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Literature summary extracted from

  • Kosaka, H.; Hoseki, J.; Nakagawa, N.; Kuramitsu, S.; Masui, R.
    Crystal structure of family 5 uracil-DNA glycosylase bound to DNA (2007), J. Mol. Biol., 373, 839-850.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.2.2.27 gene TtUDGB, expression of wild-type and selenomethionine-labeled enzymes in Escherichia coli strain BL21(DE3) Thermus thermophilus

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.2.2.27 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 Thermus thermophilus

Protein Variants

EC Number Protein Variants Comment Organism
3.2.2.27 D75A the D75A mutant shows low enzymatic activity for the removal of uracil from U-G or thymine from T-G. However, the mutant can distinguish between the C5-hydrogen and the C5-methyl group Thermus thermophilus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.2.2.27 additional information Thermus thermophilus UDG removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. The fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1 to 4 ?
-
?
3.2.2.27 additional information Thermus thermophilus HB8 / ATCC 27634 / DSM 579 UDG removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. The fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1 to 4 ?
-
?
3.2.2.27 uracil-mismatched double-stranded DNA + H2O Thermus thermophilus
-
uracil + double-stranded DNA with abasic site
-
?
3.2.2.27 uracil-mismatched double-stranded DNA + H2O Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
uracil + double-stranded DNA with abasic site
-
?

Organism

EC Number Organism UniProt Comment Textmining
3.2.2.27 Thermus thermophilus Q5SJG5 family 5 UDGB, gene TtUDGB
-
3.2.2.27 Thermus thermophilus HB8 / ATCC 27634 / DSM 579 Q5SJG5 family 5 UDGB, gene TtUDGB
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.2.2.27 recombinant wild-type and selenomethionine-labeled enzymes from Escherichia coli strain BL21(DE3) by hydrophobic interaction and anion exchange chromatography, followed by hydroxyapatite adsorption chromatography and gel filtration Thermus thermophilus

Reaction

EC Number Reaction Comment Organism Reaction ID
3.2.2.27 Hydrolyses single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil a conserved asparagine residue acts as a ligand to the catalytic water molecule, and another water molecule acts as a barrier during substrate recognition, slide-in mechanism for initial damage recognition, catalytic reaction mechanism, overview Thermus thermophilus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.2.2.27 additional information UDG removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. The fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1 to 4 Thermus thermophilus ?
-
?
3.2.2.27 additional information family 5 UDGB in complex with rAP-G DNA and rAP-A DNA, substrate specificity and binding structure analysis, modelling, overview Thermus thermophilus ?
-
?
3.2.2.27 additional information UDG removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. The fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1 to 4 Thermus thermophilus HB8 / ATCC 27634 / DSM 579 ?
-
?
3.2.2.27 additional information family 5 UDGB in complex with rAP-G DNA and rAP-A DNA, substrate specificity and binding structure analysis, modelling, overview Thermus thermophilus HB8 / ATCC 27634 / DSM 579 ?
-
?
3.2.2.27 uracil-mismatched double-stranded DNA + H2O
-
Thermus thermophilus uracil + double-stranded DNA with abasic site
-
?
3.2.2.27 uracil-mismatched double-stranded DNA + H2O
-
Thermus thermophilus HB8 / ATCC 27634 / DSM 579 uracil + double-stranded DNA with abasic site
-
?

Subunits

EC Number Subunits Comment Organism
3.2.2.27 More family 5 UDGB secondary structure elements, overview Thermus thermophilus

Synonyms

EC Number Synonyms Comment Organism
3.2.2.27 More the enzyme is an UDG family 5 enzyme belonging to the UDG superfamily Thermus thermophilus
3.2.2.27 UDG
-
Thermus thermophilus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.2.2.27 37
-
assay at Thermus thermophilus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.2.2.27 7.5
-
assay at Thermus thermophilus