BRENDA - Enzyme Database
show all sequences of 3.2.2.6

Insights into the mechanism of bovine CD38/NAD+ glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates

Egea, P.F.; Muller-Steffner, H.; Kuhn, I.; Cakir-Kiefer, C.; Oppenheimer, N.J.; Stroud, R.M.; Kellenberger, E.; Schuber, F.; PLoS ONE 7, e34918 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant expression of bovine CD38/NAD+ glycohydrolase truncated for the first 31 amino acids that encompass the transmembrane and short intracellular domains in Pichia pastoris. The construct comprises a DNA fragment encoding the ecto-domain in the expression plasmid pPICZaA in frame with the yeast alpha-factor secretion signal sequence under the transcriptional control of the AOX1 promoter and keeping its original stop codon
Bos taurus
Crystallization (Commentary)
Crystallization
Organism
mono N-glycosylated forms of soluble enzyme ecto-domain (residues 32-278) and catalytic residue mutant Glu218Gln, in apo state or bound to 2'-fluorinated NAD+ derivatives aFNAD or rFNAD, hanging drop vapour diffusion method, from 20-30% PEG 4000, 50-250 mM ammonium sulfate and 100 mM sodium cacodylate, sodium acetate or MES, pH 6.0-6.5, room temperature, soaking of crystals in 1-3 mM ligand solution, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement
Bos taurus
Engineering
Amino acid exchange
Commentary
Organism
E218Q
site-directed mutagenesis, catalytic site mutant, crystal structure analysis, almost inactive mutant
Bos taurus
K120A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Bos taurus
additional information
construction of CD38/NAD+ glycohydrolase truncated for the first 31 amino acids that encompass the transmembrane and short intracellular domains
Bos taurus
R216A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Bos taurus
S185A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Bos taurus
W168A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Bos taurus
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
steady state kinetics
Bos taurus
0.0171
-
NAD+
pH 7.4, 37C, recombinant wild-type enzyme
Bos taurus
0.0187
-
NAD+
pH 7.4, 37C, recombinant mutant S185A
Bos taurus
0.0229
-
NAD+
pH 7.4, 37C, recombinant mutant R216A
Bos taurus
0.0246
-
NAD+
pH 7.4, 37C, recombinant mutant W168A
Bos taurus
0.0247
-
NAD+
pH 7.4, 37C, recombinant mutant E218Q
Bos taurus
0.0277
-
NAD+
pH 7.4, 37C, recombinant mutant K120A
Bos taurus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
additional information
Bos taurus
the enzyme catalyses the hydrolysis of NAD+ into nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose (cADPR)
?
-
-
-
NAD+ + H2O
Bos taurus
-
ADP-D-ribose + nicotinamide
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Bos taurus
Q9TTF5
-
-
Posttranslational Modification
Posttranslational Modification
Commentary
Organism
glycoprotein
N-linked glycosylation near the active site
Bos taurus
Reaction
Reaction
Commentary
Organism
NAD+ + H2O = ADP-D-ribose + nicotinamide
structure-function analysis and reaction mechanism, overview. The nicotinamide-ribosyl bond of NAD+ is cleaved via a dissociative process with a late transition state, leading to a ribooxocarbenium ion reaction intermediate stabilized by the side-chain of invariant Glu218. This rate-determining step is followed by two nucleophilic reactions in competition: (i) an intermolecular pathway involving a rapid trapping from the b-face of this intermediate by a water molecule (NAD+ glycohydrolase activity) or by competing neutral nucleophiles such as pyridines (transglycosidation reactions) or alcohols (e.g., methanolysis), and (ii) an intramolecular reaction between N1 of the adenine ring and C19 (anomeric carbon) of the oxocarbenium ion leading to the formation of cyclic ADP-ribose (ADP-ribosyl cyclase activity). This latter reaction represents a kinetically minor step relative to solvolysis
Bos taurus
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
the enzyme catalyses the hydrolysis of NAD+ into nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose (cADPR)
732691
Bos taurus
?
-
-
-
-
NAD+ + H2O
-
732691
Bos taurus
ADP-D-ribose + nicotinamide
-
-
-
?
Temperature Optimum [C]
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
37
-
assay at
Bos taurus
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.4
-
assay at
Bos taurus
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of bovine CD38/NAD+ glycohydrolase truncated for the first 31 amino acids that encompass the transmembrane and short intracellular domains in Pichia pastoris. The construct comprises a DNA fragment encoding the ecto-domain in the expression plasmid pPICZaA in frame with the yeast alpha-factor secretion signal sequence under the transcriptional control of the AOX1 promoter and keeping its original stop codon
Bos taurus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
mono N-glycosylated forms of soluble enzyme ecto-domain (residues 32-278) and catalytic residue mutant Glu218Gln, in apo state or bound to 2'-fluorinated NAD+ derivatives aFNAD or rFNAD, hanging drop vapour diffusion method, from 20-30% PEG 4000, 50-250 mM ammonium sulfate and 100 mM sodium cacodylate, sodium acetate or MES, pH 6.0-6.5, room temperature, soaking of crystals in 1-3 mM ligand solution, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement
Bos taurus
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
E218Q
site-directed mutagenesis, catalytic site mutant, crystal structure analysis, almost inactive mutant
Bos taurus
K120A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Bos taurus
additional information
construction of CD38/NAD+ glycohydrolase truncated for the first 31 amino acids that encompass the transmembrane and short intracellular domains
Bos taurus
R216A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Bos taurus
S185A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Bos taurus
W168A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Bos taurus
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
steady state kinetics
Bos taurus
0.0171
-
NAD+
pH 7.4, 37C, recombinant wild-type enzyme
Bos taurus
0.0187
-
NAD+
pH 7.4, 37C, recombinant mutant S185A
Bos taurus
0.0229
-
NAD+
pH 7.4, 37C, recombinant mutant R216A
Bos taurus
0.0246
-
NAD+
pH 7.4, 37C, recombinant mutant W168A
Bos taurus
0.0247
-
NAD+
pH 7.4, 37C, recombinant mutant E218Q
Bos taurus
0.0277
-
NAD+
pH 7.4, 37C, recombinant mutant K120A
Bos taurus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
additional information
Bos taurus
the enzyme catalyses the hydrolysis of NAD+ into nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose (cADPR)
?
-
-
-
NAD+ + H2O
Bos taurus
-
ADP-D-ribose + nicotinamide
-
-
?
Posttranslational Modification (protein specific)
Posttranslational Modification
Commentary
Organism
glycoprotein
N-linked glycosylation near the active site
Bos taurus
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
the enzyme catalyses the hydrolysis of NAD+ into nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose (cADPR)
732691
Bos taurus
?
-
-
-
-
NAD+ + H2O
-
732691
Bos taurus
ADP-D-ribose + nicotinamide
-
-
-
?
Temperature Optimum [C] (protein specific)
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
37
-
assay at
Bos taurus
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.4
-
assay at
Bos taurus
General Information
General Information
Commentary
Organism
additional information
invariant glutamate 218 identified is the catalytic residue of the enzyme, Structure homology modelling, overview
Bos taurus
General Information (protein specific)
General Information
Commentary
Organism
additional information
invariant glutamate 218 identified is the catalytic residue of the enzyme, Structure homology modelling, overview
Bos taurus
Other publictions for EC 3.2.2.6
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
749830
Chini
The NADase CD38 is induced by ...
Homo sapiens
Biochem. Biophys. Res. Commun.
513
486-493
2019
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
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-
1
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1
-
-
-
-
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-
-
-
-
-
-
-
1
1
1
1
-
-
750282
Shu
Blockade of CD38 diminishes l ...
Mus musculus
Cell. Signal.
42
249-258
2018
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-
-
-
-
-
-
-
-
-
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4
-
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1
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1
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1
1
1
1
-
-
731357
Kuhn
Probing the catalytic mechanis ...
Bos taurus
Biochim. Biophys. Acta
1844
1317-1331
2014
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-
-
-
11
-
7
12
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-
1
-
2
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1
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3
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1
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12
1
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11
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7
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12
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1
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-
-
3
-
1
-
-
12
1
-
-
-
-
1
1
-
12
12
731882
Ma
Basal CD38/cyclic ADP-ribose-d ...
Mus musculus
Glia
62
943-955
2014
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-
-
-
-
-
-
-
-
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4
-
1
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4
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4
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1
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1
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4
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4
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4
-
1
-
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-
1
-
-
-
-
2
2
-
-
-
731987
Shrimp
Revealing CD38 cellular locali ...
Homo sapiens
J. Am. Chem. Soc.
136
5656-5663
2014
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-
-
-
2
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-
2
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3
-
1
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2
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3
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1
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1
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2
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2
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3
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2
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3
-
1
-
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-
1
-
-
-
1
1
1
1
-
-
731119
Jiang
Identification of ADP-ribosyla ...
Homo sapiens
Anal. Biochem.
433
218-226
2013
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-
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6
-
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-
1
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1
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1
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1
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1
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1
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1
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6
-
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1
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1
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-
1
-
1
-
-
-
1
-
-
-
-
1
1
-
-
-
732593
Coskun
Purification of NAD+ glycohydr ...
Homo sapiens
Oncol. Lett.
6
227-231
2013
-
-
-
-
-
-
-
-
2
-
2
3
-
1
-
-
1
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1
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3
1
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1
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2
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2
3
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1
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1
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3
1
-
-
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-
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1
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-
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-
731296
Kwong
Catalysis-based inhibitors of ...
Homo sapiens, Mus musculus, Rattus norvegicus
Biochemistry
51
555-564
2012
-
-
-
1
-
-
42
-
-
-
-
9
-
3
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-
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4
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9
-
3
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3
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1
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42
-
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9
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4
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9
-
3
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-
3
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9
9
-
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-
732501
Ikeda
Identification of a major enzy ...
Xenopus laevis
Mol. Cell. Biochem.
366
69-80
2012
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1
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3
-
2
4
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3
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1
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3
1
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4
1
1
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1
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1
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3
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2
4
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1
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3
1
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4
1
1
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-
1
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-
-
-
2
2
-
-
-
732691
Egea
Insights into the mechanism of ...
Bos taurus
PLoS ONE
7
e34918
2012
-
-
1
1
6
-
-
7
-
-
-
2
-
2
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1
-
1
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-
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2
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1
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1
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1
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1
6
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7
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2
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1
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2
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1
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1
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1
1
-
-
-
714434
Kellenberger
Flavonoids as inhibitors of hu ...
Homo sapiens
Bioorg. Med. Chem. Lett.
21
3939-3942
2011
-
-
1
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-
17
-
-
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-
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-
1
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1
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-
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2
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16
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1
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16
17
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1
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2
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714921
Congleton
ATRA-induced HL-60 myeloid leu ...
Homo sapiens
Exp. Cell Res.
317
910-919
2011
-
-
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-
1
-
1
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1
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1
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1
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1
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1
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1
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1
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1
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1
1
1
1
-
-
716910
Lee
Cyclic ADP-ribose and NAADP: f ...
Mus musculus
Sci. China Life Sci.
54
699-711
2011
-
-
-
-
-
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1
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3
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1
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1
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1
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3
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-
-
-
-
-
-
-
-
1
1
-
-
-
326409
Orsomando
NAD(P)+-glycohydrolase from hu ...
Homo sapiens
Comp. Biochem. Physiol. B
126
89-98
2000
-
-
-
-
-
2
7
3
2
3
2
1
-
3
-
-
1
1
1
1
3
3
22
1
1
1
1
-
1
1
-
-
-
1
-
-
-
-
-
-
-
2
-
7
-
3
2
3
2
1
-
-
-
1
1
1
3
3
22
1
1
1
1
-
1
1
-
1
-
-
-
-
-
-
326410
Berthelier
-
Human CD38 is an authentic NAD ...
Homo sapiens
Biochem. J.
330
1383-1390
1998
-
-
-
-
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1
6
-
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1
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1
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9
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1
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6
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1
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9
-
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-
-
-
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-
-
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-
326411
Chini
Enzymatic synthesis and degrad ...
Rattus norvegicus
Biochem. Biophys. Res. Commun.
209
167-174
1995
-
-
-
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2
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4
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1
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4
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1
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-
-
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-
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-
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-
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326406
Jorge
Carbon source regulation of ni ...
Neurospora crassa
J. Gen. Microbiol.
130
1563-1568
1984
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-
-
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1
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2
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3
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1
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3
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2
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326403
Yamasaki
-
Purification and some properti ...
Saccharomyces cerevisiae
J. Ferment. Technol.
60
131-137
1982
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2
1
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2
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1
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1
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2
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1
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2
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1
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2
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2
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1
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2
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1
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1
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326407
Skala
Elevated NAD(P) glycohydrolase ...
Homo sapiens
Blood
60
912-917
1982
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1
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1
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326408
Artman
Nicotinamide adenine dinucleot ...
Oryctolagus cuniculus, Ovis aries
Can. J. Microbiol.
28
696-702
1982
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2
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1
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326405
Broeker
-
A nicotinamide adenine dinucle ...
Streptomyces griseus
FEMS Microbiol. Lett.
6
245-247
1979
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1
2
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1
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1
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1
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1
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326404
Mather
A heat-stable nicotinamide-ade ...
Pseudomonas putida KB1
Biochem. J.
129
141-152
1972
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5
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5
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1
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5
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5
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