Literature summary for 3.2.2.27 extracted from

Hoseki, J.; Okamoto, A.; Masui, R.; Shibata, T.; Inoue, Y.; Yokoyama, S.; Kuramitsu, S.
Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8 (2003), J. Mol. Biol., 333, 515-526.

Search for more literature for 3.2.2.27

Cloned(Commentary)

Cloned (Comment)	Organism
gene udg	Thermus thermophilus

Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Thermus thermophilus

Inhibitors

Inhibitors	Comment	Organism	Structure
G-U dsDNA	product inhibition	Thermus thermophilus

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	kinetic analysis	Thermus thermophilus
0.001	-	uracil-mismatched single-stranded DNA	pH 7.5, 37°C, family 4 UDG	Thermus thermophilus

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Fe2+	the UDG possesses a [4Fe-4S] cluster, distant from the active site, which interacts with loop structures and is unessential to the activity but necessary for stabilizing the loop structures	Thermus thermophilus

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
additional information	Thermus thermophilus	UDG is an essential enzyme for maintaining the integrity of genomic information, it is the first enzyme of a base excision repair, BER, pathway that corrects uracil lesions. TthUDG specifically recognizes uracil that is flipped out from double-stranded DNA, in a manner similar to that of the family 1 human UDG, rather than binding to the guanine base of the complementary strand in mismatched DNA, as does the family 2 Escherichia coli MUG	?	-	?
additional information	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	UDG is an essential enzyme for maintaining the integrity of genomic information, it is the first enzyme of a base excision repair, BER, pathway that corrects uracil lesions. TthUDG specifically recognizes uracil that is flipped out from double-stranded DNA, in a manner similar to that of the family 1 human UDG, rather than binding to the guanine base of the complementary strand in mismatched DNA, as does the family 2 Escherichia coli MUG	?	-	?
uracil-mismatched double-stranded DNA + H2O	Thermus thermophilus	-	uracil + double-stranded DNA with abasic site	-	?
uracil-mismatched double-stranded DNA + H2O	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	-	uracil + double-stranded DNA with abasic site	-	?
uracil-mismatched single-stranded DNA + H2O	Thermus thermophilus	-	uracil + single-stranded DNA with abasic site	-	?
uracil-mismatched single-stranded DNA + H2O	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	-	uracil + single-stranded DNA with abasic site	-	?

Organism

Organism	UniProt	Comment	Textmining
Thermus thermophilus	Q7WYV4	gene udg	-
Thermus thermophilus HB8 / ATCC 27634 / DSM 579	Q7WYV4	gene udg	-

Reaction

Reaction	Comment	Organism	Reaction ID
Hydrolyses single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil	catalytic reaction mechanism, the active side comprises the GEGPG motif, residues 40-44, the side-chain of Arg161 in family 4 TthUDG might play a role in binding AP-DNA after catalysis	Thermus thermophilus	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	UDG is an essential enzyme for maintaining the integrity of genomic information, it is the first enzyme of a base excision repair, BER, pathway that corrects uracil lesions. TthUDG specifically recognizes uracil that is flipped out from double-stranded DNA, in a manner similar to that of the family 1 human UDG, rather than binding to the guanine base of the complementary strand in mismatched DNA, as does the family 2 Escherichia coli MUG	Thermus thermophilus	?	-	?
additional information	UDG is an essential enzyme for maintaining the integrity of genomic information, it is the first enzyme of a base excision repair, BER, pathway that corrects uracil lesions. TthUDG specifically recognizes uracil that is flipped out from double-stranded DNA, in a manner similar to that of the family 1 human UDG, rather than binding to the guanine base of the complementary strand in mismatched DNA, as does the family 2 Escherichia coli MUG	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	?	-	?
uracil-mismatched double-stranded DNA + H2O	-	Thermus thermophilus	uracil + double-stranded DNA with abasic site	-	?
uracil-mismatched double-stranded DNA + H2O	UDG removes uracil from DNA to initiate DNA base excision repair, Thermus thermophilus UDG processes both single-stranded and double-stranded DNA containing uracil, regardless of opposing base, but does not process G-T mismatched DNA, nor does it possess AP endonuclease activity, uracil bases in U-A mismatches are excised less efficiently, due to the stability of that particular base-pair. The UDG possesses a [4Fe-4S] cluster, distant from the active site, which interacts with loop structures and is unessential to the activity but necessary for stabilizing the loop structures. Uracil recognition mechanism, overview	Thermus thermophilus	uracil + double-stranded DNA with abasic site	-	?
uracil-mismatched double-stranded DNA + H2O	-	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	uracil + double-stranded DNA with abasic site	-	?
uracil-mismatched double-stranded DNA + H2O	UDG removes uracil from DNA to initiate DNA base excision repair, Thermus thermophilus UDG processes both single-stranded and double-stranded DNA containing uracil, regardless of opposing base, but does not process G-T mismatched DNA, nor does it possess AP endonuclease activity, uracil bases in U-A mismatches are excised less efficiently, due to the stability of that particular base-pair. The UDG possesses a [4Fe-4S] cluster, distant from the active site, which interacts with loop structures and is unessential to the activity but necessary for stabilizing the loop structures. Uracil recognition mechanism, overview	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	uracil + double-stranded DNA with abasic site	-	?
uracil-mismatched single-stranded DNA + H2O	-	Thermus thermophilus	uracil + single-stranded DNA with abasic site	-	?
uracil-mismatched single-stranded DNA + H2O	UDG removes uracil from DNA to initiate DNA base excision repair, Thermus thermophilus UDG processes both single-stranded and double-stranded DNA containing uracil, regardless of opposing base, but does not process G-T mismatched DNA, nor does it possess AP endonuclease activity, uracil bases in U-A mismatches are excised less efficiently, due to the stability of that particular base-pair. The UDG possesses a [4Fe-4S] cluster, distant from the active site, which interacts with loop structures and is unessential to the activity but necessary for stabilizing the loop structures. Uracil recognition mechanism, overview	Thermus thermophilus	uracil + single-stranded DNA with abasic site	-	?
uracil-mismatched single-stranded DNA + H2O	-	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	uracil + single-stranded DNA with abasic site	-	?
uracil-mismatched single-stranded DNA + H2O	UDG removes uracil from DNA to initiate DNA base excision repair, Thermus thermophilus UDG processes both single-stranded and double-stranded DNA containing uracil, regardless of opposing base, but does not process G-T mismatched DNA, nor does it possess AP endonuclease activity, uracil bases in U-A mismatches are excised less efficiently, due to the stability of that particular base-pair. The UDG possesses a [4Fe-4S] cluster, distant from the active site, which interacts with loop structures and is unessential to the activity but necessary for stabilizing the loop structures. Uracil recognition mechanism, overview	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	uracil + single-stranded DNA with abasic site	-	?

Subunits

Subunits	Comment	Organism
More	the UDG possesses a [4Fe-4S] cluster, distant from the active site, which interacts with loop structures and is unessential to the activity but necessary for stabilizing the loop structures, salt-bridges and ion pairs on the molecular surface and the presence of proline on loops and turns contribute to the enzyme's thermostability	Thermus thermophilus

Synonyms

Synonyms	Comment	Organism
More	the enzyme belongs to the UDG family 4	Thermus thermophilus
UDG	-	Thermus thermophilus

Temperature Optimum [°C]

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

Temperature Stability [°C]

Temperature Stability Minimum [°C]	Temperature Stability Maximum [°C]	Comment	Organism
additional information	-	salt-bridges and ion pairs on the molecular surface and the presence of proline on loops and turns contribute to the enzyme's thermostability	Thermus thermophilus

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.17	-	uracil-mismatched single-stranded DNA	pH 7.5, 37°C, family 4 UDG	Thermus thermophilus

pH Optimum

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

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor	Structure
0.000088	-	pH 7.5, 37°C, family 4 UDG	Thermus thermophilus	G-U dsDNA

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Release 2023.1 (January 2023)