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Information on EC 6.3.1.5 - NAD+ synthase
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EC Tree
6.3.1.5 NAD+ synthaseIUBMB Comments
L-Glutamine also acts, more slowly, as amido-donor [cf. EC 6.3.5.1].
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Word Map
- 6.3.1.5
- adenylyltransferase
- nmnat
-
glutamine-dependent
-
nucleolus-associated
- analysis
- pharmacology
- drug development
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
nads, nad synthetase, nad+ synthetase, nad synthase, nicotinamide adenine dinucleotide synthetase, nad+ synthase, nh3-dependent nad+ synthetase, ammonia-specific nad synthetase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ammonia-dependent NADS
ammonia-specific NAD synthetase
Diphosphopyridine nucleotide synthetase
-
-
-
-
draNADS
MJ1352
mj_NADS
NAD synthase
NAD synthetase
NAD+ synthetase
NadE
NADS
NH3-dependent NAD+ synthetase
Nicotinamide adenine dinucleotide synthetase
Qns1
-
couples a glutamine amidotransferase domain to a second active site that requires ammonia as a reactant
Synthetase, nicotinamide adenine dinucleotide
-
-
-
-
draNADS
Deinococcus radiodurans ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
-
-
NAD synthetase
-
-
-
-
NAD+ synthetase
-
-
-
-
NadE
Deinococcus radiodurans ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
-
-
NH3-dependent NAD+ synthetase
Deinococcus radiodurans ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
-
-
Nicotinamide adenine dinucleotide synthetase
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+
-
-
-
-
ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+
flexible active site loops of residues 82-7 and 204-225, stabilization of the loop and active site structure, mechanism
-
ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+
mechanism of two-step procedure, reaction intermediate
ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+
reaction mechanism, determination of deamido-NAD+-binding site, Asp173 is the key residue in both deprotonation of the primarily bound ammonium ion, and stabilization of the tetrahedral transition-state intermediate
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Acid amide hydrolysis
-
-
carboxylic
-
amide bond formation
amide group transfer
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SYSTEMATIC NAME
IUBMB Comments
deamido-NAD+:ammonia ligase (AMP-forming)
L-Glutamine also acts, more slowly, as amido-donor [cf. EC 6.3.5.1].
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CAS REGISTRY NUMBER
COMMENTARY
9032-69-3
-
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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
2-fluoro-ATP + deamido-NAD+ + NH3
2-fluoro-AMP + diphosphate + NAD+
-
-
-
-
?
ATP + deamido-NAD+ + glutamine
AMP + diphosphate + glutamate + NAD+
-
-
-
?
ATP + deamido-NAD+ + glutamine
AMP + diphosphate + NAD+ + glutamate
-
-
-
?
ATP + deamido-NAD+ + NH4+
AMP + diphosphate + NAD+ + H+
-
-
-
?
ATP + deamido-NMN + NH3
AMP + diphosphate + NMN
existence of an alternative route of NAD synthesis where the amidation of NaMN to nicotinamide mononucleotide occurs before the adenylylation reaction, which converts the intermediate to the NAD cofactor. The first step is catalyzed by Francisella tularensis NadE
-
-
?
ATP + deamido-NAD+ + Asp
AMP + diphosphate + NAD+ + oxaloacetate
-
slightly active as nitrogen donor
-
-
?
ATP + deamido-NAD+ + Asp
AMP + diphosphate + NAD+ + oxaloacetate
Escherichia coli B / ATCC 11303
-
slightly active as nitrogen donor
-
-
?
ATP + deamido-NAD+ + Glu
AMP + diphosphate + NAD+ + 2-oxoglutarate
-
slightly active as nitrogen donor
-
-
?
ATP + deamido-NAD+ + Glu
AMP + diphosphate + NAD+ + 2-oxoglutarate
Escherichia coli B / ATCC 11303
-
slightly active as nitrogen donor
-
-
?
ATP + deamido-NAD+ + L-Gln
AMP + diphosphate + NAD+ + Glu
-
ineffective as amide donor
-
-
?
ATP + deamido-NAD+ + L-Gln
AMP + diphosphate + NAD+ + Glu
-
-
-
-
?
ATP + deamido-NAD+ + NH3
?
-
last step in the metabolic pathway for the biosynthesis of NAD+
-
-
?
ATP + deamido-NAD+ + NH3
?
-
last step in the metabolic pathway for the biosynthesis of NAD+
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
-
dependent on NH3
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
NAD-adenylate intermediate, two step reaction
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
NAD-adenylate intermediate, key two step reaction in NAD+ biosynthesis
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
-
NH3 is the preferred nitrogen donor
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
Escherichia coli B / ATCC 11303
-
NH3 is the preferred nitrogen donor
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
E07950
-
-
ir
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
E07950
specific for NH3, no activity with L-glutamine or other L-amino acids, no activity with urea, uric acid, or creatinine
-
ir
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
E07950
-
-
ir
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
E07950
specific for NH3, no activity with L-glutamine or other L-amino acids, no activity with urea, uric acid, or creatinine
-
ir
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
last step of NAD synthesis
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
no activity with glutamine as the amide donor
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
last step of NAD synthesis
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
no activity with glutamine as the amide donor
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
-
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
-
NH3 is the preferred nitrogen donor
-
-
?
dATP + deamido-NAD+ + NH3
dAMP + diphosphate + NAD+
-
20% of the activity relative to ATP
-
-
?
dATP + deamido-NAD+ + NH3
dAMP + diphosphate + NAD+
Escherichia coli B / ATCC 11303
-
20% of the activity relative to ATP
-
-
?
additional information
?
-
-
2 possible substrates, NH3 or glutamine, to perform the final step in the Preiss-Handler pathway for NAD+ biosynthesis
-
?
additional information
?
-
-
enzyme induces lymphocyte polyclonal activation, it stimulates murine B cells after in vitro treatment of spleen cell cultures
-
?
additional information
?
-
-
enzyme induces lymphocyte polyclonal activation, it stimulates murine B cells after in vitro treatment of spleen cell cultures
-
?
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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
ATP + deamido-NAD+ + glutamine
AMP + diphosphate + glutamate + NAD+
-
-
-
?
ATP + deamido-NAD+ + NH4+
AMP + diphosphate + NAD+ + H+
-
-
-
?
ATP + deamido-NAD+ + NH3
?
-
last step in the metabolic pathway for the biosynthesis of NAD+
-
-
?
ATP + deamido-NAD+ + NH3
?
-
last step in the metabolic pathway for the biosynthesis of NAD+
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
NAD-adenylate intermediate, key two step reaction in NAD+ biosynthesis
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
E07950
-
-
ir
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
E07950
-
-
ir
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
last step of NAD synthesis
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
last step of NAD synthesis
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
-
-
-
?
additional information
?
-
-
2 possible substrates, NH3 or glutamine, to perform the final step in the Preiss-Handler pathway for NAD+ biosynthesis
-
?
additional information
?
-
-
enzyme induces lymphocyte polyclonal activation, it stimulates murine B cells after in vitro treatment of spleen cell cultures
-
?
additional information
?
-
-
enzyme induces lymphocyte polyclonal activation, it stimulates murine B cells after in vitro treatment of spleen cell cultures
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K+
required, 2 binding sites near the bound diphosphate at the ATP-binding site, can be substituted by Tl+
Mg2+
Mn2+
-
can satisfy the metal ion requirement, Mn2+ is more effective than Mg2+ at low concentrations, at high concentrations Mn2+ markedly inhibits, but Mg2+ does not
Mg2+
-
required, binding structure and mechanism, 2 binding sites per molecule of enzyme
Mg2+
-
can satisfy the metal ion requirement, Mn2+ is more effective than Mg2+ at low concentrations, at high concentrations Mn2+ markedly inhibits, but Mg2+ does not
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1-(4-benzyloxyphenoxy)-8-(2-N,N,N-trimethylammonium-2-phenyl-1-ethyloxy)octane
-
-
1-(4-benzyloxyphenoxy)-8-(2-N,N,N-trimethylammonium-3-phenyl-1-propyloxy)octane
-
-
8-(4-benzyloxyphenoxy)-1-octyl 2-(N,N,N-trimethylammonium)-3-(1H-indol-3-yl)propionate
-
-
8-(4-benzyloxyphenoxy)-1-octyl 2-(N,N,N-trimethylammonium)-3-(4-hydroxyphenyl)propionate
-
-
8-(4-benzyloxyphenoxy)-1-octyl 2-(N,N,N-trimethylammonium)-3-phenylpropionate
-
-
Mn2+
-
can satisfy the metal ion requirement at low concentrations, at high concentrations Mn2+ markedly inhibits
N-[8-(4-benzyloxyphenoxy)-1-octyl]-2-(N,N,N-trimethylammonium)-2-phenylacetamide
-
-
N-[8-(4-benzyloxyphenoxy)-1-octyl]-2-(N,N,N-trimethylammonium)-3-phenylpropionamide
-
-
Psicofuranine
-
i.e. 9-D-psicofuranosyl-6-aminopurine, each substrate provides some protection
thrombin
-
enzyme is highly susceptible too proteolytic cleavage
-
additional information
-
clotrimazole does not inhibit in the presence of 0.01% Triton X-100
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Congenital Abnormalities
National Administrative Databases in Adult Spinal Deformity Surgery: A Cautionary Tale.
Frontotemporal Dementia
NMNAT suppresses tau-induced neurodegeneration by promoting clearance of hyperphosphorylated tau oligomers in a Drosophila model of tauopathy.
Hepatorenal Syndrome
Nonabsorbable disaccharides for hepatic encephalopathy: A systematic review and meta-analysis.
HIV Infections
High population-attributable fractions of traditional risk factors for non-AIDS-defining diseases among people living with HIV in China: a cohort study.
Infections
A genetic strategy to identify targets for the development of drugs that prevent bacterial persistence.
Infections
Nonabsorbable disaccharides for hepatic encephalopathy: A systematic review and meta-analysis.
Liver Failure
Nonabsorbable disaccharides for hepatic encephalopathy: A systematic review and meta-analysis.
Ovarian Neoplasms
Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers.
Parkinsonian Disorders
NMNAT suppresses tau-induced neurodegeneration by promoting clearance of hyperphosphorylated tau oligomers in a Drosophila model of tauopathy.
Peritonitis
Nonabsorbable disaccharides for hepatic encephalopathy: A systematic review and meta-analysis.
Starvation
Biosynthesis and recycling of nicotinamide cofactors in mycobacterium tuberculosis. An essential role for NAD in nonreplicating bacilli.
Tauopathies
Nicotinamide mononucleotide adenylyltransferase uses its NAD+ substrate-binding site to chaperone phosphorylated Tau.
Tuberculosis
A genetic strategy to identify targets for the development of drugs that prevent bacterial persistence.
Tuberculosis
Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+ synthetases.
Tuberculosis
Glutamine amidotransferase activity of NAD+ synthetase from Mycobacterium tuberculosis depends on an amino-terminal nitrilase domain.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.2
ATP
-
in 60 mM Tris-HCl pH 8.0, 10 mM NH4Cl, 10 mM MgCl2, 10 mM KCl
0.289
ATP
in 60 mM EPPS pH 8.5 with 20 mM ammonium chloride, 20 mM potassium chloride, and 10 mM magnesium chloride, at 37°C
0.0029
deamido-NAD+
-
pH 8.5, 37°C, recombinant full length enzyme
0.03
deamido-NAD+
-
in 60 mM Tris-HCl pH 8.0, 10 mM NH4Cl, 10 mM MgCl2, 10 mM KCl
0.152
deamido-NAD+
in 60 mM EPPS pH 8.5 with 20 mM ammonium chloride, 20 mM potassium chloride, and 10 mM magnesium chloride, at 37°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
the Vmax/KM-value for NADsyn2 with NH3 is 2370fold higher than the Vmax/Km-value for glutamine
-
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.011
1-(4-benzyloxyphenoxy)-8-(2-guanidino-2-phenyl-1-ethyloxy)-octane
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.011
1-(4-benzyloxyphenoxy)-8-(2-guanidino-3-phenyl-1-propyloxy)-octane
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.038
1-(4-benzyloxyphenoxy)-8-(2-N,N,N-trimethylammonium-2-phenyl-1-ethyloxy)octane
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.021
1-(4-benzyloxyphenoxy)-8-(2-N,N,N-trimethylammonium-3-phenyl-1-propyloxy)octane
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.019
8-(4-benzyloxyphenoxy)-1-octyl 2-(N,N,N-trimethylammonium)-3-(1H-indol-3-yl)propionate
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.053
8-(4-benzyloxyphenoxy)-1-octyl 2-(N,N,N-trimethylammonium)-3-(4-hydroxyphenyl)propionate
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.037 - 0.22
8-(4-benzyloxyphenoxy)-1-octyl 2-(N,N,N-trimethylammonium)-3-phenylpropionate
0.045
N-[8-(4-benzyloxyphenoxy)-1-octyl]-2-(N,N,N-trimethylammonium)-2-phenylacetamide
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.04
N-[8-(4-benzyloxyphenoxy)-1-octyl]-2-(N,N,N-trimethylammonium)-3-phenylpropionamide
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.019
N-[8-(4-benzyloxyphenoxy)-1-octyl]-2-guanidino-2-phenylacetamide
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.012
N-[8-(4-benzyloxyphenoxy)-1-octyl]-2-guanidino-3-phenylpropionamide
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
0.037
8-(4-benzyloxyphenoxy)-1-octyl 2-(N,N,N-trimethylammonium)-3-phenylpropionate
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5, in the presence of 0.01% Triton X-100
0.22
8-(4-benzyloxyphenoxy)-1-octyl 2-(N,N,N-trimethylammonium)-3-phenylpropionate
Bacillus subtilis
-
in 58.5 mM HEPPS buffer, 18.5 mM NH4Cl, 19.5 mM KCl, 9.75 mM MgCl2, 1% (v/v) EtOH, at pH 8.5
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.0003
-
mutant enzyme R112L, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.0011
-
mutant enzyme D593A/F622A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.0027
-
mutant enzyme L604A/L519A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.0033
-
mutant enzyme Y532A/M621A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.0043
-
mutant enzyme L604N, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.008
-
mutant enzyme F622A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.009
-
partially purified recombinant His-tagged enzyme expressed in insect cells, substrate NH4+
0.0143
-
mutant enzyme I111A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.015
-
mutant enzyme R112S, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.033
-
purified recombinant HIs-tagged enzyme expressed in Escherichia coli, substrate glutamine
0.0485
-
mutant enzyme Y601A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.1
-
purified recombinant His-tagged enzyme expressed in Escherichia coli, substrate NH4+
0.152
-
mutant enzyme D593A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.183
-
mutant enzyme L604A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.25
-
mutant enzyme M621A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.631
-
mutant enzyme E177A, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
0.67
-
purified recombinant His-tagged truncated enzyme expressed in Escherichia coli, substrate NH4+
0.741
-
wild type enzyme, at 37°C, with 2 mM ATP, 5 mM MgCl2, 50 mM Tris-HCl, pH 8.0, 56 mM KCl, and 0.2 mg/ml bovine serum albumin
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Deinococcus radiodurans ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
-
UniProt
brenda
wild-type and mutant strains which are defective in NAD synthetase
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
existence of an alternative route of NAD synthesis where the amidation of NaMN to nicotinamide mononucleotide occurs before the adenylylation reaction, which converts the intermediate to the NAD cofactor. The first step is catalyzed by Francisella tularensis NadE
evolution
the genes encoding the enzymes nicotinic acid mononucleotide adenylyltransferase (NaMNAT), NAD synthetase and NAD kinase responsible for the downstream conversion of nicotinic acid mononucleotide (NaMN) to NAD and NAD(P) are conserved in almost all investigated bacterial genomes
evolution
-
the genes encoding the enzymes nicotinic acid mononucleotide adenylyltransferase (NaMNAT), NAD synthetase and NAD kinase responsible for the downstream conversion of nicotinic acid mononucleotide (NaMN) to NAD and NAD(P) are conserved in almost all investigated bacterial genomes
-
malfunction
-
induced degradation of NadE enzyme shows a strong bactericidal effect which coincided with anticipated changes in relative levels of NaAD intermediate (substrate of NadE) and ultimate depletion of the NAD(H) pool. The disruption of NAD production in the cell via genetic suppression of the essential enzymes (NadD and NadE) involved in the last two steps of NAD biogenesis leads to cell death, even under dormancy conditions. Proteolytic degradation of the enzyme leads to depletion of the NAD cofactor pool, which suppresses metabolic flux through numerous NAD(P)-dependent pathways of central metabolism of carbon and energy production, phenotype, overview
malfunction
the disruption of NAD production in the cell via genetic suppression of the essential enzymes (NadD and NadE) involved in the last two steps of NAD biogenesis leads to cell death, even under dormancy conditions. Proteolytic degradation of either target enzyme leads to depletion of the NAD cofactor pool, which suppresses metabolic flux through numerous NAD(P)-dependent pathways of central metabolism of carbon and energy production
metabolism
NAD synthetases are critical as they catalyze the amidation of nicotinic acid adenine dinucleotide (NaAD) to yield the enzyme cofactor NAD, which is the last step in NAD synthesis. NAD synthetase catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide, making it a crucial intermediate enzyme linked to the biosynthesis of several amino acids, purine and pyrimidine nucleotides, coenzymes and antibiotics
metabolism
-
NaMN adenylyltransferase (NadD) and NAD synthetase (NadE) are the key enzymes of NAD biosynthesis
metabolism
NaMN adenylyltransferase (NadD) and NAD synthetase (NadE) are the key enzymes of NAD biosynthesis
metabolism
-
NAD synthetases are critical as they catalyze the amidation of nicotinic acid adenine dinucleotide (NaAD) to yield the enzyme cofactor NAD, which is the last step in NAD synthesis. NAD synthetase catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide, making it a crucial intermediate enzyme linked to the biosynthesis of several amino acids, purine and pyrimidine nucleotides, coenzymes and antibiotics
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
additional information
additional information
Deinococcus radiodurans ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
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enzyme structure analysis, overview
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additional information
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multimeric enzyme of at least two subunits
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour diffusion method using 8-12% PEG 8000, 0.505 M ammonium sulfate, 6% glycerol, 100 mM magnesium chloride, 0.05% n-octyl-beta-D-glucopyranoside, 100 mM HEPES, pH 7
enzyme in complex with ATP, ATP-Tl+, ATP-Mn2+, or NAD-adenylate, hanging-drop vapour diffusion method, 15 mg/ml protein, 5 mM ATP, 20 mM NAD+ in 0.1 M sodium acetate, pH 5.2, 22% PEG 400, and 50 mM MgCl2, thallium acetate, or MnCl2 20°C, 24 h before data collection the crystale are soaked in a cryoprotectant buffer, X-ray diffraction structure determination at 1.3 A resolution, structure analysis and modeling
free enzyme form at 2.6 A resolution and in a complex with ATP at 2.0 A resolution
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purified recombinant enzyme complexed with substrates, vapour diffusion method at 5.2 under earth gravity at pH 5.2, and microseeding under space microgravity, the latter in protein solution containing 15 mg/ml protein, 2.5 mM ATP, 5 mM deamido-NAD+, 50 mM Tris, pH 8.5, 50 mM MgCl2, 25% PEG 400 v/v, 9 days, X-ray diffractio structure determination at 1.0 A resolution and analysis of the crystal structures at pH 5.2 and pH 8.5
purified recombinant enzyme, in complex with 4 different substrates: complex I is formed by enzyme and deamido-NAD, complex II is formed by enzyme and ATP, complex III is formed by enzyme, deamido-NAD and ATP, complex is formed by enzyme and substrate analogue alpha,beta-methylene-adenosine triphosphate, crystallization from protein solution: 15 mg/ml protein, 20 mM sodium acetate, pH 5.2, 50 mM MgCl2, 2.5 mM 2-mercaptoethanol, plus equal volume of 0.1 M sodium acetate, pH 5.2, 21-23% PEG 400, 50 mM MgCl2, at room temperature, addition of substrates at different concentrations, formation of complex IV at different pH-values, in the reservoir solution: 50 mM HEPES, pH 7.5, 0.1 M MgCl2, 20-26% PEG 400, 2 mM AMP-CPP, X-ray diffraction structure determination at resolution 1.9-2.3, structure analysis
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purified recombinant detagged enzyme, sitting drop vapor diffusion method, mixing of 30 mg/ml protein in 0.2 M NaCl, 20 mM Tris-HCl, pH 8.0, 1 mM DTT, 5 mM MgCl2, and 5% glycerol, with reservoir solution containing 20% PEG 4000, 0.2 M lithium sulfate, 0.1 M MES, pH 6.0, 23°C, 3 days, method optimization, X-ray diffraction structure determination and analysis at 2.60 A resolution, molecular replacement
28 mg/ml purified recombinant enzyme, pure or in complex with substrates NAD+ and ATP, hanging-drop vapour diffusion method, 22°C room temperature, protein in 0.01 M HEPES, pH 7.5, 5 mM MgCl2, 3 mM DTT, precipitant solution: 0.1 M HEPES, pH 7.5, 1.5 M lithium sulfate, X-ray diffraction structure determination at 2.0 A resolution, compex structure determination via molecular replacement method
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crystal structures of the enzyme alone and in complex with natural substrates and with the reaction product NAD+
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crystal structures of apo- and complex forms with deamido-NAD+ and ATP to a resolution of 2.3 and 1.7 respectively. Hanging drop vapor diffusion method. Crystals of SeMet-containing NAD+ synthase belong to space group C2 with unit cell dimensions of a = 92.3, b = 47.5, c = 64.0, and beta = 110°. Crystals of NAD+ synthetase complexed with deamido-NAD+ belong to space group P3(1), with unit cell dimensions of a = b = 63.4, c = 125.7 A
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purified recombinant His-tagged enzyme enzyme, hanging drop vapour diffusion method, mixing of 0.002-0.004 ml of 10 mg/ml protein in 20 mM TrisHCl, pH 8.5, 200 mM NaCl, and 5% glycerol, with 0.002-0.004 ml of reservoir solution containing 200 mM CaCl2, 100 mM TrisHCl, pH 7.5, 22% PEG 4000, and equilibration against 0.4 ml of reservoir solution, 20°C, 1 week, X-ray diffraction structure determination and analysis at 2.03 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
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mutant enzyme with a lower temperature optimum and a non-hyperbolic kinetic versus NH4+
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Triton X-100
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inhibitory effects toward the enzyme are decreased in the presence of Triton X-100
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, recombinant truncated enzyme, overnight, loss of 59% activity
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-70°C, recombinant truncated enzyme, overnight, loss of 30% activity
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni HiTrap column chromatography, and Superdex-200 gel filtration or Superdex-75 gel filtration
recombinant His-tagged enzyme and recombinant thioredoxin-His6-fusion protein from Escherichia coli and insect cells, the His-tag is cleaved off afterwards
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recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) star pLysS by nickel affinity chromatography, tag cleavage by a protease, another step of nickel affinity chromatography, and gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, functional overexpression in Escherichia coli
E07950
functional expression in Escherichia coli strain M-15 as His-tagged enzyme, secretion to the medium
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gene nadE, recombinant expression of the His-tagged enzyme in Escherichia coli strain BL21(DE3) star pLysS
gene nadE, sequence comparisons, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
nadE gene, expression of the enzyme as a His-tagged protein and as a thioredoxin-His6-fusion protein in insect cells of Thrichoplusia ni BTI-TN-5B1-4 via baculovirus infection, for large scale production, and in Escherichia coli
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
drug development
pharmacology
analysis
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the enzyme is used for an enzymatic cycling method for ammonia assay using a system consisting of three enzymes: EC 6.3.1.5, EC 1.1.1.47 and EC 1.6.99.2
analysis
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method for measurement of allantoin in human serum. Serum allantoin is converted to allantoate by the action of allantoinase,and endogenous ammonia is simultaneously removed by the action of glutamine synthetase II. In the second step, L-methionine sulfoximine is used to inhibit glutamine synthetase II, and ammonia is liberated from allantoate by the activity of allantoate amidohydrolase. The ammonia is then converted to NAD by NAD synthetase. Subsequent action of glucose dehydrogenase and diaphorase acts to cycle the formed NAD between its oxidized and reduced forms, resulting in the production of WST-1 formazan, which is monitored at 450 nm. The assay standard curve is linear from 0 to 70 microM allantoin
analysis
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use of substrate 2-fluro-ATP as tool for 18F NMR-based activity screening
drug development
enzymes involved in NAD metabolism and synthesis are significant drug targets as NAD is a central player in several cellular processes
drug development
NadE is a antimycobacterial drug target
drug development
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enzymes involved in NAD metabolism and synthesis are significant drug targets as NAD is a central player in several cellular processes
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pharmacology
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preparation of isotopically labelled [13N]NAD+, a radiopharmaceutical designed for positron emission tomography, by the NAD+ synthetase immobilized on porous glass beads
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hughes, K.T.; Baldomero, M.O.; Roth, J.R.
Structural gene for NAD synthetase in Salmonella typhimurium
J. Bacteriol.
170
2113-2120
1988
Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Lambrecht, R.H.D.; Slegers, G.; Claeys, A.; Vuye, A.
Purification and immobilization of NAD+ synthetase from Escherichia coli
Enzyme Microb. Technol.
7
493-498
1985
Escherichia coli
-
brenda
Spencer, R.L.; Preiss, J.
Biosynthesis of diphosphopyridine nucleotide. The purification and the properties of diphosphopyridine nucleotide synthetase from Escherichia coli
J. Biol. Chem.
242
385-392
1967
Escherichia coli, Escherichia coli B / ATCC 11303
brenda
Rizzi, M.; Nessi, C.; Bolognesi, M.; Coda, A.; Galizzi, A.
Crystallization of NAD+ synthetase from Bacillus subtilis
Proteins Struct. Funct. Genet.
26
236-238
1996
Bacillus subtilis
brenda
Nessi, C.; Albertini, A.M.; Speranza, M.L.; Galizzi, A.
The outB gene of Bacillus subtilis codes for NAD synthetase
J. Biol. Chem.
17
6181-6185
1995
Bacillus subtilis
brenda
Willison, J.C.; Tissot, G.
The Escherichia coli efg gene and the Rhodobacter capsulatus adgA gene code for NH3-dependent NAD synthetase
J. Bacteriol.
176
3400-3402
1994
Escherichia coli, Rhodobacter capsulatus
brenda
Rizzi, M.; Nessi, C.; Mattevi, A.; Coda, A.; Bolognesi, M.; Galizzi, A.
Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis
EMBO J.
15
5125-5134
1996
Bacillus subtilis
brenda
Devedjiev, Y.; Symersky, J.; Singh, R.; Jedrzejas, M.; Brouillette, C.; Brouillette, W.; Muccio, D.; Chattopadhyay, D.; DeLucas, L.
Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis
Acta Crystallogr. Sect. D
57
806-812
2001
Bacillus subtilis
brenda
Symersky, J.; Devedjiev, Y.; Moore, K.; Brouillette, C.; DeLucas, L.
NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution
Acta Crystallogr. Sect. D
58
1138-1146
2002
Bacillus subtilis (P08164), Bacillus subtilis
brenda
Yamaguchi, F.; Koga, S.; Yoshioka, I.; Takahashi, M.; Sakuraba, H.; Ohshima, T.
Stable ammonia-specific NAD synthetase from Bacillus stearothermophilus: purification, characterization, gene cloning, and applications
Biosci. Biotechnol. Biochem.
66
2052-2059
2002
Geobacillus stearothermophilus (E07950), Geobacillus stearothermophilus, Geobacillus stearothermophilus H-804 (E07950)
brenda
Veiga-Malta, I.; Duarte, M.; Dinis, M.; Madureira, P.; Ferreira, P.; Videira, A.
Identification of NAD+ synthetase from Streptococcus sobrinus as a B-cell-stimulatory protein
J. Bacteriol.
186
419-426
2004
Streptococcus sobrinus, Streptococcus sobrinus 6715
brenda
Ozment, C.; Barchue, J.; DeLucas, L.J.; Chattopadhyay, D.
Structural study of Escherichia coli NAD synthetase: overexpression, purification, crystallization, and preliminary crystallographic analysis
J. Struct. Biol.
127
279-282
1999
Escherichia coli
brenda
Bellinzoni, M.; De Rossi, E.; Branzoni, M.; Milano, A.; Peverali, F.A.; Rizzi, M.; Riccardi, G.
Heterologous expression, purification, and enzymatic activity of Mycobacterium tuberculosis NAD(+) synthetase
Protein Expr. Purif.
25
547-557
2002
Mycobacterium tuberculosis
brenda
Rizzi, M.; Bolognesi, M.; Coda, A.
A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure
Structure
6
1129-1140
1998
Bacillus subtilis (P08164), Bacillus subtilis
brenda
Yamaguchi, F.; Etoh, T.; Takahashi, M.; Misaki, H.; Sakuraba, H.; Ohshima, T.
A new enzymatic cycling method for ammonia assay using NAD synthetase
Clin. Chim. Acta
352
165-173
2005
Geobacillus stearothermophilus
brenda
Jauch, R.; Humm, A.; Huber, R.; Wahl, M.C.
Structures of Escherichia coli NAD synthetase with substrates and products reveal mechanistic rearrangements
J. Biol. Chem.
280
15131-15140
2005
Escherichia coli
brenda
Kang, G.B.; Kim, Y.S.; Im, Y.J.; Rho, S.H.; Lee, J.H.; Eom, S.H.
Crystal structure of NH3-dependent NAD+ synthetase from Helicobacter pylori
Proteins
58
985-988
2005
Helicobacter pylori
brenda
McDonald, H.M.; Pruett, P.S.; Deivanayagam, C.; Protasevich, I.I.; Carson, W.M.; DeLucas, L.J.; Brouillette, W.J.; Brouillette, C.G.
Structural adaptation of an interacting non-native C-terminal helical extension revealed in the crystal structure of NAD+ synthetase from Bacillus anthracis
Acta Crystallogr. Sect. D
63
891-905
2007
Bacillus anthracis (Q81RP3), Bacillus anthracis
brenda
Yamaguchi, F.; Ohshima, T.; Sakuraba, H.
An enzymatic cycling assay for nicotinic acid adenine dinucleotide phosphate using NAD synthetase
Anal. Biochem.
364
97-103
2007
Geobacillus stearothermophilus
brenda
Heuser, F.; Schroer, K.; Luetz, S.; Bringer-Meyer, S.; Sahm, H.
Enhancement of the NAD(P)(H) pool in Escherichia coli for biotransformation
Eng. Life Sci.
7
343-353
2007
Escherichia coli
-
brenda
Wojcik, M.; Seidle, H.F.; Bieganowski, P.; Brenner, C.
Glutamine-dependent NAD+ synthetase. How a two-domain, three-substrate enzyme avoids waste
J. Biol. Chem.
281
33395-33402
2006
Saccharomyces cerevisiae
brenda
Stockman, B.J.; Lodovice, I.J.; Fisher, D.A.; McColl, A.S.; Xie, Z.
A nuclear magnetic resonance-based functional assay for nicotinamide adenine dinucleotide synthetase
J. Biomol. Screen.
12
457-463
2007
Staphylococcus aureus, Staphylococcus aureus NCTC 8325
brenda
Velu, S.E.; Mou, L.; Luan, C.H.; Yang, Z.W.; DeLucas, L.J.; Brouillette, C.G.; Brouillette, W.J.
Antibacterial nicotinamide adenine dinucleotide synthetase inhibitors: amide- and ether-linked tethered dimers with alpha-amino acid end groups
J. Med. Chem.
50
2612-2621
2007
Bacillus subtilis
brenda
Muratsubaki, H.; Enomoto, K.; Soejima, A.; Satake, K.
An enzyme cycling method for measurement of allantoin in human serum
Anal. Biochem.
378
65-70
2008
Geobacillus stearothermophilus
brenda
Stockman, B.J.
2-Fluoro-ATP as a versatile tool for 19F NMR-based activity screening
J. Am. Chem. Soc.
130
5870-5871
2008
Staphylococcus aureus
brenda
Sorci, L.; Martynowski, D.; Rodionov, D.A.; Eyobo, Y.; Zogaj, X.; Klose, K.E.; Nikolaev, E.V.; Magni, G.; Zhang, H.; Osterman, A.L.
Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis
Proc. Natl. Acad. Sci. USA
106
3083-3088
2009
Francisella tularensis (A0A0B3VMT3), Francisella tularensis
brenda
De Ingeniis, J.; Kazanov, M.D.; Shatalin, K.; Gelfand, M.S.; Osterman, A.L.; Sorci, L.
Glutamine versus ammonia utilization in the NAD synthetase family
PLoS One
7
e39115
2012
Methanocaldococcus jannaschii (Q58747), Methanocaldococcus jannaschii DSM 2661 (Q58747)
brenda
Arbade, G.K.; Srivastava, S.K.
Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of NAD synthetase from methicillin-resistant Staphylococcus aureus
Acta Crystallogr. Sect. F
71
763-769
2015
Staphylococcus aureus (Q5HEK9), Staphylococcus aureus, Staphylococcus aureus COL (Q5HEK9)
brenda
Park, Y.; Yeo, H.; Lee, J.
Structural analysis of the NH3-dependent NAD+ synthetase from Deinococcus radiodurans
Bull. Korean Chem. Soc.
35
2863-2866
2014
Deinococcus radiodurans (Q9RYV5), Deinococcus radiodurans ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 (Q9RYV5)
-
brenda
Rodionova, I.A.; Schuster, B.M.; Guinn, K.M.; Sorci, L.; Scott, D.A.; Li, X.; Kheterpal, I.; Shoen, C.; Cynamon, M.; Locher, C.; Rubin, E.J.; Osterman, A.L.
Metabolic and bactericidal effects of targeted suppression of NadD and NadE enzymes in mycobacteria
mBio
5
e00747-13
2014
Mycolicibacterium smegmatis, Mycobacterium tuberculosis (A0A0U0RRS4), Mycobacterium tuberculosis
brenda
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