Information on EC 3.6.1.58 - 8-oxo-dGDP phosphatase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.6.1.58
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RECOMMENDED NAME
GeneOntology No.
8-oxo-dGDP phosphatase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate
show the reaction diagram
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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].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
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
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-hydroxy-dADP + H2O
2-hydroxy-dAMP + phosphate
show the reaction diagram
5-formyl-dUDP + H2O
5-formyl-dUMP + phosphate
show the reaction diagram
kcat/KM is 30% of the wild-type value
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?
8-hydroxy-dADP + H2O
8-hydroxy-dAMP + phosphate
show the reaction diagram
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-
-
?
8-oxo-dADP + H2O
8-oxo-dAMP + phosphate
show the reaction diagram
8-oxo-dADP is hydrolyzed slightly more efficiently than 8-oxo-dGDP
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-
?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
show the reaction diagram
8-oxo-dGTP + H2O
8-oxo-dGDP + phosphate
show the reaction diagram
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the enzyme hardly cleaves 8-oxo-dGTP
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-
?
8-oxo-GDP + H2O
8-oxo-GMP + phosphate
show the reaction diagram
dADP + H2O
dAMP + phosphate
show the reaction diagram
kcat/KM is 16% of the wild-type value
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-
?
dGDP + H2O
dGMP + phosphate
show the reaction diagram
GDP + H2O
GMP + posphate
show the reaction diagram
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Vmax/Km is 6.5% of the value for 8-oxo-GDP
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
show the reaction diagram
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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-GDP + H2O
8-oxo-GMP + phosphate
show the reaction diagram
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?
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8-oxo-dGDP
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inhibits cleavage of ADP-ribose
ADP-ribose
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inhibits cleavage of 8-oxo-dGTP
AMP
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inhibits cleavage of 8-oxo-dGTP
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0088
2-hydroxy-dADP
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pH 8.0, 30°C
0.004
5-formyl-dUDP
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pH 8.0, 30°C
0.0029
8-oxo-dADP
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pH 8.0, 30°C
0.0021 - 0.77
8-oxo-dGDP
0.0049 - 0.0117
8-oxo-GDP
0.0126
dADP
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pH 8.0, 30°C
0.0076 - 7.1
dGDP
0.048
GDP
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pH 8.0, 30°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.004
2-hydroxy-dADP
Homo sapiens
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pH 8.0, 30°C
0.0035
5-formyl-dUDP
Homo sapiens
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pH 8.0, 30°C
0.009
8-oxo-dADP
Homo sapiens
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pH 8.0, 30°C
0.006
8-oxo-dGDP
Homo sapiens
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pH 8.0, 30°C
0.006
dADP
Homo sapiens
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pH 8.0, 30°C
0.015
dGDP
Homo sapiens
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pH 8.0, 30°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.45
2-hydroxy-dADP
Homo sapiens
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pH 8.0, 30°C
28437
0.88
5-formyl-dUDP
Homo sapiens
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pH 8.0, 30°C
41710
3.1
8-oxo-dADP
Homo sapiens
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pH 8.0, 30°C
15190
2.9
8-oxo-dGDP
Homo sapiens
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pH 8.0, 30°C
4164
0.48
dADP
Homo sapiens
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pH 8.0, 30°C
731
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10
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cleavage of 8-oxo-dGDP
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
9.5 - 12
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pH 9.5: about 50% of maximal activity, pH 12.0: about 50% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
expressed in Escherichia coli BL21 cells
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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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