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Information on EC 3.2.2.27 - uracil-DNA glycosylase and Organism(s) Deinococcus radiodurans and UniProt Accession Q9RWH9
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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 taxonomic range for the selected organisms is: Deinococcus radiodurans
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected 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
additional information
three MUGs form a distintc MUG/thymidine-DNA glycosylase subfamily, called the MUG2 family
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Hydrolyses single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Hydrolyses single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
catalytic reaction mechanism, the catalytic residue is Asp93
Hydrolyses single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
uracil-DNA glycosylases are widespread enzymes that are found in all living organisms. UDGs 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
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
uracil-containing single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
-
-
-
?
uracil-mismatched 16 nt double-stranded DNA + H2O
uracil + 16 nt double-stranded DNA with abasic site
5'-CCTGTCCAUGTCTCCG-3'
-
-
?
uracil-mismatched single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
single-stranded DNA containing uracil labeled with fluorescein in the 5'-end, sequence overview. Determination of kinetics using commercially available nick-translated calf thymus DNA with deoxy[5-3H]uridine 5'-triphosphate as substrate. To perform efficient glycoside bond cleavage, drMUG must stabilize the mismatched uracil in the specificity pocket, nucleotide stabilization by Tyr46, substrate binding mechanism, overview. Binding of thymine in the activity pocket is probably prevented by Ser36 and Ser39 in MUG, binding of cytosine is prevented by Asp84
-
-
?
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
the enzyme removes uracil from DNA, which can occur by misincorporation of dUMP in place of dTMP during DNA synthesis or by deamination of cytosine, resulting in U-A or U-G mispairs
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
30-bp dsDNA oligonucleotide substrates containing G-C, G-U, G-T, and A-U base pairs. Determination of kinetics using commercially available nick-translated calf thymus DNA with deoxy[5-3H]uridine 5'-triphosphate as substrate. To perform efficient glycoside bond cleavage, drMUG must stabilize the mismatched uracil in the specificity pocket, nucleotide stabilization by Tyr46, substrate binding mechanism, overview. Binding of thymine in the activity pocket is probably prevented by Ser36 and Ser39 in MUG, binding of cytosine is prevented by Asp84
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
drUNG is able to excise uracil from both U-A and U-G double-stranded DNA and single-stranded DNA, substrate is commercially available nick-translated calf thymus DNA with deoxy[5-3H]uridine 5'-triphosphate: DNA binding, the active-site environment, and uracil specificity, structure-activity relationship, overview
-
-
?
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-containing single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
-
-
-
?
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
the enzyme removes uracil from DNA, which can occur by misincorporation of dUMP in place of dTMP during DNA synthesis or by deamination of cytosine, resulting in U-A or U-G mispairs
-
-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0007
uracil-mismatched double-stranded DNA
pH 8.0, 37°C, recombinant enzyme
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
15.58
uracil-mismatched double-stranded DNA
pH 8.0, 37°C, recombinant enzyme
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
type 1 UNG structure analysis and comparison with the human and Escherichia coli enzymes, structure-activity relationship, overview
additional information
-
type 1 UNG structure analysis and comparison with the human and Escherichia coli enzymes, structure-activity relationship, overview
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HisTrap column chromatography and Q Sepharose column chromatography
recombinant His-tagged UNG type 1 from Escherichia coli strain BL21(DE3) by affinity chromatography
recombinant wild-type and mutant enzymes from Escherichia coli strain Bl21(DE3)
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene dr0689, expression of His-tagged UNG type 1 in Escherichia coli strain BL21(DE3)
MUG, DNA and amino acid sequence determination and analysis, phylogenetic analysis, expression of wild-type and mutant enzymes in Escherichia coli strain Bl21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Leiros, I.; Moe, E.; Smala, A.O.; McSweeney, S.
Structure of the uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans
Acta Crystallogr. Sect. D
D61
1049-1056
2005
Deinococcus radiodurans (Q9RWH9), Deinococcus radiodurans
Moe, E.; Leiros, I.; Smalas, A.O.; McSweeney, S.
The crystal structure of mismatch-specific uracil-DNA glycosylase (MUG) from Deinococcus radiodurans reveals a novel catalytic residue and broad substrate specificity
J. Biol. Chem.
281
569-577
2006
Deinococcus radiodurans (Q9RWH9), Deinococcus radiodurans
Pedersen, H.L.; Johnson, K.A.; McVey, C.E.; Leiros, I.; Moe, E.
Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA
Acta Crystallogr. Sect. D
71
2137-2149
2015
Deinococcus radiodurans (Q9RWH9), Deinococcus radiodurans, Deinococcus radiodurans ATCC 13939 (Q9RWH9)
EXTERNAL LINKS (specific for EC-Number 3.2.2.27)
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