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Literature summary for 1.1.1.361 extracted from
- Simultaneous measurement of glucose-6-phosphate 3-dehydrogenase (NtdC) catalysis and the nonenzymatic reaction of its product kinetics and isotope effects on the first step in kanosamine biosynthesis (2017), Biochemistry, 56, 2001-2009 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| expression in Escherichia coli BL21(DE3) | Bacillus subtilis |
| gene ntdC, recombinant expression in Escherichia coli BL21(DE3) Gold | Bacillus subtilis |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| additional information | 3-dehydro-D-glucose 6-phosphate and L-glutamate do not inhibit the NtdC reaction at concentrations in significant excess of those of the substrates | Bacillus subtilis | |
| NAD+ | - |
Bacillus subtilis |  |
| NADH | competitive product inhibition | Bacillus subtilis | |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | kinetic analysis and mechanism, kinetic isotope effects, overview | Bacillus subtilis | |
| 0.04 | - |
NAD+ | pH 9.5, 25°C | Bacillus subtilis | |
| 0.04 | - |
NAD+ | pH 9.5, 25°C, recombinant enzyme NtdC | Bacillus subtilis | |
| 0.043 | - |
D-glucose 6-phosphate | pH 9.5, 25°C | Bacillus subtilis | |
| 0.043 | - |
D-glucose 6-phosphate | pH 9.5, 25°C, recombinant enzyme NtdC | Bacillus subtilis | |
| 0.045 | - |
D-glucose 6-phosphate | pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA | Bacillus subtilis | |
| 0.047 | - |
NAD+ | pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA | Bacillus subtilis | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-glucose 6-phosphate + NAD+ | Bacillus subtilis | - |
3-dehydro-D-glucose 6-phosphate + NADH + H+ | - |
? | |
| D-glucose 6-phosphate + NAD+ | Bacillus subtilis | the enzyme catalyzes the first step in kanosamine biosynthesis | 3-dehydro-D-glucose 6-phosphate + NADH + H+ | - |
? | |
| D-glucose 6-phosphate + NAD+ | Bacillus subtilis 168 | - |
3-dehydro-D-glucose 6-phosphate + NADH + H+ | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus subtilis | - |
- |
- |
| Bacillus subtilis | O07564 | - |
- |
| Bacillus subtilis 168 | O07564 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
- |
Bacillus subtilis |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| D-glucose 6-phosphate + NAD+ = 3-dehydro-D-glucose 6-phosphate + NADH + H+ | NtdC follows a random sequential mechanism, consistent with our product inhibition. The equilibrium position of the NtdC-catalyzed reaction greatly favors G6P, and the rate of 3-dehydro-D-glucose 6-phosphate formation at neutral pH is very low, under more favorable basic conditions, the product of the reaction is unstable | Bacillus subtilis |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-glucose 6-phosphate + NAD+ | - |
Bacillus subtilis | 3-dehydro-D-glucose 6-phosphate + NADH + H+ | - |
? | |
| D-glucose 6-phosphate + NAD+ | the enzyme catalyzes the first step in kanosamine biosynthesis | Bacillus subtilis | 3-dehydro-D-glucose 6-phosphate + NADH + H+ | - |
? | |
| D-glucose 6-phosphate + NAD+ | the enzyme obeys a random sequential mechanism, with nearly equal Km values for NAD+ and D-glucose 6-phosphate | Bacillus subtilis | 3-dehydro-D-glucose 6-phosphate + NADH + H+ | - |
? | |
| D-glucose 6-phosphate + NAD+ | - |
Bacillus subtilis 168 | 3-dehydro-D-glucose 6-phosphate + NADH + H+ | - |
? | |
| additional information | under alkaline conditions, the product is not stable because of ring opening followed by deprotonation of the 1,3-dicarbonyl compound. Hydride transfer from carbon 3 is partially rate-limiting in the enzymatic reaction, and deuterium substitution on carbon 2 has no significant effect on the enzymatic reaction but lowers the rate of deprotonation of 3-dehydro-D-glucose 6-phosphate 4fold. Kinetics of the NtdC catalyzed reaction in the presence of the next enzyme in the pathway, NtdA. As the amount of NtdA is increased, the rate of the NtdC reaction also increases up to a maximum when NtdA exceeds a 20:1 molar ratio relative to NtdC. No change in the pH-rate profile for the coupled reaction is observed compared to that of the uncoupled assay | Bacillus subtilis | ? | - |
- |
|
| additional information | under alkaline conditions, the product is not stable because of ring opening followed by deprotonation of the 1,3-dicarbonyl compound. Hydride transfer from carbon 3 is partially rate-limiting in the enzymatic reaction, and deuterium substitution on carbon 2 has no significant effect on the enzymatic reaction but lowers the rate of deprotonation of 3-dehydro-D-glucose 6-phosphate 4fold. Kinetics of the NtdC catalyzed reaction in the presence of the next enzyme in the pathway, NtdA. As the amount of NtdA is increased, the rate of the NtdC reaction also increases up to a maximum when NtdA exceeds a 20:1 molar ratio relative to NtdC. No change in the pH-rate profile for the coupled reaction is observed compared to that of the uncoupled assay | Bacillus subtilis 168 | ? | - |
- |
|
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| G6P 3-dehydrogenase | - |
Bacillus subtilis |
| ntdC | - |
Bacillus subtilis |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 25 | - |
assay at | Bacillus subtilis |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 4.1 | - |
NAD+ | pH 9.5, 25°C | Bacillus subtilis | |
| 4.1 | - |
D-glucose 6-phosphate | pH 9.5, 25°C | Bacillus subtilis | |
| 4.1 | - |
NAD+ | pH 9.5, 25°C, recombinant enzyme NtdC | Bacillus subtilis | |
| 4.1 | - |
D-glucose 6-phosphate | pH 9.5, 25°C, recombinant enzyme NtdC | Bacillus subtilis | |
| 5.8 | - |
NAD+ | pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA | Bacillus subtilis | |
| 5.8 | - |
D-glucose 6-phosphate | pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA | Bacillus subtilis | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 9.5 | - |
- |
Bacillus subtilis |
| 9.5 | - |
the NtdC-catalyzed reaction is very slow at low and neutral pH, and its rate increases to a maximum near pH 9.5. However, under alkaline conditions, the product is not stable because of ring opening followed by deprotonation of the 1,3-dicarbonyl compound | Bacillus subtilis |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| NAD+ | - |
Bacillus subtilis | |
Ki Value [mM]
| Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0009 | - |
NAD+ | pH 9.5, 25°C | Bacillus subtilis | |
| 0.85 | - |
NADH | pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA | Bacillus subtilis | |
| 0.9 | - |
NADH | pH 9.5, 25°C, recombinant enzyme NtdC | Bacillus subtilis | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| metabolism | glucose-6-phosphate 3-dehydrogenase (NtdC) catalyzes the oxidation of glucose 6-phosphate by NtdC is the first step in kanosamine biosynthesis | Bacillus subtilis |
| metabolism | the enzyme catalyzes the first step in kanosamine biosynthesis | Bacillus subtilis |
| physiological function | glucose-6-phosphate 3-dehydrogenase (NtdC) is an NAD-dependent oxidoreductase encoded in the NTD operon of Bacillus subtilis | Bacillus subtilis |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 95.35 | - |
D-glucose 6-phosphate | pH 9.5, 25°C, recombinant enzyme NtdC | Bacillus subtilis | |
| 96 | - |
D-glucose 6-phosphate | pH 9.5, 25°C | Bacillus subtilis | |
| 100 | - |
NAD+ | pH 9.5, 25°C | Bacillus subtilis | |
| 102.5 | - |
NAD+ | pH 9.5, 25°C, recombinant enzyme NtdC | Bacillus subtilis | |
| 123.4 | - |
NAD+ | pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA | Bacillus subtilis | |
| 128.9 | - |
D-glucose 6-phosphate | pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA | Bacillus subtilis | |
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