m jannaschii genomic dna  (ATCC)

Journal: The protein journal

Article Title: Characterization of the Dihydroorotase from Methanococcus jannaschii

doi: 10.1007/s10930-017-9729-7

Figure Lengend Snippet: (a) SDS-PAGE of purified recombinant M. jannaschii DHOase. Lane A corresponds to the molecular weight markers, lane B has the purified protein. The molecular weight markers were the Precision Plus Protein unstained standards (Biorad). (b) The corresponding plot of the logarithm of the molecular weight versus relative migration distance of the standards. Based on this plot, the molecular weight of the protein was estimated to be 47503 Da.

Article Snippet: 2.1 Plasmid Preparation Clones of M. jannaschii genomic DNA encoding DHOase were obtained from the American Type Culture Collection (ATCC number 624773).

Techniques: SDS Page, Purification, Recombinant, Molecular Weight, Migration

Journal: The protein journal

Article Title: Characterization of the Dihydroorotase from Methanococcus jannaschii

doi: 10.1007/s10930-017-9729-7

Figure Lengend Snippet: Kinetic parameters of M. jannascii DHOase and of selected dihydroorotases in the degradative direction.

Article Snippet: 2.1 Plasmid Preparation Clones of M. jannaschii genomic DNA encoding DHOase were obtained from the American Type Culture Collection (ATCC number 624773).

Techniques:

Journal: The protein journal

Article Title: Characterization of the Dihydroorotase from Methanococcus jannaschii

doi: 10.1007/s10930-017-9729-7

Figure Lengend Snippet: Thermal stability of M. jannaschii DHOase at 85° C, 90° C and 98° C. Solutions of the enzyme were heated at the indicated temperature in 0.1 M Tris-acetate pH 7.5, 150 mM NaCl, 2 mM BME. At the indicated times, samples were removed and immediately placed on ice. The colorimetric assay was used to determine enzymatic activity at 37° C in the degradative direction.

Article Snippet: 2.1 Plasmid Preparation Clones of M. jannaschii genomic DNA encoding DHOase were obtained from the American Type Culture Collection (ATCC number 624773).

Techniques: Colorimetric Assay, Activity Assay

Journal: The protein journal

Article Title: Characterization of the Dihydroorotase from Methanococcus jannaschii

doi: 10.1007/s10930-017-9729-7

Figure Lengend Snippet: Molecular mass distribution plot from SEC-UV/LS/RI analysis for M. jannaschii DHOase. Molecular masses are plotted as red filled triangles (for clarity only every 5th measurement of molecular mass across the eluting peak is plotted); the blue line corresponds to the UV trace of the protein eluting from the SEC column monitored at 280 nm.

Article Snippet: 2.1 Plasmid Preparation Clones of M. jannaschii genomic DNA encoding DHOase were obtained from the American Type Culture Collection (ATCC number 624773).

Techniques:

Journal: The protein journal

Article Title: Characterization of the Dihydroorotase from Methanococcus jannaschii

doi: 10.1007/s10930-017-9729-7

Figure Lengend Snippet: Calibration curve for Zn in ICP-MS analysis used to determine the Zn content of M. jannaschii DHOase. Blue filled circles illustrate the Zn standards used to construct this curve. Red filled squares correspond to the protein samples and orange filled squares correspond to the buffer samples. Both were diluted by a factor of 10. The green filled triangles are bracketing quality controls for the protein and buffer samples. 1ppb corresponds to 1 ug/lt.

Article Snippet: 2.1 Plasmid Preparation Clones of M. jannaschii genomic DNA encoding DHOase were obtained from the American Type Culture Collection (ATCC number 624773).

Techniques: Construct

Journal: The protein journal

Article Title: Characterization of the Dihydroorotase from Methanococcus jannaschii

doi: 10.1007/s10930-017-9729-7

Figure Lengend Snippet: (a) A schematic ribbons diagram illustrating the homology model of the M. jannaschii DHOase superimposed on the enzyme from B. anthracis (pdb id: 3mpg, chain A). M. jannaschii DHOase is depicted in rainbow colors, from blue at the N-terminus to red at the C-terminus. 3mpg, chain A is depicted in dark grey. In this view, the β hairpin loop described in the text for M.jannaschii (βIX and βX) is in orange in the back of the molecule. The homology model was calculated with Modeller in the UCSF chimera environment using the dihydroorotase of B. anthracis as the template. A stereo pair. Figure was drawn with the UCSF Chimera package (b)Sequence alignment of the M. jannaschii (Mj) and B. anthracis (Ba) dihydroorotases. The figure was prepared with UCSF Chimera and is based on the structural superposition of the two proteins. Identity between the two sequences is emphasized by blocks drawn at the suitable sequence positions. Invariant residues in all dihydroorotases are highlighted; those that coordinate the two Zn ions in magenta, those with side chains involved in substrate binding in blue and the rest in green. Cyan corresponds to amino acids that are not conserved but their positions are conserved and their main chain atoms interact with the substrate. Residues Asp146 in Mj and Asp151 in Ba are outlined in black. Their carboxylate oxygens bridge the two Zn ions. An aspartate at this position is conserved in Type I DHOases [3]. The coral region covers corresponding residues in the two proteins that are within 2 Å from each other. Sequence is colored according to the secondary structure: red for α helices, blue for β strands and black for loops. The secondary structural elements of the TIM barrel are labeled from β1 to α8. The β strands in the adjacent domain are labeled as βI to βXII. Helices are not labeled unless they correspond to the (βα)8 barrel. The two sequences exhibit 32% identity.

Article Snippet: 2.1 Plasmid Preparation Clones of M. jannaschii genomic DNA encoding DHOase were obtained from the American Type Culture Collection (ATCC number 624773).

Techniques: Sequencing, Binding Assay, Labeling

Journal: Acta Crystallographica. Section F, Structural Biology Communications

Article Title: Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNA Cys synthesis

doi: 10.1107/S2053230X16009559

Figure Lengend Snippet: Macromolecule-production information

Article Snippet: The purified protein was pooled, concentrated using an Amicon Ultra 30 kDa MWCO centrifugal concentrator (Millipore) and finally stored at 193 K. table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Source organism M. jannaschii DNA source M. jannaschii genome SepCysS Cloning site NdeI–XhoI Expression vector pET-15b (Novagen) Expression host E. coli B834(DE3) plus pRARE2 (Novagen) Complete amino-acid sequence of the construct produced † MGSSHHHHHHSSGLVPRGSHN MELEGPYSKKFEVITLDINLDKYKNLTRSLTREFINLNPIQRGGILPKEAKKAVYEYWDGYSVCDYCHGRLDEVTCPPIKDFLEDIAKFLNMDCARPTHGAREGKFIVMHAICKEGDYVVLDKNAHYTSYVAAERAKLNVAEVGYEEEYPTYKINLEGYKEVIDNLEDKGKNVGLILLTHVDGEYGNLNDAKKVGKIAKEKGIPFLLNCAYTVGRMPVNGKEVKADFIVASGHKSMAASAPCGILAFSEEFSDKITKTSEKFPVKEIEMLGCTSRGLPIVTLMASFPHVVERVKKWDEELKKTRYVVDELEKIGFKQLGIKPKEHDLIKFETPVLDEIAKKDKRRGFFFYDELKKRGIGGIRAGVTKEIKMSVYGLEWEQVEYVVNAIKEIVESCK SepCysE Cloning site NdeI–XhoI Expression vector Modified pCDF-Duet-1 Additional residues Downstream box ‡ Expression host E. coli B834(DE3) plus pRARE2 (Novagen) Complete amino-acid sequence of the construct produced † MNH MRVEYSKDLIRKGISTISQLKKAKIRVEKDDKKISYKDAKPGKIDVNEFKKAIYLLIEADDFLYKKAPKHELNEEEAKEFCKLIIKCQEHLNKILANFGFEFEEKEIDEGALYIVSNKKLFKKLKNKNPNLKVVCTEGMLDIEDMRAIGVPEKALEGLKKKVEIARKNVERFIEKYKPEKIFVVVEDDKDELLYLRAKNLYNAEKLDADEILD Synthesis of DNA template for tRNA Cys Forward primer § 5′- TAATACGACTCACTATA GCCGGGGTAGTCTAGGGGCTAGGCAGCGGACT-3′ Middle primer 5′-CTAGGCAGCGGACTGCAGATCCGCCTTACGTGGGT-3′ Reverse primer ¶ 5′-T G GAGCCGGGGGTGGGATTTGAACCCACGTAAGGC-3′ Open in a separate window † Amino acids from the vector are underlined.

Techniques: Clone Assay, Expressing, Plasmid Preparation, Sequencing, Construct, Produced, Modification