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Enzyme Nomenclature
Information on EC 3.6.1.58 - 8-oxo-dGDP phosphatase
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
3.6.1.58
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RECOMMENDED NAME
GeneOntology No.
8-oxo-dGDP phosphatase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate
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SYSTEMATIC NAME
IUBMB Comments
8-oxo-dGDP phosphohydrolase
The enzyme catalyses the hydrolysis of both 8-oxo-dGDP and 8-oxo-GDP thereby preventing translational errors caused by oxidative damage. The preferred in vivo substrate is not known. The enzyme does not degrade 8-oxo-dGTP and 8-oxo-GTP to the monophosphates (cf. EC 3.6.1.55, 8-oxo-dGTP diphosphatase) [1,2]. Ribonucleotide diphosphates and deoxyribonucleotide diphosphates are hydrolysed with broad specificity. The bifunctional enzyme NUDT5 also hydrolyses ADP-ribose to AMP and D-ribose 5-phosphate (cf. EC 3.6.1.13, ADP-ribose diphosphatase) [4]. The human enzyme NUDT18 also hydrolyses 8-oxo-dADP and 2-hydroxy-dADP, the latter at a slower rate [6].
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
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the knockdown of the MTH1, MTH2, and NUDT5 proteins increases the A:T to C:G substitution mutations induced by 8-hydroxy-dGTP. In addition, the increase in the induced mutation frequency is more evident in the triple-knockdown cells
physiological function
physiological function
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NUDT5 might have a much greater role than MTH1 in preventing the occurrence of mutations that are caused by the misincorporation of 8-oxoguanine in human cells
physiological function
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all three of the human MTH1, MTH2, and NUDT5 proteins act as a defense against the mutagenesis induced by oxidized dGTP
physiological function
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is produced in cells by reactive oxygen species normally formed during cellular metabolic processes. This oxidized base can pair with both adenine and cytosine, and thus the existence of this base in messenger RNA would cause translational errors. The elimination of 8-oxoguanine-containing ribonucleotides from the precursor pool is important to ensure accurate protein synthesis. Both NUDT5 and MTH1 are involved in this process in human cells
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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
5-formyl-dUDP + H2O
5-formyl-dUMP + phosphate
kcat/KM is 30% of the wild-type value
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?
8-oxo-dADP + H2O
8-oxo-dAMP + phosphate
8-oxo-dADP is hydrolyzed slightly more efficiently than 8-oxo-dGDP
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-
?
8-oxo-dGTP + H2O
8-oxo-dGDP + phosphate
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the enzyme hardly cleaves 8-oxo-dGTP
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-
?
2-hydroxy-dADP + H2O
2-hydroxy-dAMP + phosphate
kcat/KM is 15% of the wild-type value
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-
?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
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NUDT5 might have a much greater role than MTH1 in preventing the occurrence of mutations that are caused by the misincorporation of 8-oxoguanine in human cells. NUDT5 has another role in promoting the MTH1 reaction, in removing its inhibitor, 8-oxo-dGDP
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?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
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8-oxo-dGDP is a specific substrate for the NUDT5 protein
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?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
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ADP-ribose is a better substrate for NUDT5 compared with oxidized guanine nucleotides
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-
?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
NUDT5 protein is a hydrolyzing enzyme with broad substrate specificity for oxidized deoxyribonucleoside diphosphates
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?
8-oxo-GDP + H2O
8-oxo-GMP + phosphate
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8-oxoGDP is a specific substrate for the human NUDT5 protein
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?
8-oxo-GDP + H2O
8-oxo-GMP + phosphate
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the enzyme can degrade 8-oxo-GDP as efficiently as 8-oxo-dGDP
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-
?
dGDP + H2O
dGMP + phosphate
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poor substrate. Vmax/Km is 32% of value for 8-oxo-dGDP
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?
additional information
?
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NDX-1 does not hydrolyze 8-oxo-dGTP, 2-hydroxy-dATP or 2-hydroxy-dADP
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additional information
?
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NUDT5 does not degrade 8-oxo-GTP to the monophosphate (Vmax/Km is 0.7% of the activity with 8-oxo-GDP)
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additional information
?
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NUDT5 hydrolyses 8-oxo-dGTP only at very low levels (Vmax/Km is 0.07% of the value for 8-oxo-dGDP)
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additional information
?
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the bifunctional enzyme also hydrolyses ADP-ribose to ADP-ribose and ribose 5-phosphate (cf. EC 3.6.1.13)
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additional information
?
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the hydrolyses of 2-hydroxy-dADP and 5-formyl-dUDP are less effective, with 0.4- and 0.5-fold efficiencies relative to that of 8-oxo-dGDP, respectively. The hydrolyses of the triphosphate derivatives are less efficient than those of the diphosphate counterparts
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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
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
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NUDT5 might have a much greater role than MTH1 in preventing the occurrence of mutations that are caused by the misincorporation of 8-oxoguanine in human cells. NUDT5 has another role in promoting the MTH1 reaction, in removing its inhibitor, 8-oxo-dGDP
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?
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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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
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
9.5 - 12
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pH 9.5: about 50% of maximal activity, pH 12.0: about 50% of maximal activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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PDB
SCOP
CATH
ORGANISM
UNIPROT
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystals of full-length hNUDT5 are grown at 4°C using the hanging-drop vapor diffusion method. Crystal structures of hNUDT5 in apo form, in complex with ADP-ribose, and in complex with AMP with bound Mg2+
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
HisTrap column chromatography, HiTrap heparin column chromatography, and Mono S column chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
the increase in the production of erroneous proteins by oxidative damage is 28fold over the wild-type cells in Escherichia coli mutT deficient cells. By the expression of NUDT5 in the cells, it is reduced to 1.4fold
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when NUDT5 is expressed in Escherichia coli mutT-cells as a His-tagged protein, the increased frequency of spontaneous mutations is decreased to normal levels
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LINKS TO OTHER DATABASES (specific for EC-Number 3.6.1.58)
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