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3.2.2.27: uracil-DNA glycosylase

This is an abbreviated version!
For detailed information about uracil-DNA glycosylase, go to the full flat file.

Word Map on EC 3.2.2.27

Reaction

Hydrolyses single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil =

Synonyms

5-formyluracil-DNA glycosylase, AFUDG, Afung protein, Blr0248, DNA N-glycosylase, dr0689, DR_0968, endonuclease VIII, family 1 uracil N-glycosylase, family 4 UDGa, family 4 uracil-DNA glycosylase, HMUDG, mismatch-specific uracil-DNA glycosylase, MjUDG, More, MtuNei1, MUG, Pa-UDG, PF1385, PfuUDG, single-strand selective monofunctional uracil-DNA glycosylase, single-strand selective uracil DNA glycosylase, single-strand-selective mono-functional uracil-DNA glycosylase, single-strand-selective monofunctional uracil DNA glycosylase, single-strand-selective monofunctional uracil-DNA glycosylase, single-stranded monofunctional uracil DNA N-glycosylase, SMUG1, SMUG1-like glycosylase, STK_22380, Ta0477, TD12-encoded protein, Thd1p, Thp1p, TMUDG, type 1 UDG, UDG, UDG1, UDGa, UdgB, UDGIV, UDGV, UL114, UL2, UNG, UNG-1, Ung-type uracil glycosylase, UNG1, UNG2, Unga, uracil DNA glycosylase, uracil DNA glycosylase 2, uracil DNA-glycosylase, uracil DNA-glycosylase 2, uracil-DNA glycosylase, uracil-DNA glycosylase 2, uracil-DNA glycosylase a, uracil-DNA N-glycosylase, uracil-N-glycosylase 2

ECTree

     3 Hydrolases
         3.2 Glycosylases
             3.2.2 Hydrolysing N-glycosyl compounds
                3.2.2.27 uracil-DNA glycosylase

Crystallization

Crystallization on EC 3.2.2.27 - uracil-DNA glycosylase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with DNA, vapor diffusion method, using 0.05 M sodium citrate pH 4.6, 20% (w/v) PEG 3350
purified recombinant His-tagged UNG type 1, hanging drop vapour diffusion method, 0.001 ml of 10 mg/ml protein in 70 mM Tris-HCl, 10 mM NaCl, 1 mM EDTA pH 8.0, 100 mg/ml bovine serum albumin, are mixed with 0.001 ml of precipitant solution containing 0.2 M ammonium nitrate and 17% w/v PEG 3000 at 4°C for a few days, 20% v/v glycerol as cryoprotectant, X-ray diffraction structure determination and analysis at 1.8-1.9 A resolution
purified recombinant wild-type MUG and MUG mutant D93A, crystal growth by mixing 0.001 ml drops of 10 mg/ml protein with a solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate, pH 6.5, and 30% w/v polyethylene glycol 8000, equilibration at 18°C, hexagonal crystals suitable for data collection purposes appear after 1 day, X-ray diffraction structure determination and analysis at 1.7-1.75 A resolution, molecular replacement
strain B UDG free or in complex with uracil or glycerol, X-ray diffraction structure determination and analysis at 1.60, 1.50, and 1.43 A resolution, respectively
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in complex with a bacteriophage encoded natural inhibitor, hanging drop vapor diffusion method, using 0.1 M Tris-HCl pH 7.4, 270 mM Li2SO4, 4% (w/v) PEG 550 MME, 17% (w/v) PEG 4000
in complex with a bacteriophage encoded natural inhibitor, hanging drop vapor diffusion method, using 0.1 M Tris–HCl pH 7.4, 270 mM Li2SO4, 4% (w/v) PEG 550 MME, 17% (w/v) PEG 4000
mutant D183G/K302R, hanging drop vapor diffusion method, using 0.1 M imidazole/maleate pH 7.8, 50 mM NaCl, 41 mM ammonium sulfate and 18% (w/v) PEG4000
mutant enzyme K302R, hanging drop vapor diffusion method, using 0.1 M imidazole/maleate pH 7.8, 50 mM NaCl, 41 mM ammonium sulfate and 18% (w/v) PEG4000
UDG alone and bound to uncleaved substrate and product, X-ray diffraction structure determination and analysis, molecular modelling
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enzyme in complex with 5-chlorouracil, microbatch-under-oil method, using 0.15 M potassium bromide, 30%(w/v) polyethylene glycol monomethyl ether 2000
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enzyme in complex with 5-fluorouracil, microbatch-under-oil method, using 0.2 M sodium acetate trihydrate, 0.1 MTris-HCl pH 8.5, 30%(w/v) PEG 4000, 4%(v/v) 1,3-butanediol
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enzyme in complex with uracil or 5-nitrouracil, microbatch-under-oil method, using 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 30%(w/v) PEG 8000, 5%(v/v) Jeffamine M-600 pH 7.0
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enzyme in complex with uracil, microbatch-under-oil method, using 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate pH 4.6, 30%(w/v) PEG 4000, 4%(v/v) 1,1,1,3,3,3-hexafluoro-2-propanol
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native enzyme and enzyme in complex with 2-thiouracil, microbatch-under-oil method, using 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 30%(w/v) PEG 4000
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native enzyme and enzyme in complex with 5-fluorouracil, 5-nitrouracil, 5-aminouracil or 6-aminouracil, microbatch-under-oil method, using 1.6 M sodium citrate tribasic dihydrate pH 6.5
-
free enzyme and in complex with uracil
sitting-drop vapour diffusion method, deletion mutant enzyme and deletion mutant enzyme complexed with uracil are crystallized and analyzed by X-ray crystallography. The crystals are found to belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 52.2, b = 52.3, c = 74.7 A and a = 52.1, b = 52.2, c = 74.1 A for the apoenzyme and the enzyme complexed with uracil, respectively
family 4 UDG in complex with uracil, hanging drop vapor diffusion method, mixing of 0.002 ml of 13 mg/ml of selenomethionyl protein solution with 0.002 ml of 1.2-1.5 M ammonium sulfate, 25% v/v glycerol, and 75 mM Tris-HCl, pH 8.5, and equilibration against 0.3 ml of the reservoir solution at 4°C, X-ray diffraction structure determination and analysis at 1.5 A resolution
Q7WYV4
recombinant family 5 UDGB, as free protein or selenomethionine-labeled protein, or in complex with rAP-G DNA and rAP-A DNA, hanging drop vapor diffusion method, 0.001 ml drops of 11 mg/ml TtUDGB are mixed with 0.001 ml of 9-13% v/v PEG 3350, 0.2 M ammonium acetate, 5% v/v glycerol and 0.1 M MES, pH 6.5, and equilibrated against 0.5 ml of the reservoir solution at 20°C. X-ray diffraction structure determination and analysis at 1.45-2.1 A resolution, molecular replacement
in complex with a 10-merDN Aduplex containing an abasic site resulting from the cleavage of a uracil base, hanging drop vapor diffusion method, using 0.1 M Bicine, pH 8.7, 1.5 M ammonium sulfate, 0.2 M ammonium chloride, and 10% (w/v) PEG 3350
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in complex with an undamaged double stranded DNA, hanging drop vapor diffusion method, using 16 % PEG6K, 0.08 M Tris buffer, pH 8.5, and 20% (v/v) glycerol
mutant enzymes R167A, E171G/S172G/P173G, and DELTAE171/DELTAS172, hanging drop vapor diffusion method, using of 0.6-1.0 M ammonium sulfate, 0.1 M HEPES buffer pH 7.4, 10% (v/v) glycerol or 16% (w/v) PEG 3350, 0.15 M potassium fluoride, 10% (v/v) glycerol, or 2.0 M lithium sulfate in 50 mM MES buffer pH 5.6, 5 mM magnesium chloride, 5% (v/v) ethylene glycol
purified recombinant thrombin-cleaved, detagged enzyme, crystallization in two different conditions, condition 1: 5% PEG 6000, 7.5% MPD, 0.1 M HEPES, pH 7.25, at 4°C; condition 2: 5% PEG 3000, 0.1 M NaCl, 0.1 M HEPES, pH 7.5, at 4°C, 1-3 days, or protein purified in the one-step procedure, crystallized by hanging-drop vapor diffusion, pH 7.3, 100 mM HEPES buffer, pH 7.25, 12% glycerol, and 1.5 M ammonium sulfate as precipitant, improvement of crystallization by microseeding, X-ray diffraction structure determination and analysis at 2.4 A resolution, heavy atom labeling and molecular replacement, modelling
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purified recombinant His-tagged enzyme, hanging drop vapour diffusion, mixing of 0.001 ml of protein solution containing 15 mg/ml protein in 50 mM Tris-HCl, pH 7.5, and 5 mM 2-mercaptoethanol, with 0.001 ml of reservoir solution containing 50 mM Na MES, pH 6.0, and 28% w/v PEG 3350, equilibration against a reservoir containing 1.0 ml precipitant solution, room temperature, 1 week, X-ray diffraction structure determination and analysis at 1.5 A resolution, modelling