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3.1.13.3: oligonucleotidase

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

Word Map on EC 3.1.13.3

Reaction

exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates =

Synonyms

CpsORN, EC 3.1.4.19, More, nanoRNase, NrnC, nucleotidase, oligo-, oligoribonuclease, ORN, phosphodiesterase, REXO2, RNase T, small fragment nuclease, XC847, YtqI

ECTree

     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.13 Exoribonucleases producing 5′-phosphomonoesters
                3.1.13.3 oligonucleotidase

Crystallization

Crystallization on EC 3.1.13.3 - oligonucleotidase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant unliganded wild-type enzyme and pNP-TMP-bound D163A mutant, and uridine-bound wild-type and mutant enzymes, sitting drop vapour diffusion method, crystals of unliganded CpsORN are obtained from 15% w/v PEG 3350 and 0.1 M magnesium formate, 20°C, for larger single crystals, by hanging-drop vapour-diffusion method, the drop volume is increased from 200 nl to 0.001 ml against 0.5 ml reservoir solution, optimised single crystals are obtained in the same condition as that of initial screening. The crystals of pNP-TMP-bound CpsORN are observed under several conditions. Among them, the most suitable crystals are obtained from the 1.4 M ammonium tartrate dibasic and 0.1 M Tris, pH 8.5, condition. The crystals of linked RNA-bound form are obtained with 0.04 M citric acid, 0.06 M Bis-Tris propane pH 6.4, and 20% w/v PEG 3350. Crystals of uridine-bound form are obtained with 0.2 M potassium thiocyanate and 20% w/v PEG 3350. X-ray diffraction structure determination and analysis at 2.0-2.7 A resolution, molecular replacement and modelling
belongs to space group I422, with unit cell parameters a = 213.1, b = 213.1, c = 149.2, 90.0, 90.0, 90.0, to 30.0-3.1 A resolution, opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer
both native and selenomethionine-labeled enzyme
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belongs to space group P21, with unit cell parameters a = 49.9, b = 76.6, c = 61.7, 90.0, 93.55, 90.0, to 19.97-2.09 A resolution, opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer
by sitting-drop vapor diffusion method, to a resolution of 2.1 A, orn monomer comprises 9 alpha-helices and 5 beta-strands, helix H is oriented opposingly from similar helices in all reported 3'-5' DNases discovered so far, possibly to prevent steric hindrance of accommodating oligoribonucleotide substrates. Amino acids Leu135, Leu143, Ile140, and Leu174 form a hydrophobic cluster, side chains of Glu142/Arg133 and Thr139/Asp136 form salt bridges and H-bonds in the dimer interface, while side chains of Arg145, and Lys157 interact with the ribose 2'-OH or phosphate oxygen atoms of U5 substrates
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sitting-drop vapour-diffusion method, 2.1 A resolution, crystals are tetragonal and belong to space group P4(3)2(1)2 with unit cell parameters a = b = 67.5 A, c = 89.8 A. One molecule is present per asymmetric unit
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