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Information on EC 3.2.2.27 - uracil-DNA glycosylase
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3.2.2.27 uracil-DNA glycosylaseIUBMB Comments
Uracil-DNA glycosylases are widespread enzymes that are found in all living organisms. EC 3.2.2.27 and double-stranded uracil-DNA glycosylase (EC 3.2.2.28) form a central part of the DNA-repair machinery since they initiate the DNA base-excision repair pathway by hydrolysing the N-glycosidic bond between uracil and the deoxyribose sugar thereby catalysing the removal of mis-incorporated uracil from DNA.
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Word Map
- 3.2.2.27
-
deamination
- cytosine
- glycosylases
- endonuclease
- thymine
-
abasic
-
misincorporation
- ung2
-
uracil-containing
- duplex
-
hypermutation
- dump
- deoxyuridine
-
activation-induced
-
excises
- mispairs
-
base-excision
- dutpase
- 8-oxoguanine
-
apyrimidinic
- 5-methylcytosine
- 5-hydroxymethyluracil
-
g-quadruplexes
-
transversions
- ape1
-
thymine-dna
- formamidopyrimidine
- 5-hydroxyuracil
-
short-patch
- xrcc1
-
apurinic
-
class-switching
- 3,n4-ethenocytosine
-
translesion
-
post-replicative
- ap-endonuclease
-
aid-induced
- apobec3g
- drug development
- molecular biology
- analysis
- medicine
The enzyme appears in viruses and cellular organisms
Reaction Schemes
Hydrolyses single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Synonyms
uracil-dna glycosylase, smug1, dna n-glycosylase, ung-1, ul114, uracil dna-glycosylase, uracil-dna n-glycosylase, uracil dna glycosylase 2, thd1p, mjudg, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
SYSTEMATIC NAME
IUBMB Comments
uracil-DNA deoxyribohydrolase (uracil-releasing)
Uracil-DNA glycosylases are widespread enzymes that are found in all living organisms. EC 3.2.2.27 and double-stranded uracil-DNA glycosylase (EC 3.2.2.28) form a central part of the DNA-repair machinery since they initiate the DNA base-excision repair pathway by hydrolysing the N-glycosidic bond between uracil and the deoxyribose sugar thereby catalysing the removal of mis-incorporated uracil from DNA.
CAS REGISTRY NUMBER
COMMENTARY
59088-21-0
cf. EC 3.2.2.28
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
M6-FAM-labeled single stranded oligonucleotide + H2O
uracil + ?
T12-AGUA-T12
-
-
?
uracil-containing calf thymus DNA + H2O
uracil + calf thymus DNA with abasic site
-
-
-
?
uracil-mismatched single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
-
-
-
?
uracil-containing single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
-
-
-
?
uracil-containing single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
isoform UNG1, which in contrast to isoform UNG2 lacks a PCNA-binding motif, may be specialized to act on single stranded DNA (ssDNA) through its ability to bind ssDNA-binding protein RPA
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
-
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
uracil-mismatched single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
-
-
-
?
uracil-containing single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
-
-
-
?
uracil-containing single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
isoform UNG1, which in contrast to isoform UNG2 lacks a PCNA-binding motif, may be specialized to act on single stranded DNA (ssDNA) through its ability to bind ssDNA-binding protein RPA
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
-
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
-
-
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
DNA containing 1'-cyano-2'-deoxyuridine
CNdU, a UDG inhibitor whose respective nucleotide triphosphate is also a substrate for DNA polymerase
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00157
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 37°C
-
0.0021
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 37°C
-
0.0022
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 15°C
-
0.00226
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 15°C
-
0.00238
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 15°C
-
0.0024
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 22°C
-
0.00265
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 37°C
-
0.00276
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 22°C
-
0.00277
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 22°C
-
0.00157
uracil-mismatched single-stranded DNA
mutant enzyme G183G, at pH 7.4 and 37°C
-
0.0021
uracil-mismatched single-stranded DNA
wild type enzyme, at pH 7.4 and 37°C
-
0.0022
uracil-mismatched single-stranded DNA
wild type enzyme, at pH 7.5 and 15°C
-
0.00265
uracil-mismatched single-stranded DNA
mutant enzyme G183G/K302R, at pH 7.4 and 37°C
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.45
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 15°C
-
1.65
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 15°C
-
2.37
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 15°C
-
4.07
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 22°C
-
4.55
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 22°C
-
5.33
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 22°C
-
7.73
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 37°C
-
10.78
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 37°C
-
16.85
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 37°C
-
2.4
uracil-mismatched single-stranded DNA
wild type enzyme, at pH 7.5 and 15°C
-
7.7
uracil-mismatched single-stranded DNA
mutant enzyme G183G, at pH 7.5 and 37°C
-
10.8
uracil-mismatched single-stranded DNA
wild type enzyme, at pH 7.5 and 37°C
-
16.9
uracil-mismatched single-stranded DNA
mutant enzyme G183G/K302R, at pH 7.5 and 37°C
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00065
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 15°C
-
0.0007
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 15°C
-
0.0011
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 15°C
-
0.00147
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 22°C
-
0.00163
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 22°C
-
0.00225
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 22°C
-
0.0052
uracil-containing calf thymus DNA
wild type enzyme, at pH 7.5 and 37°C
-
0.0064
uracil-containing calf thymus DNA
mutant enzyme D183G/K302R, at pH 7.5 and 37°C
-
0.06
uracil-containing calf thymus DNA
mutant enzyme D183G, at pH 7.5 and 37°C
-
1100
uracil-mismatched single-stranded DNA
wild type enzyme, at pH 7.5 and 15°C
-
4917
uracil-mismatched single-stranded DNA
mutant enzyme G183G, at pH 7.4 and 37°C
-
5150
uracil-mismatched single-stranded DNA
wild type enzyme, at pH 7.4 and 37°C
-
6367
uracil-mismatched single-stranded DNA
mutant enzyme G183G/K302R, at pH 7.4 and 37°C
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
isoform UNG1 supports antibody class switching and repairs genomic uracil in the cell nucleus
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). UNG_HUMAN
313
0
34645
Swiss-Prot
Mitochondrion (Reliability: 3)
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
structure of wild-type enzyme in complex with DNA, modelling, overview
additional information
-
structure of wild-type enzyme in complex with DNA, modelling, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with a bacteriophage encoded natural inhibitor, hanging drop vapor diffusion method, using 0.1 M TrisHCl 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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D183G
D183G/K302R
R276X
mutations at Arg276 transform uracil-DNA glycosylase into a single-stranded DNA-specific uracil-DNA glycosylase. The kcat of the R276 mutants is comparable to wild-type UNG on single-stranded DNA and differentially affected by NaCl, however, kcat on double-stranded DNA substrate is reduced 4-12-fold and decreases sharply at NaCl concentrations as low as 20 mM, the mutant proteins exhibit a 2.6 to 7.7fold reduction in affinity for a doubled-stranded oligonucleotide containing a pseudouracil residue opposite 2-aminopurine compared to the wild-type UNG
D183G
the mutant shows a slight increase in stability with concomitant reduction in the enzyme activity
D183G
-
the mutant shows a slight increase in stability with concomitant reduction in the enzyme activity
D183G/K302R
the mutant shows a slight increase in stability with concomitant reduction in the enzyme activity
D183G/K302R
-
the mutant shows a slight increase in stability with concomitant reduction in the enzyme activity
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
53.9
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
HEPES pH 7.5, Tris pH 7.5, and imidazole pH 8.0 are the most stabilizing buffers
HEPES pH 7.5, Tris pH 7.5, and imidazole pH 8.0 are the most stabilizing buffers for the enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Q-Sepharose column chromatography, SP Sepharose column chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli NR8052 cells
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
fluorescence method for sensitive detection of uracil-DNA glycosylase using TdT-activated Endonuclease IV-assisted hyperbranched signal amplification. The method exhibits high sensitivity with a limit of detection of 0.090 U/ml for pure uracil-DNA glycosylase and shows a dynamic range from 0.1 to 50 U/ml, and can be applied for accurate detection of uracil-DNA glycosylase in HeLa nuclear extract. The method can be used for discrimination of uracil-DNA glycosylase from other DNA glycosylases
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Chen, C.-Y.; Mosbaugh, D.W.; Bennett, S.E.
Mutations at arginine 276 transform human uracil-DNAglycosylase into a single-stranded DNA-specific uracil-DNA glycosylase
DNA Repair
4
793-805
2005
Homo sapiens (P13051), Homo sapiens
Huang, H.; Stivers, J.T.; Greenberg, M.M.
Competitive inhibition of uracil DNA glycosylase by a modified nucleotide whose triphosphate is a substrate for DNA polymerase
J. Am. Chem. Soc.
131
1344-1345
2009
Escherichia coli, Homo sapiens (P13051)
Assefa, N.G.; Niiranen, L.; Johnson, K.A.; Leiros, H.K.; Smalas, A.O.; Willassen, N.P.; Moe, E.
Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi)
Acta Crystallogr. Sect. D
70
2093-2100
2014
Homo sapiens (P13051), Homo sapiens, Gadus morhua (Q9I983), Gadus morhua
Assefa, N.; Niiranen, L.; Willassen, N.; Smals, A.; Moe, E.
Thermal unfolding studies of cold adapted uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). A comparative study with human UNG
Comp. Biochem. Physiol. B
161
60-68
2012
Gadus morhua, Homo sapiens (P13051), Homo sapiens
Franco, D.; Sgrignani, J.; Bussi, G.; Magistrato, A.
Structural role of uracil DNA glycosylase for the recognition of uracil in DNA duplexes. Clues from atomistic simulations
J. Chem. Inf. Model.
53
1371-1387
2013
Homo sapiens (P13051)
Assefa, N. G.; Niiranen, L.; Willassen, N. P.; Smalas, A.; Moe, E.
Thermal unfolding studies of cold adapted uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). A comparative study with human UNG
Comp. Biochem. Physiol. B
161
60-68
2012
Gadus morhua, Homo sapiens (P13051), Homo sapiens
Sarno, A.; Lundbaek, M.; Liabakk, N.B.; Aas, P.A.; Mjelle, R.; Hagen, L.; Sousa, M.M.L.; Krokan, H.E.; Kavli, B.
Uracil-DNA glycosylase UNG1 isoform variant supports class switch recombination and repairs nuclear genomic uracil
Nucleic Acids Res.
47
4569-4585
2019
Mus musculus, Homo sapiens (P13051), Homo sapiens
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