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Literature summary 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.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.2.2.27 gene udg Thermus thermophilus

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.2.2.27 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

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

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.2.2.27 additional information
-
 additional information kinetic analysis Thermus thermophilus
3.2.2.27 0.001
-
 uracil-mismatched single-stranded DNA pH 7.5, 37°C, family 4 UDG Thermus thermophilus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.2.2.27 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)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.2.2.27 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 ?
-
 ?
3.2.2.27 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 ?
-
 ?
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
-
 ?
3.2.2.27 uracil-mismatched single-stranded DNA + H2O Thermus thermophilus
-
 uracil + single-stranded DNA with abasic site
-
 ?
3.2.2.27 uracil-mismatched single-stranded DNA + H2O Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
 uracil + single-stranded DNA with abasic site
-
 ?

Organism

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

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 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)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.2.2.27 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 ?
-
 ?
3.2.2.27 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 ?
-
 ?
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 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
-
 ?
3.2.2.27 uracil-mismatched double-stranded DNA + H2O
-
 Thermus thermophilus HB8 / ATCC 27634 / DSM 579 uracil + double-stranded DNA with abasic site
-
 ?
3.2.2.27 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
-
 ?
3.2.2.27 uracil-mismatched single-stranded DNA + H2O
-
 Thermus thermophilus uracil + single-stranded DNA with abasic site
-
 ?
3.2.2.27 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
-
 ?
3.2.2.27 uracil-mismatched single-stranded DNA + H2O
-
 Thermus thermophilus HB8 / ATCC 27634 / DSM 579 uracil + single-stranded DNA with abasic site
-
 ?
3.2.2.27 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

EC Number Subunits Comment Organism
3.2.2.27 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

EC Number Synonyms Comment Organism
3.2.2.27 More the enzyme belongs to the UDG family 4 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

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.2.2.27 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]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.2.2.27 0.17
-
 uracil-mismatched single-stranded DNA pH 7.5, 37°C, family 4 UDG Thermus thermophilus

pH Optimum

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

IC50 Value

EC Number IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
3.2.2.27 0.000088
-
 pH 7.5, 37°C, family 4 UDG Thermus thermophilus G-U dsDNA