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Literature summary extracted from

  • Turgimbayeva, A.; Abeldenov, S.; Zharkov, D.O.; Ishchenko, A.A.; Ramankulov, Y.; Saparbaev, M.; Khassenov, B.
    Characterization of biochemical properties of an apurinic/apyrimidinic endonuclease from Helicobacter pylori (2018), PLoS ONE, 13, e0202232 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.2.99.18 gene xth, DNA and amino acid sequence determination and analysis, phylogenetic analysis, recombinant N-terminally His-tagged enzyme expression in Escherichia coli strains BH110 (DE3) and Rosetta 2 (DE3) Helicobacter pylori

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.2.99.18 Ca2+ higher concentrations of Mn2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage Helicobacter pylori
4.2.99.18 Cu2+ activates at 0.01 mM, inhibits at 0.1 mM Helicobacter pylori
4.2.99.18 Fe2+ activates at 0.01 mM, inhibits at 0.1 mM Helicobacter pylori
4.2.99.18 Mg2+ higher concentrations of Mg2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage Helicobacter pylori
4.2.99.18 Mn2+ higher concentrations of Mn2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage Helicobacter pylori
4.2.99.18 Ni2+ activates at 0.01 mM, inhibits at 0.1 mM Helicobacter pylori
4.2.99.18 Zn2+ activates at 0.01 mM, inhibits at 0.1 mM Helicobacter pylori

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.2.99.18 additional information
-
 additional information steady-state kinetic analysis Helicobacter pylori
4.2.99.18 0.000015
-
 30mer THF-T duplex pH 8.0, 37°C, recombinant His-tagged enzyme Helicobacter pylori

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.2.99.18 Ca2+ presence of 1 or 5 mM Ca2+ causes much less efficient stimulation of HpXth's AP site cleavage activity as compared to Mg2+ or Mn2+ Helicobacter pylori
4.2.99.18 Cu2+ activates at 0.01 mM, inhibits at 0.1 mM Helicobacter pylori
4.2.99.18 Fe2+ activates at 0.01 mM, inhibits at 0.1 mM Helicobacter pylori
4.2.99.18 Mg2+ required, activates, best at 5 mM Helicobacter pylori
4.2.99.18 Mn2+ activates Helicobacter pylori
4.2.99.18 additional information in the presence of 1 or 5 mM Mg2+ or Mn2+, the purified recombinant His-tagged HpXth protein exerts an efficient AP site cleavage activity by generating fast-migrating 10mer cleavage fragments. But higher concentrations of Mg2+ or Mn2+ (10-20 mM) result in a strong decrease in the HpXth-catalyzed AP site cleavage Helicobacter pylori
4.2.99.18 Ni2+ activates at 0.01 mM, inhibits at 0.1 mM Helicobacter pylori
4.2.99.18 Zn2+ activates at 0.01 mM, inhibits at 0.1 mM Helicobacter pylori

Organism

EC Number Organism UniProt Comment Textmining
4.2.99.18 Helicobacter pylori Q9ZJ98 i.e. Campylobacter pylori
-
4.2.99.18 Helicobacter pylori J99 / ATCC 700824 Q9ZJ98 i.e. Campylobacter pylori
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.2.99.18 recombinant His-tagged enzyme from Escherichia coli strain Rosetta 2 (DE3) by nickel affinity chromatography Helicobacter pylori

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.2.99.18 30mer THF-T duplex 5'-[32P]labeled 30mer THF-T duplex Helicobacter pylori ?
-
 ?
4.2.99.18 30mer THF-T duplex 5'-[32P]labeled 30mer THF-T duplex Helicobacter pylori J99 / ATCC 700824 ?
-
 ?
4.2.99.18 31mer oligonucleotide duplex 3'-[alpha-32P]-dAMP-labeled 31mer oligonucleotide duplex Helicobacter pylori ?
-
 ?
4.2.99.18 31mer oligonucleotide duplex 3'-[alpha-32P]-dAMP-labeled 31mer oligonucleotide duplex Helicobacter pylori J99 / ATCC 700824 ?
-
 ?
4.2.99.18 additional information enzyme HpXth removes the AP site, 3'-blocking sugar-phosphate, and 3'-terminal phosphate in DNA strand breaks with good efficiency (kcat/KM = 1.240, 0.044, and 0.0054 mM/min, respectively). In the presence of 1 or 5 mM Mg2+ or Mn2+, the purified recombinant His-tagged HpXth protein exerts an efficient AP site cleavage activity by generating fast-migrating 10mer cleavage fragments. 3'-Repair phosphodiesterase, 3'-phosphatase, and nucleotide incision activities of the HpXth protein, overview Helicobacter pylori ?
-
 ?
4.2.99.18 additional information enzyme HpXth removes the AP site, 3'-blocking sugar-phosphate, and 3'-terminal phosphate in DNA strand breaks with good efficiency (kcat/KM = 1.240, 0.044, and 0.0054 mM/min, respectively). In the presence of 1 or 5 mM Mg2+ or Mn2+, the purified recombinant His-tagged HpXth protein exerts an efficient AP site cleavage activity by generating fast-migrating 10mer cleavage fragments. 3'-Repair phosphodiesterase, 3'-phosphatase, and nucleotide incision activities of the HpXth protein, overview Helicobacter pylori J99 / ATCC 700824 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
4.2.99.18 ? x * 31600, about, His-tagged enzyme, sequence calculation Helicobacter pylori
4.2.99.18 More tryptic enzyme peptide mapping, LC-MS/MS analysis Helicobacter pylori

Synonyms

EC Number Synonyms Comment Organism
4.2.99.18 apurinic/apyrimidinic endonuclease
-
 Helicobacter pylori
4.2.99.18 HpXth
-
 Helicobacter pylori
4.2.99.18 XTH
-
 Helicobacter pylori

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.2.99.18 30
-
-
 Helicobacter pylori

Temperature Range [°C]

EC Number Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
4.2.99.18
-
 80 activity range, profile overview Helicobacter pylori

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.2.99.18 0.308
-
 30mer THF-T duplex pH 8.0, 37°C, recombinant His-tagged enzyme Helicobacter pylori

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.2.99.18 8
-
-
 Helicobacter pylori

pH Range

EC Number pH Minimum pH Maximum Comment Organism
4.2.99.18 6 9 activity range, profile overview Helicobacter pylori

General Information

EC Number General Information Comment Organism
4.2.99.18 malfunction mutation of active site residue D144 in HpXth predicted to be essential for catalysis results in a complete loss of enzyme activities Helicobacter pylori
4.2.99.18 additional information enzyme HpXth homology modeling Helicobacter pylori
4.2.99.18 physiological function apurinic/apyrimidinic (AP) endonucleases play critical roles in the repair of abasic sites and strand breaks in DNA. Helicobacter pylori contains one single AP endonuclease. The DNA substrate specificity of Helicobacter pylori AP endonuclease HpXth counteracts the genotoxic effects of DNA damage generated by endogenous and host-imposed factors. The presence of Helicobacter pylori Xth protein in AP endonuclease-deficient Escherichia coli xth nfo strain significantly reduces the sensitivity to an alkylating agent and H2O2 Helicobacter pylori

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
4.2.99.18 20555
-
 30mer THF-T duplex pH 8.0, 37°C, recombinant His-tagged enzyme Helicobacter pylori