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Information on EC 6.3.1.5 - NAD+ synthase and Organism(s) Bacillus subtilis and UniProt Accession P08164
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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 taxonomic range for the selected organisms is: Bacillus subtilis
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
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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topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Diphosphopyridine nucleotide synthetase
-
-
-
-
NAD synthetase
NAD+ synthetase
-
-
-
-
Nicotinamide adenine dinucleotide synthetase
Synthetase, nicotinamide adenine dinucleotide
-
-
-
-
NAD synthetase
-
-
-
-
Nicotinamide adenine dinucleotide synthetase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
amide group transfer
amide bond formation
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -, -, -
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].
CAS REGISTRY NUMBER
COMMENTARY
9032-69-3
-
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
ATP + deamido-NAD+ + L-Gln
AMP + diphosphate + NAD+ + Glu
-
ineffective as amide donor
-
-
?
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
?
-
last step in the metabolic pathway for the biosynthesis of NAD+
-
-
?
ATP + deamido-NAD+ + NH3
AMP + diphosphate + NAD+
-
dependent on NH3
-
?
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+ + NH3
AMP + diphosphate + NAD+
NAD-adenylate intermediate, key two step reaction in NAD+ biosynthesis
-
?
ATP + deamido-NAD+ + NH3
?
-
last step in the metabolic pathway for the biosynthesis of NAD+
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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+
Mg2+
-
required, binding structure and mechanism, 2 binding sites per molecule of enzyme
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
-
-
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
-
-
additional information
-
clotrimazole does not inhibit in the presence of 0.01% Triton X-100
-
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
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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
free enzyme form at 2.6 A resolution and in a complex with ATP at 2.0 A resolution
-
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
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
mutant enzyme with a lower temperature optimum and a non-hyperbolic kinetic versus NH4+
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Triton X-100
-
inhibitory effects toward the enzyme are decreased in the presence of Triton X-100
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
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
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
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
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
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
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
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