmid pGT5 (3,444 bp) from the hyperthermophilic archaeon Pyrococcus abyssi GE5 has been completely sequenced...
  52. Blaise M, Fr chin M, Oli ric V, Charron C, Sauter C, Lorber B, et al. Crystal structure of the archaeal asparagine synthetase: interrelation with aspartyl-tRNA and asparaginyl-tRNA synthetases. J Mol Biol. 2011;412:437-52 pubmed publisher
  53. Yatime L, Schmitt E, Blanquet S, Mechulam Y. Structure-function relationships of the intact aIF2alpha subunit from the archaeon Pyrococcus abyssi. Biochemistry. 2005;44:8749-56 pubmed publisher
    ..Thereby, the observed structural mobility within the e- and aIF2alpha molecules would be an integral part of the biological function of this subunit in the heterotrimeric e- and aIF2alphabetagamma factors...
  54. 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...
  55. Schmitt E, Panvert M, Blanquet S, Mechulam Y. Structural basis for tRNA-dependent amidotransferase function. Structure. 2005;13:1421-33 pubmed publisher
    ..Comparison of GatD and L-asparaginase structures shows how the motion of a beta hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE...
  56. Iwasaki W, Sekine S, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S. Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase. J Mol Biol. 2006;360:329-42 pubmed publisher
    ..We performed a mutational analysis of this particular arginine residue, and confirmed its significance in the tRNA recognition...
  57. Fukunaga R, Yokoyama S. Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. J Mol Biol. 2005;346:57-71 pubmed publisher
  58. Qureshi S, Jackson S. Sequence-specific DNA binding by the S. shibatae TFIIB homolog, TFB, and its effect on promoter strength. Mol Cell. 1998;1:389-400 pubmed
    ..shibatae TFB mediates sequence-specific interactions with DNA flanking the A box. Thus, sequence-specific DNA recognition by TFB and TBP are codeterminants of promoter strength in Archaea...
  59. Liu B, Bartlam M, Gao R, Zhou W, Pang H, Liu Y, et al. Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii. Biophys J. 2004;86:420-7 pubmed publisher
    ..The identification of structural features that make PPases more adaptable to extreme temperature should prove helpful for future biotechnology applications...
  60. Wang C, Jia Q, Zeng J, Chen R, Xie W. Structural insight into the methyltransfer mechanism of the bifunctional Trm5. Sci Adv. 2017;3:e1700195 pubmed publisher
    ..Last, through structure comparison with its ortholog Methanococcus jannaschii Trm5b (MjTrm5b), we propose a reaction mechanism for the double methylation capability of this unique enzyme. ..
  61. 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...
  62. de Cr cy Lagard V, Brochier Armanet C, Urbonavicius J, Fernandez B, Phillips G, Lyons B, et al. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol Biol Evol. 2010;27:2062-77 pubmed publisher
    ..Finally, we proposed that the duplication of the trm5 gene in some Archaea led to a change in function from N1 methylation of guanosine to C7 methylation of 4-demethylwyosine (imG-14)...
  63. Perrochia L, Guetta D, Hecker A, Forterre P, Basta T. Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t6A tRNA modification. Nucleic Acids Res. 2013;41:9484-99 pubmed publisher
    ..Overall, our data support a mechanistic model in which the final step in the biosynthesis of t(6)A relies on a strictly catalytic component, Kae1, and three partner proteins necessary for dimerization, tRNA binding and regulation...
  64. Hayashi I, Oyama T, Morikawa K. Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus. EMBO J. 2001;20:1819-28 pubmed publisher
  65. 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...
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