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2.7.7.8: polyribonucleotide nucleotidyltransferase

This is an abbreviated version!
For detailed information about polyribonucleotide nucleotidyltransferase, go to the full flat file.

Word Map on EC 2.7.7.8

Reaction

RNAn+1
+
phosphate
=
RNAn
 +
a nucleoside diphosphate

Synonyms

AtcpPNPase, AtmtPNPase, chloroplast PNPase, cpPNPase, hPNPase(old-35), hPNPaseold-35, nucleoside diphosphate:polynucleotidyl transferase, nucleotidyltransferase, polyribonucleotide, PNP, PNPase, PNPT1, polynucleotide phosphorylase, polyribonucleotide phosphorylase, RNase PH

ECTree

     2 Transferases
         2.7 Transferring phosphorus-containing groups
             2.7.7 Nucleotidyltransferases
                2.7.7.8 polyribonucleotide nucleotidyltransferase

Crystallization

Crystallization on EC 2.7.7.8 - polyribonucleotide nucleotidyltransferase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
modeling of structure based on Escherichia coli PNPase crystal structure. Residues Glu20, Arg35, Asp323, Glu331, and Arg546 are hypothesized to be involved in the RNase Y interaction
-
purified recombinant RNA-free and RNA-bound PNPase, as protein-peptide and protein-RNA complexes, mixing of PNPase recognition peptide from RNase E, KPRRGWWRR, with apo-PNPase in a 2:1 ratio, sitting drop vapour diffusion method, mixing of equal volumes of protein solution and cyrstallization solution, containing w/v PEG 3350, 0.1 M Bis-Tris, pH 5.5, 0.1 M ammonium acetate for RNA-bound crystals, and with the apo-enzyme containing w/v PEG3000, 0.1 M trisodium citrate, pH 5.5, for hexagonal crystals and w/v PEG 3350, 0.15 M DL-malic acid for rhombohedral crystals, 18°C, 1 week, X-ray diffraction structure determination aand analysis at 2.6-3.3 A resolution, molecular replacement
-
PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA, hanging droplet vapor diffusion method, crystals for the PNPase core/RNase E micro-domain crystals are grown using 0.2 M ammonium nitrate, and 20% (w/v) PEG 3350, crystals for the PNPase core/RNase E microdomain-RNA complex are produced using 0.2 M diammonium hydrogen citrate, and 17% PEG 3350. The optimal reservoir buffer for the PNPase core/RNase E micro-domain-RNA-tungstate crystals is composed of 0.2 M di-ammonium hydrogen citrate, 17% PEG 3350, about pH 4.5, 50 mM disodium tungstate. Crystals for the PNPase core/RNase E micro-domain-Mn2+ co-crystals are prepared using 2.5 M NaCl, 9% (w/v) PEG 6000, 20 mM sodium citrate, and 20 mM manganese acetate tetrahydrate
three-dimensional modeling of enzyme based on Streptomyces antibioticus protein structure. The binding domain for RNase E is located on the monomer surface, facing outward from the trimeric tertiary structure
wild-type and C-terminal KH/S1 domain truncated mutant at resolutions of 2.6 and 2.8 A, respectively. The six PH domains assemble into a ring-like structure containing a central channel
homology modeling based on structure of Streptomyces antibioticus ortholog. Enzyme displays a doughnut-shaped trimer with a central channel to accommodate a single-stranded RNA molecule. The circular structure is composed of the first and second core domains, while the KH and S1 RNA binding domains are located at the top, adjacent to the gate entrance into the circle
-
wild-type and S1 domain-truncated hPNPase, hanging-drop vapor diffusion method, mixxing of 0.001 ml of 10 mg/ml protein in 50 mM Tris, pH 8.0, and 150 mM NaCl, with 0.001 ml of reservoir solution containing 0.1 M citrate, pH 5.0, 10% v/v 2-propanol and 26% v/v PEG 400, room temperature, X-ray diffraction structure determination and analysis at 2.1 A resolution, molecular replacement method
structure reveals a bound phosphate in the PH2 domain of each protomer coordinated by three adjacent serine residues. Phosphate coordination by these serine residues is essential to maintain the catalytic center in an active conformation
protein solution mixed at 3/1 ratio with well solution consisting of 2 M ammonium sulfate, 100 mM Tris-HCl, pH 8.5, 5 mM dithiothreitol and 0.75 mM Na2AsO4, crystals are harvested in a so called mirror solution from equilibrated droplets with buffer replacing enzyme solution and no added Na2AsO4, crystals of native PNPase, a tungstate derivative and a seleno-methionyl derivative