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Information on EC 1.1.1.361 - glucose-6-phosphate 3-dehydrogenase
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1.1.1.361 glucose-6-phosphate 3-dehydrogenaseIUBMB Comments
The enzyme, found in the bacterium Bacillus subtilis, is involved in a kanosamine biosynthesis pathway.
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The enzyme appears in viruses and cellular organisms
Synonyms
glucose-6-phosphate 3-dehydrogenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
G6P 3-dehydrogenase
ntdC
ntdC
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
D-glucose 6-phosphate + NAD+ = 3-dehydro-D-glucose 6-phosphate + NADH + H+
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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
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
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
D-glucose-6-phosphate:NAD+ oxidoreductase
The enzyme, found in the bacterium Bacillus subtilis, is involved in a kanosamine biosynthesis pathway.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
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-
-
-
?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
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-
-
?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
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-
-
?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
the enzyme catalyzes the first step in kanosamine biosynthesis
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-
?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
the alpha-anomer form is the substrate for the enzyme. Kinetics of NtdC by itself and with the next enzyme in the pathway, NtdA, which converts 3-oxo-D-glucose 6-phosphate to kanosamine 6-phosphate through a glutamate-coupled PLP-dependent transamination, have shown that the equilibrium of both the NtdC reaction and the NtdC-NtdA-coupled reaction lies heavily toward D-glucose 6-phosphate
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?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
the enzyme obeys a random sequential mechanism, with nearly equal Km values for NAD+ and D-glucose 6-phosphate
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?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
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-
-
?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
the alpha-anomer form is the substrate for the enzyme. Kinetics of NtdC by itself and with the next enzyme in the pathway, NtdA, which converts 3-oxo-D-glucose 6-phosphate to kanosamine 6-phosphate through a glutamate-coupled PLP-dependent transamination, have shown that the equilibrium of both the NtdC reaction and the NtdC-NtdA-coupled reaction lies heavily toward D-glucose 6-phosphate
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?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
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additional information
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the NtdC-catalyzed reaction is unusual because 3-oxo-D-glucose 6-phosphate undergoes rapid ring opening, resulting in a 1,3-dicarbonyl compound that is inherently unstable due to enolate formation. Synthesis of carbocyclic G6P analogues by two routes, one based upon the Ferrier II rearrangement to generate the carbocycle and one based upon a Claisen rearrangement. Both pseudo-anomers of carbaglucose 6-phosphate (C6P) are synthesized using the Ferrier approach, and activity assays reveal that the pseudo-alpha-anomer is a good substrate for NtdC, while the pseudo-beta-anomer and the open-chain analogue, sorbitol 6-phosphate (S6P), are not substrates. A more efficient synthesis of alpha-C6P is achieved using the Claisen rearrangement approach, which allows for a thorough evaluation of the NtdC-catalyzed oxidation of alpah-C6P
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additional information
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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
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additional information
?
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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
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additional information
?
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the NtdC-catalyzed reaction is unusual because 3-oxo-D-glucose 6-phosphate undergoes rapid ring opening, resulting in a 1,3-dicarbonyl compound that is inherently unstable due to enolate formation. Synthesis of carbocyclic G6P analogues by two routes, one based upon the Ferrier II rearrangement to generate the carbocycle and one based upon a Claisen rearrangement. Both pseudo-anomers of carbaglucose 6-phosphate (C6P) are synthesized using the Ferrier approach, and activity assays reveal that the pseudo-alpha-anomer is a good substrate for NtdC, while the pseudo-beta-anomer and the open-chain analogue, sorbitol 6-phosphate (S6P), are not substrates. A more efficient synthesis of alpha-C6P is achieved using the Claisen rearrangement approach, which allows for a thorough evaluation of the NtdC-catalyzed oxidation of alpah-C6P
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additional information
?
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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
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
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-
?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
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-
?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
the enzyme catalyzes the first step in kanosamine biosynthesis
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?
D-glucose 6-phosphate + NAD+
3-dehydro-D-glucose 6-phosphate + NADH + H+
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?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
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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
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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
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.045
D-glucose 6-phosphate
pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA
0.047
NAD+
pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA
additional information
additional information
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kinetic analysis and mechanism, kinetic isotope effects, overview
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additional information
additional information
kinetic analysis and mechanism, kinetic isotope effects, overview
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additional information
additional information
steady-state kinetics. Kinetics of NtdC by itself and with the next enzyme in the pathway, NtdA, which converts 3-oxo-D-glucose 6-phosphate to kanosamine 6-phosphate through a glutamate-coupled PLP-dependent transamination, have shown that the equilibrium of both the NtdC reaction and the NtdC-NtdA-coupled reaction lies heavily toward D-glucose 6-phosphate
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5.8
D-glucose 6-phosphate
pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA
5.8
NAD+
pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
128.9
D-glucose 6-phosphate
pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA
123.4
NAD+
pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.85
NADH
pH 9.5, 25°C, recombinant enzyme NtdC coupled to enzyme NtdA
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
9.5
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
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
evolution
the requirement for the alpha-anomer as substrate indicates that NtdC and NtdA, the subsequent enzyme in the pathway, have co-evolved to recognize the alpha-anomer in order to avoid mutarotation between enzymatic steps
evolution
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the requirement for the alpha-anomer as substrate indicates that NtdC and NtdA, the subsequent enzyme in the pathway, have co-evolved to recognize the alpha-anomer in order to avoid mutarotation between enzymatic steps
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metabolism
glucose-6-phosphate 3-dehydrogenase (NtdC) catalyzes the oxidation of glucose 6-phosphate by NtdC is the first step in kanosamine biosynthesis
metabolism
NtdC is an NAD-dependent dehydrogenase that catalyzes the conversion of glucose 6-phosphate (G6P) to 3-oxoglucose 6-phosphate, the first step in kanosamine biosynthesis in Bacillus subtilis and other closely-related bacteria. Kanosamine biosynthesis in Bacillus subtilis, overview
metabolism
the enzyme catalyzes the first step in kanosamine biosynthesis
metabolism
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NtdC is an NAD-dependent dehydrogenase that catalyzes the conversion of glucose 6-phosphate (G6P) to 3-oxoglucose 6-phosphate, the first step in kanosamine biosynthesis in Bacillus subtilis and other closely-related bacteria. Kanosamine biosynthesis in Bacillus subtilis, overview
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metabolism
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glucose-6-phosphate 3-dehydrogenase (NtdC) catalyzes the oxidation of glucose 6-phosphate by NtdC is the first step in kanosamine biosynthesis
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physiological function
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the ntd operon is essential for biosynthesis of the unusual disaccharide 3,3'-neotrehalosadiamine. The enzymes catalyze the biosynthesis of kanosamine from D-glucose 6-phosphate. NtdC is a D-glucose-6-phosphate-3-dehydrogenase, NtdA is a pyridoxal phosphate-dependent 3-oxo-glucose-6-phosphate:glutamate aminotransferase, and NtdB is a kanosamine-6-phosphate phosphatase
physiological function
glucose-6-phosphate 3-dehydrogenase (NtdC) is an NAD-dependent oxidoreductase encoded in the NTD operon of Bacillus subtilis
physiological function
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glucose-6-phosphate 3-dehydrogenase (NtdC) is an NAD-dependent oxidoreductase encoded in the NTD operon of Bacillus subtilis
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Show AA Sequence and Transmembrane Helices (219 entries)
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Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene ntdC, recombinant expression in Escherichia coli BL21(DE3) Gold
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Vetter, N.D.; Langill, D.M.; Anjum, S.; Boisvert-Martel, J.; Jagdhane, R.C.; Omene, E.; Zheng, H.; van Straaten, K.E.; Asiamah, I.; Krol, E.S.; Sanders, D.A.; Palmer, D.R.
A previously unrecognized kanosamine biosynthesis pathway in Bacillus subtilis
J. Am. Chem. Soc.
135
5970-5973
2013
Bacillus subtilis
brenda
Vetter, N.; Jagdhane, R.; Richter, B.; Palmer, D.
Carbocyclic substrate analogues reveal kanosamine biosynthesis begins with the alpha-anomer of glucose 6-phosphate
ACS Chem. Biol.
15
2205-2211
2020
Bacillus subtilis (O07564), Bacillus subtilis 168 (O07564)
brenda
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
Biochemistry
56
2001-2009
2017
Bacillus subtilis, Bacillus subtilis (O07564), Bacillus subtilis 168 (O07564)
brenda
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Release 2023.1 (January 2023)
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