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Literature summary for 3.6.1.61 extracted from
- The Nudix hydrolase Ndx1 from Thermus thermophilus HB8 is a diadenosine hexaphosphate hydrolase with a novel activity (2004), J. Biol. Chem., 279, 21732-21739.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| overexpressed in Escherichia coli | Thermus thermophilus |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| E46Q | 2200fold reduction in kcat | Thermus thermophilus |
| E49Q | mutation has very little effect on activity | Thermus thermophilus |
| E50Q | 130000fold reduction in kcat | Thermus thermophilus |
| W26S | no decrease in fluorescence intensity upon the addition of ATP | Thermus thermophilus |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| ATP | - |
Thermus thermophilus |  |
| dATP | - |
Thermus thermophilus | |
| fluoride | non-competitive inhibition | Thermus thermophilus | |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0014 | - |
P1,P6-bis(5'-adenosyl)hexaphosphate | pH 7.0, 25°C | Thermus thermophilus | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Co2+ | Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+ | Thermus thermophilus | |
| Mg2+ | Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+ | Thermus thermophilus | |
| Mn2+ | Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+ | Thermus thermophilus | |
| additional information | Ca2+, Ni2+, and Cu2+ are not able to activate Ndx1 | Thermus thermophilus | |
| Zn2+ | Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+ | Thermus thermophilus | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 14170 | - |
1 * 14170, calculated from sequence | Thermus thermophilus |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| P1,P6-bis(5'-adenosyl)hexaphosphate + H2O | Thermus thermophilus | - |
2 ATP | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Thermus thermophilus | Q75UV1 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
- |
Thermus thermophilus |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| P1,P4-bis(5'-adenosyl)tetraphosphate + H2O = ATP + AMP | nucleophilic double, not single, displacement catalytic forward reaction mechanism via oxocarbenium ion intermediate, detailed overview | Thermus thermophilus | |
| P1,P5-bis(5'-adenosyl)pentaphosphate + H2O = ATP + ADP | (2) | Thermus thermophilus | |
| P1,P6-bis(5'-adenosyl)hexaphosphate + H2O = 2 ATP | (1) | Thermus thermophilus |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| P1,P4-bis(5'-adenosyl)tetraphosphate + H2O | - |
Thermus thermophilus | ATP + AMP | - |
? | |
| P1,P5-bis(5'-adenosyl)pentaphosphate + H2O | - |
Thermus thermophilus | ATP + ADP | - |
? | |
| P1,P6-bis(5'-adenosyl)hexaphosphate + H2O | - |
Thermus thermophilus | 2 ATP | - |
? | |
| P1,P6-bis(5'-adenosyl)hexaphosphate + H2O | P1,P6-bis(5'-adenosyl)hexaphosphate is the most preferred substrate. Glu46 and Glu50 are conserved residues in the Nudix motif and are involved in catalysis | Thermus thermophilus | 2 ATP | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| monomer | 1 * 14170, calculated from sequence | Thermus thermophilus |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| Ndx1 | - |
Thermus thermophilus |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 70 | - |
hydrolysis of P1,P6-bis(5'-adenosyl)hexaphosphate | Thermus thermophilus |
Temperature Stability [°C]
| Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 95 | - |
pH 7.5, stable up to | Thermus thermophilus |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 4.1 | - |
P1,P6-bis(5'-adenosyl)hexaphosphate | pH 7.0, 25°C | Thermus thermophilus | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8 | - |
hydrolysis of P1,P6-bis(5'-adenosyl)hexaphosphate | Thermus thermophilus |
pH Stability
| pH Stability | pH Stability Maximum | Comment | Organism |
|---|---|---|---|
| 2 | 12 | 25°C, stable | Thermus thermophilus |
Ki Value [mM]
| Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.013 | - |
ATP | pH 7.0, 25°C | Thermus thermophilus | |
| 0.041 | - |
dATP | pH 7.0, 25°C | Thermus thermophilus | |
| 0.424 | - |
fluoride | pH 7.0, 25°C | Thermus thermophilus | |
pI Value
| Organism | Comment | pI Value Maximum | pI Value |
|---|---|---|---|
| Thermus thermophilus | calculated from sequence | - |
4.8 |
IC50 Value
| IC50 Value | IC50 Value Maximum | Comment | Organism | Inhibitor | Structure |
|---|---|---|---|---|---|
| 0.08 | - |
pH 7.0, 25°C | Thermus thermophilus | fluoride | |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2929 | - |
P1,P6-bis(5'-adenosyl)hexaphosphate | pH 7.0, 25°C | Thermus thermophilus | |
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