Pyrococcus abyssi

NIS measurements have been performed on the rubredoxin (FeSa) type mutant Rm 2-A from Pyrococcus abyssi [103], on Pyrococcus furiosus rubredoxin [104], on Fe2S2 - and Fe4S4 - proteins and model compounds [105, 106], and on the P-cluster and FeMo-cofactor of nitrogenase [105, 107]. 

For example, Fig. 9.40 shows the NIS spectra of the oxidized and reduced FeS4 centers of a rubredoxin mutant from Pyrococcus abyssi obtained at 25 K together with DFT simulations using different models for the Fe-S center [103]. The spectrum from the oxidized protein Fe S4 (S = 5/2) reveals broad bands around 15-25 meV (121-202 cm ) and 42-48 meV (339-387 cm ) consistent with the results on rubredoxin from Pyrococcus furiosus [104]. 

Fig. 9.40 NIS spectra of oxidized (filled circle) and reduced rubredoxin mutant Rm 2-4 (filled triangle) from Pyrococcus abyssi obtained at 25 K. The protein samples have been prepared with Fe concentrations of about 10 mM. Theoretically calculated NIS spectra based on DFT calculations (B3LYP/CEP-3IG) of 9, 21 and 49 atoms are shown below. The dotted lines represent calculated NIS spectra for the oxidized Fe S4 center and the dashed lines for the reduced Fe°S4 center. (Taken from [103])...

A nitrilase from the hyperthermophile Pyrococcus abyssi, which exhibits optimal growth at 100 °C, was cloned and overexpressed. Characterization of this nitrilase revealed that it is operational as a dimer (rather than the more common multimeric structure for nitrilases), with optimal pH at 7.4 and optimal apparent activity at 80 °C with Tm (DSC) at 112.7 °C. The substrate specificity of the nitrilase is narrow and it does not accept aromatic nitriles. The nitrilase converts the dinitriles fumaronitrile and malononitrile to their corresponding mononitriles [58],... 

Mueller, P, Egorova, K., Vorgias, C.E. et al. (2006) Cloning, overexpression, and characterization of a thermoactive nitrilase from the hyperthermophilic archaeon Pyrococcus abyssi. Protein Expression and Purification, 47, 672-668. 

Purcarea, C., Simon, V., Prieur, D., and Herve, G. (1996). Purification and characterization of carbamoyl-phosphate synthetase from the deep-sea hyperthermophilic archaebac-terium Pyrococcus abyssi. Eur. J. Biochem., 236, 189—199. 

Purcarea, C., Evans, D. R., and Herve, G. (1999). Channeling of carbamoyl phosphate to the pyrimidine and arginine biosynthetic pathways in the deep sea hyperthermophilic archaeon Pyrococcus abyssi. J. Biol. Chem., 274, 6122—6129. 

As a second example, Mossbauer spectra of a rubredoxin-type protein mutant from Pyrococcus abyssi are shown in Figure 11. This protein contains a tetrahedral sulfur-coordinated high-spin ferrous site. Owing to the covalent character of the Fe-S bond, an isomer shift of 0.70 mm s is observed at 4.2 K. This value is characteristic for almost all tetrahedral sulfur-coordinated high-spin ferrous sites. 

Figure 13 Mossbauer spectra of the oxidized rubredoxin-type protein mutant RM-2-4 from the archaeon Pyrococcus abyssi taken at 4.2 K in applied field perpendicular (a) and parallel (b) to y -ray. The solid lines have been obtained by simultaneous fitting of the Mossbauer spectra with the software package VINDA assuming an Y = 5/2 ground state. The parameters are described in text. (From Wegner et al With kind permission from Springer Science Business Media)...

Pyrococcus abyssi y subunit of initiation factor, e/all2 Translation IKJZ Cysp 2 CysL 8 Cysp 2 CysL... 

A further striking example is given by the Pyrococcus abyssi Sm core (PA Sm). In the free state and in complex with RNA, the PA Sm has point symmetry 72 and consists of a sandwich of two heptameric rings in the same orientation and dyadically related [20]. In the two states, the folding of the monomers differs only slightly, so that the corresponding molecular forms of PA Sm heptamer (central hole and envelope) are the same. 

Figure 11-5. The form lattice of the double heptameric ring of the pyrococcus abyssi Sm core in the free state conformation is isometric heptagonal. The lattice parameter is given by the distance u of each heptamer from a twofold axis (from [16], courtesy lUCr)...

Figure 11-6. The double heptameric ring of pyrococcus abyssi Sm core in complex with RNA (not shown) has the same form lattice as in the free state. Only the distance d between the heptamers is doubled d = Au instead of 2u (from [19], courtesy lUCr)...

The number of amino acids in each intein is indicated, while the absence of an intein is indicated by a dash (—). Pab, Pyrococcus abyssi Pho, Pyrococcus horikoshii OT3 PJu, Pymcoccusfuriosus Mja, Methanococcus jannaschii Mth, Methanobacterium thermoautoirophicum (delta H strain) Ape, Aempynm pemix. 

HINT Hedgehog inteins. For exteins and inteins in archaeabacterium, Pyrococcus abyssi, click Du Z Liu J Albrecht CD et al. 

Geslin C, Gaillard M, Flament D, Roault K, Le Romancer M, Prieur D, Erauso G. Analysis of the first genome of a hyperthermophilic marine virus-like particle, RAVI, isolated from Pyrococcus abyssi. J Bacteriol. 2007 189 4510-9. 

Crepin T, Schmitt E, Blanquet S, Mechulam Y Three-dimensional structure of methionyl-tRNA synthetase from Pyrococcus abyssi. Biochemistry 2004, 43(9) 2635-2644. 

Investigation of the structure-function relationships in nitrilases was largely based on sequence analyses, homology modeling, and mutational studies, as the crystal structures of nitrile-hydrolyzing enzymes have not been available except for an aliphatic nitrilase from Pyrococcus abyssi [13]. Other crystallized members of the nitrilase superfamily (amidases, N-carbamoyl-D-amino acid amidohydrolases, etc. [9]) shared only low levels of identity with experimentally confirmed nitrilases. 

A propynyl moiety instead of methyl also has been transferred to tRNA and pre-mRNA catalyzed by RNA 2 -0-MTase from Pyrococcus abyssi, a thermophilic archaeon, using a synthetic cofactor [55]. Terminal aUcyne groups can be subjected to click reaction in order to introduce chromophores or affinity tags. 

Deep sea hydrothermal vents Staphilothermus marimus, Pyrococcus abyssi... 

---