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Enzyme Nomenclature
Information on EC 3.6.1.13 - ADP-ribose diphosphatase
for references in articles please use BRENDA:EC3.6.1.13
Word Map on EC 3.6.1.13
- 3.6.1.13
-
diadenosine
- polyphosphate
-
mutt
-
pyrophosphatases
-
decapping
-
dinucleoside
-
sanitization
- radiodurans
-
diphosphoinositol
- ap6a
- oligophosphate
-
melastatin
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
3.6.1.13
-
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RECOMMENDED NAME
GeneOntology No.
ADP-ribose diphosphatase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
-
-
-
-
ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
molecular catalytic mechanism involving Arg51, Arg111, Glu112, and Glu116, active site structure, substrate binding involving Arg51, Leu98, Trp28 and Trp46 and transition-state structure, structure-function relationship, and kinetic analysis
-
ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
substrate binding mode in the active site of the ADPRase domain and catalytic mechanism
Q5NHR1;
ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
substrate binding mode in the active site of the ADPRase domain and catalytic mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phosphorous acid anhydride hydrolysis
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
ADP-D-ribose ribophosphohydrolase
-
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CAS REGISTRY NUMBER
COMMENTARY
9024-83-3
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
enzyme displays both nicotinamide mononucleotide deamidase and ADP-ribose diphosphatase activities
Q5SHB0
UniProt
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
enzyme displays both nicotinamide mononucleotide deamidase and ADP-ribose diphosphatase activities
Q5SHB0
UniProt
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
NUDX7 contributes to 23% of the total diphosphohydrolase activity toward ADP-ribose under normal conditions, while under oxidative stress, the contribution of NUDX7 to the activity increases to 34%. Additionally, NUDX7 accounts for 53% of the total pyrophosphohydrolase activity toward NADH under normal conditions and the activity is increased by oxidative stress with NUDX7 contributing 57%
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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
1,Nepsilon-etheno-ADP-ribose + H2O
1,Nepsilon-etheno-AMP-ribose + phosphate
-
fluorogenic substrate
the product is converted to fluorescent 1,Nepsilon-etheno-adenosine by alkaline phosphatase for detection
-
?
ADPribose 2'-phosphate + H2O
adenosine 2',5'-diphosphate + D-ribose 5-phosphate
-
-
-
-
?
CDP-glucose + H2O
CMP + glucose 5-phosphate
-
at 5% of the activity with ADPribose
-
-
?
CDP-ribose + H2O
CMP + D-ribose 5-phosphate
-
kcat/Km is 2.5% of the kcat/Km for ADP-ribose
-
-
?
diadenosine 5',5''-diphosphate + H2O
?
20% the activity with ADP-ribose
-
-
?
GDP-glucose + H2O
GMP + glucose
7% of the activity with ADP-ribose
-
-
?
GDP-ribose + H2O
GMP + D-ribose 5-phosphate
-
kcat/Km is 3% of the kcat/Km for ADP-ribose
-
-
?
IDP-ribose + H2O
IMP + D-ribose 5-phosphate
-
138% of the activity with ADPribose
-
-
?
IDPribose + H2O
IMP + D-ribose 5-phosphate
77% of the activity with ADPribose
-
-
?
NAD+ + H2O
?
-
ADPRibase-Mn in presence of Mn2+, no activity with ADPRibase I and ADPRibase II
-
-
?
UDP-galactose + H2O
UDP + galactose
7% of the activity with ADP-ribose
-
-
?
ADP-glucose + H2O
AMP + alpha-D-glucose 1-phosphate
-
at 21% of the activity with ADPribose
-
-
?
ADP-glucose + H2O
AMP + alpha-D-glucose 1-phosphate
56% of the activity with ADP-ribose
-
-
?
ADP-glucose + H2O
AMP + alpha-D-glucose 1-phosphate
-
about 70% of the activity with ADP-mannose
-
-
?
ADP-glucose + H2O
AMP + alpha-D-glucose 1-phosphate
-
about 70% of the activity with ADP-ribose
-
-
?
ADP-glucose + H2O
AMP + alpha-D-glucose 1-phosphate
-
ADPRibase II, very low activity with ADPRibase I
-
-
?
ADP-glucose + H2O
AMP + alpha-D-glucose 1-phosphate
9% of the activity with ADPribose
-
-
?
ADP-glucose + H2O
AMP + alpha-D-glucose 1-phosphate
-
kcat/Km is 3% of the kcat/Km for ADP-ribose
-
-
?
ADP-mannose + H2O
AMP + D-mannose 1-phosphate
-
at 70% of the activity with ADPribose
-
-
?
ADP-mannose + H2O
AMP + D-mannose 1-phosphate
103% of the activity with ADP-ribose
-
-
?
ADP-mannose + H2O
AMP + D-mannose 1-phosphate
-
about 80% of the activity with ADP-ribose
-
-
?
ADP-mannose + H2O
AMP + D-mannose 1-phosphate
-
ADPRibase II, low activity with ADPRibase I
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
Growth Factor Gene 1 (GFG1, At4g12720) encodes a nudix hydrolase, that is an NADH pyrophosphatase and ADP-ribose pyrophosphatase
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
AtNUDT10 shows both ADP-ribose and NADH pyrophosphatase activity
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
AtNUDT2 shows both ADP-ribose and NADH pyrophosphatase activity
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
AtNUDT6 shows both ADP-ribose and NADH pyrophosphatase activity
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
AtNUDT7 shows both ADP-ribose and NADH pyrophosphatase activity
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
-
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
Q5NHR1;
substrate binding structure, overview
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may have a predominant role in free ADP-ribose turnover and as a protective agent preventing the accumulation of this potential dangerous metabolite
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
protective enzyme whose function is to limit the intracellular accumulation of ADP-ribose
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme plays important roles in controlling the intracellular levels of ADPR and preventing non-enzymatic ADP-ribosylation of proteins by hydrolyzing ADPR to AMP and ribose 5?-phosphate
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
ADP-ribose pyrophosphatase Sll1054 hydrolyzes ADP-ribose specifically
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
ADP-ribose pyrophosphatase Slr0920 hydrolyzes ADP-ribose specifically
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
ADP-ribose pyrophosphatase Slr1134 hydrolyzes ADP-ribose, NADH and flavin adenine dinucleotide
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
substrate binding structure, overview
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme plays a key role in regulating the intracellular ADPribose levels, and prevents nonenzymatic ADP-ribosylation
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
highly specific substrate
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
interactions responsible for the substrate recognition are located at the terminal moieties of the substrate. The adenine moiety is recognized by Ile-19 and the main chain carbonyl group of Glu-29 and/or Gly-104. The terminal ribose moiety is recognized by the sum of some weak interactions with multiple residues that are close in space. Glu-82 and Glu-86 are essential for catalysis but unlikely to act as a catalytic base. Two-metal ion mechanism for the catalysis of ADPRase in which a water molecule is activated to act as a nucleophile by the cations coordinated by Glu-82 and Glu-86. Arg-54, Glu-70, Arg-81, and Glu-85 are predicted to support this nucleophilic attack on the R-phosphate of the substrate
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
preferred substrate, substrate recognition and binding structure, overview
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
the enzyme plays a key role in regulating the intracellular ADPribose levels, and prevents nonenzymatic ADP-ribosylation
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
preferred substrate, substrate recognition and binding structure, overview
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
highly specific substrate
-
-
?
ADP-ribose + H2O
AMP + ribose 5-phosphate
the function of the enzyme might be to remove free ADP-ribose arising from NAD+ and protein-bound poly- and non-enzymic protein glycation
-
-
?
ADP-ribose + H2O
AMP + ribose 5-phosphate
-
about 65% of the activity with ADP-mannose
-
-
?
ADP-ribose + H2O
AMP + ribose 5-phosphate
-
ADP-ribose is a better substrate compared with 8-oxo-dGDP
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
nucleophilic attack at the adenosyl phosphate. The enzyme cycles between an open free enzyme and a closed substrate-metal complex conformation. This cycling may be important in preventing nonspecific hydrolysis of other nucleotides
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play an important role in the regulation of intracellular steady-state of free ADPribose
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
-
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play a role in tellurite resistance
-
-
?
FAD + H2O
?
-
ADPRibase-Mn and ADPRibase II, very low activity with ADPRibase I in presence of Mn2+
-
-
?
GDP-glucose + H2O
GMP + glucose 5-phosphate
-
about 15% of the activity with ADP-mannose
-
-
?
GDP-glucose + H2O
GMP + glucose 5-phosphate
-
about 15% of the activity with ADP-ribose
-
-
?
GDP-mannose + H2O
GMP + D-mannose 1-phosphate
at 59% of the activity with ADPribose
-
-
?
GDP-mannose + H2O
GMP + D-mannose 1-phosphate
-
at 40% of the activity with ADPribose
-
-
?
GDP-mannose + H2O
GMP + D-mannose 1-phosphate
-
about 15% of the activity with ADP-mannose
-
-
?
GDP-mannose + H2O
GMP + D-mannose 1-phosphate
-
about 20% of the activity with ADP-ribose
-
-
?
GDP-mannose + H2O
GMP + D-mannose 1-phosphate
-
at 9% of the activity with ADPribose
-
-
?
GDP-mannose + H2O
GMP + D-mannose 1-phosphate
-
at 1% of the activity with ADPribose
-
-
?
IDP-ribose + H2O
IMP + ribose 5-phosphate
-
77% of the activity with ADPribose
-
-
?
IDP-ribose + H2O
IMP + ribose 5-phosphate
-
at 59% of the activity with ADPribose
-
-
?
IDP-ribose + H2O
IMP + ribose 5-phosphate
9% of the activity with ADP-ribose
-
-
?
NADH + H2O
?
-
ADPRibase I, ADPribase II and ADPRibase-Mn in presence of Mn2+
-
-
?
UDP-glucose + H2O
UMP + glucose 5-phosphate
-
at 5% of the activity with ADPribose
-
-
?
UDP-glucose + H2O
UMP + glucose 5-phosphate
-
about 12% of the activity with ADP-mannose
-
-
?
UDP-glucose + H2O
UMP + glucose 5-phosphate
-
about 5% of the activity with ADP-ribose
-
-
?
UDP-mannose + H2O
UMP + D-mannose 1-phosphate
-
at 20% of the activity with ADPribose
-
-
?
UDP-mannose + H2O
UMP + D-mannose 1-phosphate
-
about 15% of the activity with ADP-mannose
-
-
?
UDP-mannose + H2O
UMP + D-mannose 1-phosphate
-
about 5% of the activity with ADP-ribose
-
-
?
additional information
?
-
-
no or very poor substrates: ADP-glucose, UDP-glucose, CDP-glucose, CDP, CMP, AMP, and 3',5'-cAMP
-
-
-
additional information
?
-
no or very poor substrates: ADP-glucose, UDP-glucose, CDP-glucose, CDP, CMP, AMP, and 3',5'-cAMP
-
-
-
additional information
?
-
-
the enzyme is a bifunctional NMN adenylyltransferase/ADP-ribose diphosphatase, NMN specificity of the enzyme, overview
-
-
-
additional information
?
-
Q5NHR1;
the enzyme is a bifunctional NMN adenylyltransferase/ADP-ribose diphosphatase, NMN specificity of the enzyme, overview
-
-
-
additional information
?
-
-
no activity with ADPglucose, ADPmannose, UDPglucose
-
-
-
additional information
?
-
-
hNUDT5 can utilize a variety of ADP-sugar conjugates as substrate, with a preference for ADPR
-
-
-
additional information
?
-
-
three diphosphatases: 1.ADPRibase-I: an ADP-ribose diphosphatase highly specific for ADPribose and IDPribose in presence of Mg2+, but active also on non-reducing ADP-hexoses and dinucleotides, not on NAD+, when Mg2+ is replaced with Mn2+, 2. ADPRibase-Mn: a Mn2+-dependent diphosphatase active on ADPribose and IDPribose, dinucleotides and CDP alcohols, 3. ADPribase-II: a rather unspecific diphosphatase that, with Mg2+, is active on AMP or IMP containing NDP sugars and dinucleotides, not on NAD+, and with Mn2+ also active on non-adenine NDP-sugars and CDP-alcohols
-
-
-
additional information
?
-
the enzyme is a bifunctional NMN adenylyltransferase/ADP-ribose diphosphatase, NMN specificity of the enzyme, overview
-
-
-
additional information
?
-
-
the enzyme is a bifunctional NMN adenylyltransferase/ADP-ribose diphosphatase, NMN specificity of the enzyme, overview
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
ADP-ribose + H2O
AMP + ribose 5-phosphate
Q9UKK9
the function of the enzyme might be to remove free ADP-ribose arising from NAD+ and protein-bound poly- and non-enzymic protein glycation
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
-
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may have a predominant role in free ADP-ribose turnover and as a protective agent preventing the accumulation of this potential dangerous metabolite
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
protective enzyme whose function is to limit the intracellular accumulation of ADP-ribose
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme plays important roles in controlling the intracellular levels of ADPR and preventing non-enzymatic ADP-ribosylation of proteins by hydrolyzing ADPR to AMP and ribose 5?-phosphate
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme plays a key role in regulating the intracellular ADPribose levels, and prevents nonenzymatic ADP-ribosylation
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
the enzyme plays a key role in regulating the intracellular ADPribose levels, and prevents nonenzymatic ADP-ribosylation
-
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
P54570
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
P44684
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play an important role in the regulation of intracellular steady-state of free ADPribose
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play a role in tellurite resistance
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
-
the enzyme may play a role in tellurite resistance
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Mg2+
Mn2+
Zn2+
Co2+
-
absolute requirement for divalent metal ion is satisfied by Mn2+, Co2+ or Mg2+
Mg2+
-
divalent cation required, Mg2+ or Mn2+. Mg2+ is much more effective than Mn2+
Mg2+
-
absolutely required, activates at 5 mM
Mg2+
-
strictly requires Mg2+ (more than 1 mM) or Mn2+ for full activity. Treatment with H2O2 changes the specificity of both ADP-ribose activities for the activating divalent cation, giving them a marked preference for Mn2+ and rendering them virtually inactive with Mg2+
Mg2+
-
absolute requirement for divalent metal ion is satisfied by Mn2+, Co2+ or Mg2+
Mg2+
-
ADPRibase-I is highly specific for ADPribose and IDPribose in presence of Mg2+, but active also on non-reducing ADP-hexoses and dinucleotides when Mg2+ is replaced with Mn2+. ADPRibase-Mn is a Mn2+-dependent diphosphatase active on ADPribose and IDPribose, dinucleotides and CDP alcohols. ADPribase-II is a rather unspecific diphosphatase that, with Mg2+, is active on AMP or IMP containing NDP sugars and dinucleotides, and with Mn2+ also active on non-adenine NDP-sugars and CDP-alcohols
Mg2+
-
divalent cation required, Mg2+ is most effective, ADP-ribose pyrophosphatase Sll1054; divalent cation required, Mg2+ is most effective, ADP-ribose pyrophosphatase Slr0920; divalent cation required, Mg2+ is most effective, ADP-ribose pyrophosphatase Slr1134
Mn2+
-
divalent cation required, Mg2+ or Mn2+. Mg2+ is much more effective than Mn2+
Mn2+
-
maximal activity at 0.02-0.05 mM with a steep decrease at increasing pH-values, Mg2+ or Mn2+ required
Mn2+
-
strictly requires Mg2+ or Mn2+ (0.05 mM) for full activity. Treatment with H2O2 changes the specificity of both ADP-ribose activities for the activating divalent cation, giving them a marked preference for Mn2+ and rendering them virtually inactive with Mg2+
Mn2+
-
absolute requirement for divalent metal ion is satisfied by Mn2+, Co2+ or Mg2+
Mn2+
-
ADPRibase-I is highly specific for ADPribose and IDPribose in presence of Mg2+, but active also on non-reducing ADP-hexoses and dinucleotides when Mg2+ is replaced with Mn2+. ADPRibase-Mn is a Mn2+-dependent diphosphatase active on ADPribose and IDPribose, dinucleotides and CDP alcohols. ADPribase-II is a rather unspecific diphosphatase that, with Mg2+, is active on AMP or IMP containing NDP sugars and dinucleotides, and with Mn2+ also active on non-adenine NDP-sugars and CDP-alcohols
Mn2+
divalent cation required, Mn2+ results in 22% of the activity observed in presence of Mg2+
Zn2+
divalent cation required, Zn2+ results in 9% of the activity observed in presence of Mg2+
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5-amino-3-(morpholin-4-yl)-1,2,3-oxadiazol-3-ium
-
3-morpholinosynonimine increases Km and slightly decreases Vmax
8-oxo-dGDP
-
the ADP-ribose cleavage is competitively inhibited by 8-oxo-dGDP (68% relative cleavage efficiency at 0.01 mM)
8-oxo-dGMP
-
the ADP-ribose cleavage is competitively inhibited by 8-oxo-dGMP (89% relative cleavage efficiency at 0.01 mM)
ADP-ribose
-
the 8-oxo-dGDP cleavage is competitively inhibited by ADP-ribose (22% relative cleavage efficiency at 0.005 mM)
AMP
-
the 8-oxo-dGDP cleavage is competitively inhibited by AMP (30% relative cleavage efficiency at 0.005 mM)
fluoride
-
inhibition of Mg2+-dependent activity of ADP-ribose pyrophosphatase. the Mn2+-dependent activity is not affected by fluoride
N-acetyl-p-benzoquinoneimine
1 mM, almost complete inhibition of activity towards ADPribose. The inhibitor is a useful tool for distinguishing the specific ADP-ribose diphosphatase from the less specific ADP-sugar diphosphatases
N-acetyl-p-benzoquinoneimine
-
decreases Vmax to 30% of control values and increases the Km for ADPribose 2-3fold
nitroprusside
-
nitroprusside in presence of dithiothreitol diminishes Vmax and increases Km
nitroprusside
-
sodium nitroprusside increases Km without appreciably affecting Vmax
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
nitric oxide
-
NO stimulates non-enzymatic ADP-ribosylation, at cysteine residues in the presence of reductant, of NUDT5 using ADP-ribose and consequently activates its ADPRase activity. ADPRase activity in J774 macrophage cells is increased by the treatment with SNP, an exogenous NO generator, or TNF-alpha/IFN-gamma, endogenous NO inducers. NO has a regulatory role, overview
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.76
2',3'-cAMP
wild-type, pH 7.5, temperature not specified in the publication
1.7
2',3'-cAMP
mutant H97A, pH 7.5, temperature not specified in the publication
0.053
ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
0.071
ADP-ribose
mutant H97A, pH 7.5, temperature not specified in the publication
0.1
ADP-ribose
-
25°C, pH 7.6, mutant enzyme E86Q; 25°C, pH 7.6, mutant enzyme S153A
0.11
ADP-ribose
-
25°C, pH 7.6, mutant enzyme E82Q; 25°C, pH 7.6, wild-type enzyme
0.4
ADP-ribose
-
25°C, pH 7.6, mutant enzyme E63Q; 25°C, pH 7.6, mutant enzyme Y28Q
1.15
ADP-ribose
mutant F37A/L196A, pH 7.5, 37°C; mutant F37A, pH 7.5, 37°C
0.19
cADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
12
CDP-choline
wild-type, pH 7.5, temperature not specified in the publication
43
CDP-choline
mutant H97A, pH 7.5, temperature not specified in the publication
3.9
CDP-ethanolamine
wild-type, pH 7.5, temperature not specified in the publication
31
CDP-ethanolamine
mutant H97A, pH 7.5, temperature not specified in the publication
2
CDP-glycerol
wild-type, pH 7.5, temperature not specified in the publication
6.3
CDP-glycerol
mutant H97A, pH 7.5, temperature not specified in the publication
additional information
additional information
-
effect of N-acetyl-p-benzoquinoneimine on Km
-
additional information
additional information
-
kinetic analysis, Trp28 and Trp46 function synergistically in substrate binding and catalysis, overview
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
16.9
2',3'-cAMP
wild-type, pH 7.5, temperature not specified in the publication
29.7
2',3'-cAMP
mutant H97A, pH 7.5, temperature not specified in the publication
0.2
ADP
mutant H97A, pH 7.5, temperature not specified in the publication
0.4
ADP-ribose
mutant H97A, pH 7.5, temperature not specified in the publication
0.7
ADP-ribose
-
mutant enzyme D126N, in presence of Mg2+; mutant enzyme E129Q, in presence of Mg2+
18
ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
0.0005
cADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
0.8
CDP-choline
mutant H97A, pH 7.5, temperature not specified in the publication
67.2
CDP-choline
wild-type, pH 7.5, temperature not specified in the publication
2.1
CDP-ethanolamine
mutant H97A, pH 7.5, temperature not specified in the publication
125.2
CDP-ethanolamine
wild-type, pH 7.5, temperature not specified in the publication
0.8
CDP-glycerol
mutant H97A, pH 7.5, temperature not specified in the publication
95.6
CDP-glycerol
wild-type, pH 7.5, temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4
2',3'-cAMP
mutant F37A/L196A, pH 7.5, 37°C; mutant F37A/L196F/C253A, pH 7.5, 37°C
18
2',3'-cAMP
mutant H97A, pH 7.5, temperature not specified in the publication
22
2',3'-cAMP
wild-type, pH 7.5, temperature not specified in the publication
0.0011
ADP
mutant H97A, pH 7.5, temperature not specified in the publication
5.9
ADP-ribose
mutant H97A, pH 7.5, temperature not specified in the publication
340
ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
0.028
cADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
0.9
cADP-ribose
mutant F37A/L196A, pH 7.5, 37°C; mutant L196A, pH 7.5, 37°C
0.002
CDP-choline
mutant H97A, pH 7.5, temperature not specified in the publication
5.6
CDP-choline
wild-type, pH 7.5, temperature not specified in the publication
0.007
CDP-ethanolamine
mutant H97A, pH 7.5, temperature not specified in the publication
32
CDP-ethanolamine
wild-type, pH 7.5, temperature not specified in the publication
0.12
CDP-glycerol
mutant H97A, pH 7.5, temperature not specified in the publication
48
CDP-glycerol
wild-type, pH 7.5, temperature not specified in the publication
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5 - 9
-
activity at pH 8.0 is about 90% of the activity at pH 6.5 and at pH 9.0, activity with ADP-ribose
7 - 9
8.2
9.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.5 - 10
-
pH 4.5: about 55% of maximal activity, pH 10.0: about 50% of maximal activity, activity with ADP-mannose
6 - 10
-
pH 6.0: about 25% of maximal activity, pH 10.0: about 60% of maximal activity, activity with ADP-ribose
7 - 9
-
linearly decreasing activity profile from pH 7 to pH 9, with activity at pH 9 being 50% of that at pH 7
7.5 - 10
-
pH 7.5: about 60% of maximal activity with ADP-ribose, about 50% of maximal activity with ADP-mannose, pH 10.0: about 70% of maximal activity with activity with ADP-ribose or ADP-mannose
8 - 10
pH 8.0: about 40% of maximal activity, pH 10.0: about 60% of maximal activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37 - 75
-
rate of hydrolysis of ADPribose is 15fold higher than at 37°C, incubations at higher temperatures are impractical because of the spontaneous hydrolysis of the substrate
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.9
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
activity in leaves is lower than in stem and root, AtNUDT10; activity in roots is lower than in leaves and stem, AtNUDT6; AtNUDT2; AtNUDT7
-
activity in leaves is lower than in stem and root, AtNUDT10; activity in roots is lower than in leaves and stem, AtNUDT6; AtNUDT2; AtNUDT7
-
activity in leaves is lower than in stem and root, AtNUDT10; activity in roots is lower than in leaves and stem, AtNUDT6; AtNUDT2; AtNUDT7
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100);
Q9RSC1
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422);
Escherichia coli (strain K12);
Homo sapiens;
I6X235
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv);
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh);
Thermus thermophilus;
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q6MIH8
Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100);
Q6MIH8
Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100);
Q6MIH8
Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100);
O33199
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh);
O33199
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh);
O33199
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh);
O33199
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh);
O33199
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
Q5SKW5
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579);
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
32000
40000
47000
85000
-
dimeric thioredoxin fusion protein expressed in Escherichia coli, gel filtration
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
hexamer
6 * 26735, calculation from nucleotide sequence; 6 * 28000, SDS-PAGE
additional information
additional information
-
ADPRase Nudix domain of NadM-Nudix and bacterial monofunctional ADPRase are connected by a long alpha helix with ADPRase active site facing away from the NMNATase domain, while the NMNATase active site opens partially toward the ADPRase domain, structure of the ADPRase domain, overview
additional information
Q5NHR1;
ADPRase Nudix domain of NadM-Nudix and bacterial monofunctional ADPRase are connected by a long alpha helix with ADPRase active site facing away from the NMNATase domain, while the NMNATase active site opens partially toward the ADPRase domain, structure of the ADPRase domain, overview
additional information
ADPRase Nudix domain of NadM-Nudix and bacterial monofunctional ADPRase are connected by a long alpha helix with ADPRase active site facing away from the NMNATase domain, while the NMNATase active site opens partially toward the ADPRase domain, structure of the ADPRase domain, overview
additional information
-
ADPRase Nudix domain of NadM-Nudix and bacterial monofunctional ADPRase are connected by a long alpha helix with ADPRase active site facing away from the NMNATase domain, while the NMNATase active site opens partially toward the ADPRase domain, structure of the ADPRase domain, overview
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
substrate-docking to zebrafish wild-type protein, and H97A mutant point to a role of His-97 in catalysis by orientation, and to a bidentate water bridging the dinuclear metal center as the potential nucleophile
gadolinium derivative, to 2.0 A resolution. The crystal structure of DR2204 consists of the conserved alpha/beta/alpha sandwich fold typical of Nudix hydrolases, the Nudix box, residues 94-115, holding the alpha1 helix sits between two loops accessible to the solvent, while the other two helices, alpha2 and alpha3, lie on the other side of the central beta-sheet and participate in dimer-interface formation
hanging-drop vapor diffusion at 18°C. The structure of the apo enzyme, the active enzyme and the complex with ADP-ribose are determined to 1.9 A, 2.7 A and 2.3 A, respectively. The Nudix motif residues, folded as a loop-helix-loop tailored for diphosphate hydrolysis, compose the catalytic center
-
purified recombinant enzyme in complex with the product AMP and Mn2+ ions in its Nudix active site, sitting drop vapor diffusion method, 20°C, 0.001 ml of 15 mg/ml protein solution is mixed with an equal volume of reservoir solution containing 0.1 M Tris, pH 7.5, 200 mM MgCl2, and 19% PEG 3350, with or without 30 mM AMP, equilibration against the reservoir, X-ray diffraction structure determination and analysis at 2.3 A resolution, molecular replacement method
Q5NHR1;
complexed with 8-oxo-dGMP, 8-oxo-dGDP and 8-oxo-dADP, hanging drop vapor diffusion method, using 0.8 M NaH2PO4/1.2M K2HPO4 and 0.1 M acetate (pH 4.5), and 0.2M ammonium acetate, 35-40% (w/v) polyethylene glycol 3350 and 0.1 M sodium citrate (pH 6.2)
-
in apo form, in complex with ADP-D-ribose, and in complex with AMP with bound Mg2+, hanging drop vapor diffusion method, using 160 mM sodium acetate (pH 5.5), and 25% (w/v) 2-methyl-2,4-pentanediol, or 300 mM di-ammonium hydrogen citrate, 6% (w/v) n-propanol and 15% (w/v) polyethylene glycol 3350, or 200 mM sodium acetate, 100 mM Tris-HCl (pH 8.0) and 30% (w/v) polyethylene glycol 4000
-
in complex with alpha,beta-methyleneadenosine diphosphoribose and 3 Mg2+ ions, hanging drop vapor diffusion method, using 250 mM sodium acetate, 100 mM Tris-HCl, pH 8.0, and 29% (w/v) polyethylene glycol 4000; purified recombinant wild-type and truncated mutant NUDT5 in complex with a non-hydrolyzable ADPR analogue, alpha,beta-methyleneadenosine diphosphoribose, and three Mg2+ ions representing the transition state of the enzyme during catalysis, 20 mg/ml protein is incubated with 5 mM AMPCPR and 10 mM MgCl2 at 4 °C overnight, followed by hanging drop vapour diffusion method, wild-type enzyme in complex with AMPCPR, and truncation mutant DELTAhNUDT5 in complex with AMPCPR and Mg2+, 4 °C, mixing of equal volumes of the protein solution and the reservoir solution containing 250 mM NaAc, 100 mM Tris-HCl, pH 8.0, and 29% PEG 4000, ingle crystals of the plate-shape morphology grow after 1 month, X-ray diffraction structure determination and anaylsis at 2.0 A resolution, molecular modelling
-
substrate docking on a homology model suggests possible interactions of ADP-ribose with seven residues located, with one exception (Cys253), either within the metallo-dependent phosphatases signature (Gln27, Asn110, His111), or in unique structural regions of the ADPRibase-Mn family: s2s3 (Phe37 and Arg43) and h7h8 (Phe210), around the active site entrance. Residue Phe37 is needed for ADP-ribose preference without catalytic effect. Arg43 is essential for catalysis. Cys253 is hindering for cADPR phosphohydrolase
purified recombinant His-tagged enzyme in complex with co-purified NAD and diphosphate complexed in the NadM-domain active site, and with ADPR substrate complexed in the Nudix-domain, hanging drop vapor diffusion method, 0.0015 ml of 15 mg/ml protein solution is mixed with an equal volume of reservoir solution containing 100 mM Tris, pH 7.5, and 1.5 M Li2SO4, 20°C, 3 days to 2 weeks, X-ray diffraction structure determination and analysis at 2.6 A resolution, selenomethionyl MAD phasing method
crystallized in absence or presence of ADP-ribose by hanging-drop vapour-diffusion method. 1.5 A resolution from the apo form using synchrotron radiation and 2.0 A resolution from the complexed form. Both crystals belong to space group P3(1)21 or P3(2)21 and contain one molecule in the asymmetric unit
-
in complex with alpha,beta-methyleneadenosine diphosphoribose, sitting drop vapor diffusion method, using 18% (w/v) PEG 4000, 0.1 M sodium acetate buffer pH 5.3, 20% (w/v) glycerol, 0.2 M ammonium sulfate, at 20°C
-
Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue, hanging-drop vapor diffusion method, 20 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 100 mM KCl, 0.001 ml of protein solution is mixed with the equal volume of reservoir solution and equilibrated against the reservoir, containing 0.1 M MES, pH 6.5, 0.16 M sodium acetate or magnesium acetate for the complexed enzyme, 14% PEG 8000, and 20% glycerol, at 20°C, soaking of crystals in 50 mM KAu(CN)2, X-ray diffraction structure determination and anaylsis at 2.0 A resolution, MAD phasing, model building, and refinement
-
to 2.16 A resolution. The crystal structure shows an unusual asymmetric dimer, with three domains for each chain. The C-terminal domain harbors the nicotinamide mononucleotide deamidase activity. The N-terminal domain belongs to the COG1058 family and is associated with the ADP-ribose diphosphatase activity. The mechanism for the ADP-ribose diphosphatase reaction involves a rotation of the COG1058 domain dimer as part of the reaction cycle
Q5SHB0;
Zn2+-bound enzyme, binary complex with ADPribose, ternary complex with Zn2+ and ADPribose, ternary complex with Gd3+ and ADPribose, product complex with AMP and Mg2+, product complex with ribose 5'-phosphate and Zn2+, mutant enzyme E82Q with ligands Mg2+ and SO42-, mutant enzyme E86Q with ligands Mg2+ and ADPribose, mutant enzyme E82Q with ligands Zn2+ and SO42-, mutant enzyme E86Q with ligands Zn2+ and ADPribose
-
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
acetaminophen-treated animals and controls; ADPribose pyrophosphatase I; partial
-
ADP-ribose pyrophosphatase Sll1054; ADP-ribose pyrophosphatase Slr0920; ADP-ribose pyrophosphatase Slr1134
-
ammonium sulfate precipitation, Toyopearl Phenyl-650M column chromatography, and Q Sepharose column chromatography
-
Ni-Sepharose 6 column chromatography, HisTrap column chromatography, and Superdex 75 gel filtration
-
partial
recombinant enzyme
recombinant GST-tagged enzyme from Escherichia coli by glutathione affinity chromatography, the tag is cleaved off by TEV protease, and the detagged protein is further purified by anion exchange chromatography
Q5NHR1;
recombinant His-tagged enzyme from Escherichia coli strain Bl21 by nickel affinity and anion exchange chromatography, and gel filtration
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant His6-tagged NUDT5 from Escherichia coli strain BL21 by nickel affinity chromatography
-
recombinant Ndx2 from Escherichia coli strain BL21(DE3) by heat treatment at 70°C for 15 min and ion exchange chromatography
-
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expression in Escherichia coli
expression in Escherichia coli, ADP-ribose pyrophosphatase Sll1054; expression in Escherichia coli, ADP-ribose pyrophosphatase Slr0920; expression in Escherichia coli, ADP-ribose pyrophosphatase Slr1134
-
expression in Escherichia coli, AtNUDT10; expression in Escherichia coli, AtNUDT2; expression in Escherichia coli, AtNUDT6; expression in Escherichia coli, AtNUDT7
-
expression of ORF38 as His6-tagged protein in Escherichia coli strain Bl21(DE3)
-
expression of the His-tagged enzyme in Escherichia coli strain Bl21
gene NUDT5, expression in murine J774A.1 macrophage cells, expression of His6-tagged NUDT5 in Escherichia coli strain BL21
-
hexahistidine-tagged recombinant enzyme expressed in Escherichia coli
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
oxidative stress caused by 0.003 mM paraquat for 7 days causes an increase in the total ADP-ribose diphosphohydrolase activity of NUDX7
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H97A
mutant shows 60fold decrease in activity for substrates ADP-ribose and ADP and 300–500fold for CDP-alcohols. For H97A, 2',3'-cAMP is a better substrate than ADP-ribose
C139A
-
site-directed mutagenesis, mutation causes a 2.1fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme; the mutant shows reduced catalytic efficiency compared to the wild type enzyme
C253A
mutant displays a tenfold increased efficiency for cADP-ribose, with no or modest effect on the other substrates
D133A
-
site-directed mutagenesis, mutation causes a 4.0fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme; the mutant shows reduced catalytic efficiency compared to the wild type enzyme
D133N
-
site-directed mutagenesis, mutation causes a 2.1fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme; the mutant shows reduced catalytic efficiency compared to the wild type enzyme
D164A
-
the mutant shows reduced catalytic efficiency compared to the wild type enzyme
D164N
-
the mutant shows increased catalytic efficiency compared to the wild type enzyme
E112Q
-
the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme
E115Q
-
the mutant shows reduced catalytic efficiency compared to the wild type enzyme
E116Q
-
the mutant shows reduced catalytic efficiency compared to the wild type enzyme
E166Q
-
the mutant shows reduced catalytic efficiency compared to the wild type enzyme
E93Q
-
site-directed mutagenesis, mutation causes a 1.8fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme; the mutant shows reduced catalytic efficiency compared to the wild type enzyme
F210A
lowers 40-70fold the catalytic efficiency for ADP-ribose, CDP-choline and 2',3'-cAMP hydrolysis, and 500fold for cADP-ribose
F37A
19fold increased Km for ADP-ribose, with only a 2-3fold increase of the CDP-choline and 2',3'-cAMP Km values
F37