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Information on EC 3.6.1.58 - 8-oxo-dGDP phosphatase
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3.6.1.58 8-oxo-dGDP phosphataseIUBMB Comments
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) . The human enzyme NUDT18 also hydrolyses 8-oxo-dADP and 2-hydroxy-dADP, the latter at a slower rate .
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
MTH3, MutT homologue 3, NDX-1, NUDT, NUDT5, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
NUDT5
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate
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-
-
-
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PATHWAY SOURCE
PATHWAYS
MetaCyc
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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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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
-
-
?
8-oxo-dADP + H2O
8-oxo-dAMP + phosphate
8-oxo-dADP is hydrolyzed slightly more efficiently than 8-oxo-dGDP
-
-
?
8-oxo-dGTP + H2O
8-oxo-dGDP + phosphate
-
the enzyme hardly cleaves 8-oxo-dGTP
-
-
?
2-hydroxy-dADP + H2O
2-hydroxy-dAMP + phosphate
kcat/KM is 15% of the wild-type value
-
-
?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
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
-
-
?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
8-oxo-dGDP is a specific substrate for the NUDT5 protein
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-
?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
-
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
-
8-oxoGDP is a specific substrate for the human NUDT5 protein
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-
?
8-oxo-GDP + H2O
8-oxo-GMP + phosphate
-
the enzyme can degrade 8-oxo-GDP as efficiently as 8-oxo-dGDP
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-
?
dGDP + H2O
dGMP + phosphate
poor substrate. Vmax/Km is 32% of value for 8-oxo-dGDP
-
-
?
additional information
?
-
-
NDX-1 does not hydrolyze 8-oxo-dGTP, 2-hydroxy-dATP or 2-hydroxy-dADP
-
-
?
additional information
?
-
-
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
?
-
NUDT5 hydrolyses 8-oxo-dGTP only at very low levels (Vmax/Km is 0.07% of the value for 8-oxo-dGDP)
-
-
?
additional information
?
-
-
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
?
-
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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-
?
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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
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
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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INHIBITOR
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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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
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
all three of the human MTH1, MTH2, and NUDT5 proteins act as a defense against the mutagenesis induced by oxidized dGTP
physiological function
-
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
physiological function
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
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). MUTT1_MYCS2
Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
322
0
35923
Swiss-Prot
-
ADPP_MYCTU
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
207
0
22893
Swiss-Prot
-
NUD18_DANRE
325
0
36900
Swiss-Prot
other Location (Reliability: 1)
NUD18_HUMAN
323
0
35501
Swiss-Prot
Secretory Pathway (Reliability: 5)
NUD18_MOUSE
323
0
35694
Swiss-Prot
other Location (Reliability: 5)
NUD18_MOUSE
323
0
35694
Swiss-Prot
other Location (Reliability: 5)
NUD18_RAT
323
0
35647
Swiss-Prot
other Location (Reliability: 5)
NUDT5_HUMAN
219
0
24328
Swiss-Prot
other Location (Reliability: 1)
NUDT5_MOUSE
218
0
23984
Swiss-Prot
other Location (Reliability: 1)
NUDT5_PONAB
216
0
24070
Swiss-Prot
other Location (Reliability: 1)
NUDT5_RAT
219
0
24117
Swiss-Prot
other Location (Reliability: 1)
A0A6J8ASD0_MYTCO
321
0
35942
TrEMBL
other Location (Reliability: 1)
A0A1Y0XXY1_ACEPA
139
0
14760
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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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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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kamiya, H.; Hori, M.; Arimori, T.; Sekiguchi, M.; Yamagata, Y.; Harashima, H.
NUDT5 hydrolyzes oxidized deoxyribonucleoside diphosphates with broad substrate specificity
DNA Repair
8
1250-1254
2009
Homo sapiens (Q9UKK9)
brenda
Ishibashi, T.; Hayakawa, H.; Sekiguchi, M.
A novel mechanism for preventing mutations caused by oxidation of guanine nucleotides
EMBO Rep.
4
479-483
2003
Homo sapiens (Q9UKK9)
brenda
Hori, M.; Satou, K.; Harashima, H.; Kamiya, H.
Suppression of mutagenesis by 8-hydroxy-2'-deoxyguanosine 5'-triphosphate (7,8-dihydro-8-oxo-2'-deoxyguanosine 5'-triphosphate) by human MTH1, MTH2, and NUDT5
Free Radic. Biol. Med.
48
1197-1201
2010
Homo sapiens (Q9UKK9)
brenda
Ito, R.; Sekiguchi, M.; Setoyama, D.; Nakatsu, Y.; Yamagata, Y.; Hayakawa, H.
Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein
J. Biochem.
149
731-738
2011
Homo sapiens
brenda
Zha, M.; Zhong, C.; Peng, Y.; Hu, H.; Ding, J.
Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity
J. Mol. Biol.
364
1021-1033
2006
Homo sapiens (Q9UKK9)
brenda
Ishibashi, T.; Hayakawa, H.; Ito, R.; Miyazawa, M.; Yamagata, Y.; Sekiguchi, M.
Mammalian enzymes for preventing transcriptional errors caused by oxidative damage
Nucleic Acids Res.
33
3779-3784
2005
Homo sapiens
brenda
Sanada, U.; Yonekura, S.; Kikuchi, M.; Hashiguchi, K.; Nakamura, N.; Yonei, S.; Zhang-Akiyama, Q.M.
NDX-1 protein hydrolyzes 8-oxo-7,8-dihydrodeoxyguanosine-5-diphosphate to sanitize oxidized nucleotides and prevent oxidative stress in Caenorhabditis elegans
J. Biochem.
150
649-657
2011
Caenorhabditis elegans
brenda
Takagi, Y.; Setoyama, D.; Ito, R.; Kamiya, H.; Yamagata, Y.; Sekiguchi, M.
Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine and deoxyguanosine diphosphates: comparison with MTH1 and MTH2
J. Biol. Chem.
287
21541-21549
2012
Homo sapiens
brenda
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