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Information on EC 3.2.2.27 - uracil-DNA glycosylase and Organism(s) Pyrobaculum aerophilum and UniProt Accession Q8ZYS2
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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: Pyrobaculum aerophilum
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
additional information
the UDG from Pyrobaculum aerophilum represents the fifth UDG family
additional information
cf. EC 3.2.2.15, the UDGb from Pyrobaculum aerophilum represents a fifth UDG family
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-mismatched single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
-
-
-
?
5-fluorouracil-mismatched double-stranded DNA + H2O
5-fluorouracil + double-stranded DNA with abasic site
UDGb is active on 5-fluorouracil-G pairs
-
-
?
5-hydroxymethyl-uracil-mismatched double-stranded DNA + H2O
5-hydroxymethyl-uracil + double-stranded DNA with abasic site
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates
-
-
?
5-hydroxymethyl-uracil-mismatched single-stranded DNA + H2O
5-hydroxymethyl-uracil + single-stranded DNA with abasic site
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates
-
-
?
ethenocytosine-mismatched double-stranded DNA + H2O
3,N4-ethenocytosine + double-stranded DNA with abasic site
UDGb is active on ethenocytosine-G
-
-
?
hypoxanthine-mismatched double-stranded DNA + H2O
hypoxanthine + double-stranded DNA with abasic site
the UDGb from Pyrobaculum aerophilum, belonging to a fifth UDG family, catalyzes the removal of uracil as well as of hypoxanthine from DNA by cleavage of e.g. hypoxanthine-thymine pairs, possessing an active site, that lacks the polar amino acid residue, see also EC 3.2.2.15, substrate specificity and active site structure, overview
-
-
?
uracil-mismatched single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
UDGs of the four UDG families catalyze the removal of uracil from DNA by flipping it out of the double helix into their binding pockets, where the glycosidic bond is hydrolyzed by a water molecule activated by an aromatic amino acid, while the UDGb from Pyrobaculum aerophilum, belonging to a fifth UDG family, catalyzes the removal of uracil, possessing an active site, that lacks the polar amino acid residue, see also EC 3.2.2.15, substrate specificity and active site structure, overview
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
the highly preferred substrate of UDGa is uracil mispaired with guanine, followed by A-U pairs, no activity with hydroxymethyl-uracil mispaired with guanine, overview
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
UDGs of the four UDG families, uracil-DNA glycosylase including Pyrobaculum aerophilum UDGa, catalyze the removal of uracil from DNA by flipping it out of the double helix into their binding pockets, where the glycosidic bond is hydrolyzed by a water molecule activated by an aromatic amino acid, while the UDGb from Pyrobaculum aerophilum, belonging to a fifth UDG family, also catalyzes the removal of hypoxanthine from DNA possessing an active site, that lacks the polar amino acid residue, substrate specificity and active site structure, overview
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
uracil residues in G/U mispairs, in A/U pairs. Preference for G/U substrate over A/U substrate and uracil in single-stranded DNA
-
-
?
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
UDGs of the four UDG families catalyze the removal of uracil from DNA by flipping it out of the double helix into their binding pockets, where the glycosidic bond is hydrolyzed by a water molecule activated by an aromatic amino acid, while the UDGb from Pyrobaculum aerophilum, belonging to a fifth UDG family, catalyzes the removal of uracil, possessing an active site, that lacks the polar amino acid residue, see also EC 3.2.2.15, substrate specificity and active site structure, overview
-
-
?
additional information
?
-
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates, no activity on G-T pairs, overview
-
-
?
additional information
?
-
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates, no activity on G-T pairs, overview
-
-
?
additional information
?
-
-
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates, no activity on G-T pairs, 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-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
the highly preferred substrate of UDGa is uracil mispaired with guanine, followed by A-U pairs, no activity with hydroxymethyl-uracil mispaired with guanine, overview
-
-
?
5-fluorouracil-mismatched double-stranded DNA + H2O
5-fluorouracil + double-stranded DNA with abasic site
UDGb is active on 5-fluorouracil-G pairs
-
-
?
5-hydroxymethyl-uracil-mismatched double-stranded DNA + H2O
5-hydroxymethyl-uracil + double-stranded DNA with abasic site
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates
-
-
?
5-hydroxymethyl-uracil-mismatched single-stranded DNA + H2O
5-hydroxymethyl-uracil + single-stranded DNA with abasic site
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates
-
-
?
ethenocytosine-mismatched double-stranded DNA + H2O
3,N4-ethenocytosine + double-stranded DNA with abasic site
UDGb is active on ethenocytosine-G
-
-
?
hypoxanthine-mismatched double-stranded DNA + H2O
hypoxanthine + double-stranded DNA with abasic site
the UDGb from Pyrobaculum aerophilum, belonging to a fifth UDG family, catalyzes the removal of uracil as well as of hypoxanthine from DNA by cleavage of e.g. hypoxanthine-thymine pairs, possessing an active site, that lacks the polar amino acid residue, see also EC 3.2.2.15, substrate specificity and active site structure, overview
-
-
?
uracil-mismatched double-stranded DNA + H2O
uracil + double-stranded DNA with abasic site
-
-
-
?
uracil-mismatched single-stranded DNA + H2O
uracil + single-stranded DNA with abasic site
UDGs of the four UDG families catalyze the removal of uracil from DNA by flipping it out of the double helix into their binding pockets, where the glycosidic bond is hydrolyzed by a water molecule activated by an aromatic amino acid, while the UDGb from Pyrobaculum aerophilum, belonging to a fifth UDG family, catalyzes the removal of uracil, possessing an active site, that lacks the polar amino acid residue, see also EC 3.2.2.15, substrate specificity and active site structure, overview
-
-
?
additional information
?
-
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates, no activity on G-T pairs, overview
-
-
?
additional information
?
-
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates, no activity on G-T pairs, overview
-
-
?
additional information
?
-
-
the preferred substrate of UDGb is hydroxymethyl-uracil mispaired with guanine, followed by G-U and A-U, UDGb is active on ethenocytosine-G and 5-fluorouracil-G pairs, and UDGb also performs processing of uracil and hydroxymethyluracil from single-stranded DNA, but highly prefers double-stranded DNA substrates, no activity on G-T pairs, overview
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
no inhibition by UGD inhibition protein from Bacillus subtilis-peptide
-
additional information
no inhibition by UGD inhibition protein from Bacillus subtilis-peptide
-
additional information
-
no inhibition by UGD inhibition protein from Bacillus subtilis-peptide
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
mutagenesis of motifs A and B strongly attenuates the enzyme activity of UDGb
additional information
mutagenesis of motifs A and B strongly attenuates the enzyme activity of UDGb
additional information
-
mutagenesis of motifs A and B strongly attenuates the enzyme activity of UDGb
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged UDGb from Escherichia coli strain BL21(DE3)
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
UDGb, DNA and amino acid sequence determination and analysis, expression of His6-tagged UDGb in Escherichia coli strain BL21(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Sartori, A.A.; Fitz-Gibbon, S.; Yang, H.; Miller, J.H.; Jiricny, J.
A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site
EMBO J.
21
3182-3191
2002
Pyrobaculum aerophilum (Q8ZXE0), Pyrobaculum aerophilum (Q8ZYS2), Pyrobaculum aerophilum
Sartori, A.A.; Schr, P.; Fitz-Gibbon, S.; Miller, J.H.; Jiricny, J.
Biochemical characterization of uracil processing activities in the hyperthermophilic archaeon Pyrobaculum aerophilum
J. Biol. Chem.
276
29979-29986
2001
Pyrobaculum aerophilum (Q8ZYS2), Pyrobaculum aerophilum, Pyrobaculum aerophilum DSM 7523 (Q8ZYS2)
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