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  • 1
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray crystallographic analysis of archaeal O6-methylguanine–DNA methyltransferase (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 1395-1396 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Crystals of archaeal O6-methylguanine–DNA methyltransferase (MGMT) from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1 have been grown at room temperature using polyethylene glycol as a precipitant. The diffraction pattern of the crystal extends to 2.0 Å resolution at room temperature upon exposure to Cu K\alpha radiation. The crystal belongs to the space group P212121 with unit-cell dimensions of a = 52.8, b = 86.6 and c = 39.9 Å. The presence of one molecule per asymmetric unit gives a crystal volume per protein mass (Vm) of 2.3 Å3 Da−1 and a solvent content of 48% by volume. A full set of X-ray diffraction data was collected to 2.0 Å Bragg spacings from the native crystal.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998001346
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  • 2
    Electronic Resource
    Electronic Resource
    Crystallographic study of intein homing endonuclease II encoded in the archaeal DNA polymerase gene (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1185-1186 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Intein homing endonucleases are proteins spliced out from a precursor protein and site-specific enzymes that make double-strand breaks in inteinless alleles. Crystals of intein homing endonuclease II from the hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1 (PI-PkoII) have been grown at room temperature using ammonium sulfate as a precipitant. The diffraction pattern of the crystal extends to 3.0 Å resolution at room temperature upon exposure to synchrotron X-rays at KEK-PF, Japan. The crystals have symmetry consistent with space group C2221, with unit-cell parameters a = 107.6, b = 150.5, c = 146.8 Å. A full set of X-ray diffraction data were collected to 3.0 Å Bragg spacing from a native crystal with an overall Rmerge of 4.8% and a completeness of 96.6%.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900008672
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  • 3
    Electronic Resource
    Electronic Resource
    Surface histidine residue of archaeal histone affects DNA compaction and thermostability (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 224 (2003), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Archaeal histone, which possesses only the core domain part of eukaryal histone, induced DNA compaction by binding to DNA. Based on structural modeling, tetramer formation by dimer–dimer interaction is considered to require two intermolecular ion pairs formed between histidine and aspartate. To examine the role of the ion pairs on DNA compaction, mutant histones were constructed and analyzed using HpkB from Thermococcus kodakaraensis KOD1 as a model protein. The mutant histones, HpkB-H50A, HpkB-H50V, and HpkB-H50G were constructed by replacing conserved surface His50 with Ala, Val, and Gly, respectively. Circular dichroism analysis indicated no significant difference between wild-type and mutants in their structures. Gel mobility shift assays showed that all mutants possessed DNA binding ability, like wild-type HpkB, however all mutants compacted DNA less efficiently than the wild-type. Moreover, all mutants could not maintain the nucleosome-like structure (compacted form of DNA) above 80°C. These results suggest that surface ion pairs between His and Asp play an important role in maintenance of nucleosome structure and DNA stabilization at high temperature.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0378-1097(03)00358-6
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  • 4
    Electronic Resource
    Electronic Resource
    Sequence and transcriptional studies of five clustered flagellin genes from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 (1999)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 178 (1999), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Five clustered genes (flaB1, flaB2, flaB3, flaB4 and flaB5) for multiple subunits of flagellar filaments from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 were cloned and sequenced. Deduced amino acid sequences were aligned and it was revealed that five flagellin genes are homologous especially in the N-terminal hydrophobic region which might be important for interaction among flagellin subunits. Phylogenetic analysis was performed among archaeal flagellins from methanogens, an extreme halophile and our hyperthermophile, indicating that KOD1 flagellins were grouped together with methanogenic counterparts and were distinguishable from halophilic flagellins. Northern analysis of transcripts from flagellin genes from P. 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1999.tb13776.x
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  • 5
    Electronic Resource
    Electronic Resource
    Comparison of two glutamate producing enzymes from the hyperthermophilic archaeon Pyrococcus sp. KOD1 (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 158 (1998), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The glutamate dehydrogenase from Pyrococcus sp. KOD1 (Pk-GDH) was purified to homogeneity and its enzymatic characteristics for glutamate production were analyzed. Pk-GDH exhibited glutamate producing activity from glutamine, which was found in some higher eukaryotic GDHs. However, the kcat/Km values for ammonia and glutamine were 15×103 min−1 mM and 0.4×103 min−1 mM, respectively, indicating that the enzyme utilizes ammonia predominantly for glutamate production. Kinetic parameters of Pk-GDH were compared with those of Pk-GltA, which was previously identified as a glutamate synthase homologue. The turnover number for glutamine of Pk-GltA (4.1×103 min−1 mM) was 10-fold higher than that of Pk-GDH (0.4×103 min−1 mM). Therefore, Pk-GDH is less efficient than Pk-GltA for glutamate production. Pk-GDH utilized both NADPH and NADH as a cofactor, Pk-GltA utilized only NADPH.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1998.tb12827.x
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