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Literature summary for 1.1.1.361 extracted from

  • Vetter, N.D.; Palmer, D.R.J.
    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 .
    View publication on PubMed
Search for more literature for 1.1.1.361

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
a

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