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Literature summary for 3.6.1.13 extracted from

  • Ooga, T.; Yoshiba, S.; Nakagawa, N.; Kuramitsu, S.; Masui, R.
    Molecular mechanism of the Thermus thermophilus ADP-ribose pyrophosphatase from mutational and kinetic studies (2005), Biochemistry, 44, 9320-9329.
    View publication on PubMed
Search for more literature for 3.6.1.13

Crystallization (Commentary)

Crystallization (Comment) Organism
-
 Thermus thermophilus

Protein Variants

Protein Variants Comment Organism
E108Q kcat/Km is 9.6fold lower than wild-type value Thermus thermophilus
E63Q kcat/Km is 173fold lower than wild-type value Thermus thermophilus
E70Q kcat/Km is 8.9fold lower than wild-type value Thermus thermophilus
E73Q kcat/Km is 1.8fold lower than wild-type value Thermus thermophilus
E82Q kcat/Km is 118171fold lower than wild-type value Thermus thermophilus
E85Q kcat/Km is 3.8fold lower than wild-type value Thermus thermophilus
E86Q kcat/Km is 6722fold lower than wild-type value Thermus thermophilus
H33A kcat/Km is 10fold lower than wild-type value Thermus thermophilus
I19A kcat/Km is 22fold lower than wild-type value Thermus thermophilus
L68A kcat/Km is 5.3fold lower than wild-type value Thermus thermophilus
Q52A kcat/Km is 3.5fold lower than wild-type value Thermus thermophilus
R18Q kcat/Km is 1.5fold higher than wild-type value Thermus thermophilus
R27Q kcat/Km is 1.04fold lower than wild-type value Thermus thermophilus
R54Q kcat/Km is 1589fold lower than wild-type value Thermus thermophilus
R81Q kcat/Km is 77fold lower than wild-type value Thermus thermophilus
S102A kcat/Km is 28.3fold lower than wild-type value Thermus thermophilus
S153A kcat/Km is 2.9fold lower than wild-type value Thermus thermophilus
T110A kcat/Km is 2.3fold lower than wild-type value Thermus thermophilus
T155A kcat/Km is 1.9fold lower than wild-type value Thermus thermophilus
Y28Q kcat/Km is 4fold lower than wild-type value Thermus thermophilus
Y99F kcat/Km is 2.6fold lower than wild-type value Thermus thermophilus

Inhibitors

Inhibitors Comment Organism Structure
fluoride mixed inhibition mechanism Thermus thermophilus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.018
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E70Q Thermus thermophilus
0.027
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R81Q Thermus thermophilus
0.036
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E73Q Thermus thermophilus
0.043
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E85Q Thermus thermophilus
0.05
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme T155A Thermus thermophilus
0.06
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme T110A Thermus thermophilus
0.09
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme Y99F Thermus thermophilus
0.1
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E86Q Thermus thermophilus
0.1
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme S153A Thermus thermophilus
0.11
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E82Q Thermus thermophilus
0.11
-
 ADP-ribose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus
0.12
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R18Q Thermus thermophilus
0.14
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R27Q Thermus thermophilus
0.24
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme Q52A Thermus thermophilus
0.29
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E108Q Thermus thermophilus
0.31
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme L68A Thermus thermophilus
0.4
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E63Q Thermus thermophilus
0.4
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme Y28Q Thermus thermophilus
0.42
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme H33A Thermus thermophilus
0.65
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R54Q Thermus thermophilus
0.69
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme S102A Thermus thermophilus
1.1
-
 GDP-ribose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus
1.24
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme I19A Thermus thermophilus
1.36
-
 CDP-ribose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus
3.16
-
 ADP-glucose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus

Organism

Organism UniProt Comment Textmining
Thermus thermophilus
-
-
-

Purification (Commentary)

Purification (Comment) Organism
-
 Thermus thermophilus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ADP-glucose + H2O kcat/Km is 3% of the kcat/Km for ADP-ribose Thermus thermophilus AMP + alpha-D-glucose 1-phosphate
-
 ?
ADP-ribose + H2O interactions responsible for the substrate recognition are located at the terminal moieties of the substrate. The adenine moiety is recognized by Ile-19 and the main chain carbonyl group of Glu-29 and/or Gly-104. The terminal ribose moiety is recognized by the sum of some weak interactions with multiple residues that are close in space. Glu-82 and Glu-86 are essential for catalysis but unlikely to act as a catalytic base. Two-metal ion mechanism for the catalysis of ADPRase in which a water molecule is activated to act as a nucleophile by the cations coordinated by Glu-82 and Glu-86. Arg-54, Glu-70, Arg-81, and Glu-85 are predicted to support this nucleophilic attack on the R-phosphate of the substrate Thermus thermophilus AMP + D-ribose 5-phosphate
-
 ?
CDP-ribose + H2O kcat/Km is 2.5% of the kcat/Km for ADP-ribose Thermus thermophilus CMP + D-ribose 5-phosphate
-
 ?
GDP-ribose + H2O kcat/Km is 3% of the kcat/Km for ADP-ribose Thermus thermophilus GMP + D-ribose 5-phosphate
-
 ?

Synonyms

Synonyms Comment Organism
ADP-ribose pyrophosphatase
-
 Thermus thermophilus
ADPRase
-
 Thermus thermophilus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
additional information
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme I19A Thermus thermophilus
0.000939
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E82Q Thermus thermophilus
0.00153
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E86Q Thermus thermophilus
0.035
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R81Q Thermus thermophilus
0.0411
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R54Q Thermus thermophilus
0.052 2.1 ADP-ribose 25°C, pH 7.6, mutant enzyme Y28Q Thermus thermophilus
0.057 0.65 ADP-ribose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus
0.23
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E63Q Thermus thermophilus
0.41
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E70Q Thermus thermophilus
0.97
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R18Q Thermus thermophilus
1.12
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E85Q Thermus thermophilus
2.07
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E73Q Thermus thermophilus
2.42
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme T155A Thermus thermophilus
2.43
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme S102A Thermus thermophilus
2.65
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme T110A Thermus thermophilus
2.97
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme E108Q Thermus thermophilus
3.3
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme S153A Thermus thermophilus
3.32
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme Y99F Thermus thermophilus
3.36
-
 CDP-ribose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus
3.57
-
 GDP-ribose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus
4.16
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme H33A Thermus thermophilus
5.68
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme I19A Thermus thermophilus
5.93
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme L68A Thermus thermophilus
6.74
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme Q52A Thermus thermophilus
9.1
-
 ADP-glucose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus
10.04
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme Y28Q Thermus thermophilus
10.65
-
 ADP-ribose 25°C, pH 7.6, wild-type enzyme Thermus thermophilus
12.9
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R27Q Thermus thermophilus
17.05
-
 ADP-ribose 25°C, pH 7.6, mutant enzyme R18Q Thermus thermophilus

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.015
-
 fluoride 25°C, pH 7.6, Ki(2), Ki(1) is 0.15 mM Thermus thermophilus
0.15
-
 fluoride 25°C, pH 7.6, Ki(1), Ki(2) is 0.015 mM Thermus thermophilus