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Information on EC 3.6.1.23 - dUTP diphosphatase and Organism(s) Escherichia coli and UniProt Accession P06968
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3.6.1.23 dUTP diphosphataseIUBMB Comments
The enzyme catalyses the Mg2+-dependent hydrolysis of dUTP to dUMP, providing the substrate for EC 2.1.1.45, thymidylate synthase, leading to production of thymidine nucleotides. By reducing the effective ratio of dUTP to TTP, the enzyme also reduces the possibility of dUTP incorporation into DNA.
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Word Map
- 3.6.1.23
- uracil
- dump
- trimer
- thymidylate
-
misincorporation
- glycosylase
-
herpes
-
uracil-dna
- simplex
- drug development
-
homotrimeric
- herpesviruses
-
integrase
-
fluoropyrimidines
-
uracil-containing
- lentiviruses
- pyrophosphatases
-
sapis
-
ebv-encoded
- herv-k
- 2'-deoxyuridine
-
varicella-zoster
- fiv
- diagnostics
- medicine
- pharmacology
- synthesis
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
dutpase, deoxyuridine triphosphatase, deoxyuridine triphosphate nucleotidohydrolase, deoxyuridine 5'-triphosphate nucleotidohydrolase, dut-n, deoxyuridine 5'-triphosphate, dutp pyrophosphatase, dutp nucleotidohydrolase, orf 54, dcd-dut, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
desoxyuridine 5'-triphosphatase
-
-
-
-
desoxyuridine 5'-triphosphate nucleotidohydrolase
-
-
-
-
desoxyuridine-triphosphatase
-
-
-
-
dUTP pyrophosphatase
dUTPase
P18
-
-
-
-
PIP4
-
-
-
-
additional information
-
the enzyme belongs to the Nudix superfamily of enzymes
dUTP pyrophosphatase
-
-
-
-
dUTPase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dUTP + H2O = dUMP + diphosphate
structural and catalytic mechanism involving Mg2+
-
dUTP + H2O = dUMP + diphosphate
structural organization and substrate binding modes
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phosphorous acid anhydride hydrolysis
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
dUTP nucleotidohydrolase
The enzyme catalyses the Mg2+-dependent hydrolysis of dUTP to dUMP, providing the substrate for EC 2.1.1.45, thymidylate synthase, leading to production of thymidine nucleotides. By reducing the effective ratio of dUTP to TTP, the enzyme also reduces the possibility of dUTP incorporation into DNA.
CAS REGISTRY NUMBER
COMMENTARY
37289-34-2
-
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
dUTP + H2O
dUMP + diphosphate
removes dUTP from the nucleotide triphosphate pool and therefore prevents the incorporation of uracil into the DNA
-
-
?
dUTP + H2O
dUMP + diphosphate
a preventive DNA repair enzyme, contributes to maintain the appropriate cellular dUTP/dTTP ratio by catalyzing dUTP hydrolysis, dUTPase is essential for viability
-
-
?
dUTP + H2O
dUMP + diphosphate
substrate binding structure, the strictly conserved residue Ser72 is involved in phosphate chain binding, overview
-
-
?
dUTP + H2O
?
-
the enzyme prevents a deleterious incorporation of uracil into DNA
-
-
?
dUTP + H2O
?
-
lethality of a mutation in the dut gen, deoxyuridine triphosphatase. The dut gene product might have an essential function apart from its deoxyuridine triphosphatase activity
-
-
?
dUTP + H2O
dUMP + diphosphate
-
-
-
-
?
dUTP + H2O
dUMP + diphosphate
-
removes dUTP from the nucleotide triphosphate pool and therefore prevents the incorporation of uracil into the DNA
-
-
?
dUTP + H2O
dUMP + diphosphate
-
the essential enzyme is responsible for preventive DNA repair via exclusion of uracil, overview, lack of negative enzyme regulation leads to thymine-less cell death in cells performing active DNA synthesis
-
-
?
dUTP + H2O
dUMP + diphosphate
-
the enzyme is highly specific for dUTP
-
-
?
additional information
?
-
-
biological functions in housekeeping, overview
-
-
?
additional information
?
-
-
comparison of the Drosophila melanogaster and the Escherichia coli enzymes
-
-
?
additional information
?
-
-
substrate specificity, no hydrolysis of canonical NTPs, overview
-
-
?
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
additional information
?
-
-
biological functions in housekeeping, overview
-
-
?
dUTP + H2O
dUMP + diphosphate
removes dUTP from the nucleotide triphosphate pool and therefore prevents the incorporation of uracil into the DNA
-
-
?
dUTP + H2O
dUMP + diphosphate
a preventive DNA repair enzyme, contributes to maintain the appropriate cellular dUTP/dTTP ratio by catalyzing dUTP hydrolysis, dUTPase is essential for viability
-
-
?
dUTP + H2O
?
-
the enzyme prevents a deleterious incorporation of uracil into DNA
-
-
?
dUTP + H2O
?
-
lethality of a mutation in the dut gen, deoxyuridine triphosphatase. The dut gene product might have an essential function apart from its deoxyuridine triphosphatase activity
-
-
?
dUTP + H2O
dUMP + diphosphate
-
removes dUTP from the nucleotide triphosphate pool and therefore prevents the incorporation of uracil into the DNA
-
-
?
dUTP + H2O
dUMP + diphosphate
-
the essential enzyme is responsible for preventive DNA repair via exclusion of uracil, overview, lack of negative enzyme regulation leads to thymine-less cell death in cells performing active DNA synthesis
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
Mg2+
-
Mg2+ enhances binding to dUTPase of dUTP by a factor of 100 and dUDP by a factor of 10
Mg2+
-
slight stimulation at low concentrations of dUTP, no stimulation at concentrations of dUTP above 0.1 mM
Mg2+
-
binding as dUTP-Mg2+ at the C-terminus induces the closure of the C-terminal arm which opens up again after hydrolysis to expel the product
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3'-deoxy-5'-O-(hydroxy{[hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl)uridine
competitive inhibition
3'-deoxy-5'-O-[hydroxy(phosphonoamino)phosphoryl]uridine
competitive inhibition
alpha,beta-imido-dUTP
substrate analogue, inhibits the wild-type enzyme, not mutant S72A
guanidine hydrochloride
kinetics of GuHCl-induced denaturation of the two dUTPase isozymes at pH 7.5, 4 °C and 1.5-4 M
additional information
the wild type enzyme is not inhibited by staphylococcal repressor StlSaPIbov1 protein
-
additional information
-
the wild type enzyme is not inhibited by staphylococcal repressor StlSaPIbov1 protein
-
additional information
-
binding of alpha,beta-imino-dUTP does not induce allosteric conformational changes and does not protect the enzyme against tryptic digestion
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
ligand binding constants
-
additional information
additional information
transient state kinetics of substrate binding to the S72A mutant dUTPase, stopped-flow measurements, overview. Comparative kinetics of formation of the enzyme-substrate complexes of the wild-type and S72A
-
additional information
additional information
-
transient state kinetics of substrate binding to the S72A mutant dUTPase, stopped-flow measurements, overview. Comparative kinetics of formation of the enzyme-substrate complexes of the wild-type and S72A
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
24.2
dUTP
-
pH 7.5, 25°C, in the presence of bis(acetylacetonato)oxovanadium(IV)
27.3
dUTP
-
pH 7.5, 25°C, in the presence of VO2+ or bis(acetylacetonato)oxovanadium(IV)
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0093
3'-azido-2',3'-dideoxy-UTP
-
0.02 mM 3'-azido-2',3'-dideoxy-UTP in 0.05 mM bicine, with 5 mM MgCl2, pH and temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.1 - 8
-
pH 5.0: no activity, pH 6.1-7.5: optimum, pH 8.0: about 60% of maximal activity
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotrimer
trimer
homotrimer
with interfaces formed between subunit surfaces, in the central channel, and by C-terminal beta-strand swapping. Analysis of intersubunit interactions reveals an important cohesive role for the C-terminus
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme in complex with inhibitors, i.e. dUTPase-alpha,beta-methylene-dUDP and dUTPase-dUDP-Mn complexes, 20°C, hanging-drop vapor diffusion, 3 mg/ml of enzyme in 10 mM Tris/HCl buffer, pH 7.0, and 50 mM NaCl, as well as 1.25 mM alpha,beta-methylene-dUDP or dUDP and 10 mM MgCl2 or MnCl2, respectively, mixing with an equal volume of reservoir solution 0.1 M Tris/HCl buffer, pH 7.8, containing 18-20% PEG 3350, and 400 mM Na-acetate, X-ray diffraction structure determination and analysis at 1.7-1.84 resolution, analysis of the different alpha-phosphate sites, overview
Q93H mutant in complex with a non-hydrolysable substrate analogue, alpha,beta-imido-dUTP, hanging drop vapor diffusion method, using 0.1 M Tris, 18-33.75 % polyethylene glycol 3350, 400 mM NaAc, pH 7.5
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D90N
Q93H
the mutant enzyme is significantly inhibited by staphylococcal repressor StlSaPIbov1 protein (Ki 0.00000483 mM)
Q93R
the mutant enzyme is significantly inhibited by staphylococcal repressor StlSaPIbov1 protein (Ki 0.0000059 mM)
S72A
site-directed mutagenesis, steady-state kinetic characterization, S72A mutation causes a 725fold reduction in kcat and a 35fold reduction in KM.
additional information
D90N
no effect on Km, strong decrease in catalytic activity, H-bonding significantly altered
additional information
mutations of a suggested hinge proline destabilize Escherichia coli dUTPase without preventing trimeric organization
additional information
-
mutations of a suggested hinge proline destabilize Escherichia coli dUTPase without preventing trimeric organization
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cloning of the dut gene in the runaway-replication plasmid pKN402A and in the lambdapL-promoter plasmid pHUB2
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
the enzyme is a target for development of antimicrobial agents
drug development
-
inhibitor development against the enzyme can be useful in antiviral and anticancer therapy
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Greenberg, R.G.; Somerville, R.L.
Deoxyuridylate kinase activity and deoxyuridinetriphosphatase in Escherichia coli
Biochemistry
48
247-257
1962
Escherichia coli, Escherichia coli R2
Bertani, L.E.; Haeggmark, A.; Reichard, P.
Enzymatic synthesis of deoxyribonucleotides. II. Formation and interconversion of deoxyuridine phosphates
J. Biol. Chem.
238
3407-3413
1963
Escherichia coli, Escherichia coli B / ATCC 11303
Shlomai, J.; Kornberg, A.
Deoxyuridine triphosphatase of Escherichia coli. Purification, properties, and use as a reagent to reduce uracil incorporation into DNA
J. Biol. Chem.
253
3305-3312
1978
Escherichia coli
Taylor, A.F.; Siliciano, P.G.; Weiss, B.
Cloning of the dut (deoxyuridine triphosphatase) gene of Escherichia coli
Gene
9
321-336
1980
Escherichia coli
Lundberg, L.G.; Karlstroem, O.H.; Nyman, P.O.; Neuhard, J.
Isolation and characterization of the dut gene of Escherichia coli. I. Cloning in thermoinducible plasmids
Gene
22
115-126
1983
Escherichia coli
Hoffmann, I.; Widstroem, J.; Zeppezauer, M.; Nyman, P.O.
Overproduction and large-scale preparation of deoxyuridine triphosphate nucleotidohydrolase from Escherichia coli
Eur. J. Biochem.
164
45-51
1987
Escherichia coli, Escherichia coli overproducing
El-Hajj, H.H.; Zhang, H.; Weiss, B.
Lethality of a dut (deoxyuridine triphosphatase) mutation in Escherichia coli
J. Bacteriol.
170
1069-1075
1988
Escherichia coli
Larsson, G.; Svensson, L.A.; Nyman, P.O.
Crystal structure of the Escherichia coli dUTP in complex with a substrate analogue (dUDP)
Nature Struct. Biol.
3
532-538
1996
Escherichia coli
Larsson, G.; Nyman, P.O.; Kvassman, J.O.
Kinetic characterization of dUTPase from Escherichia coli
J. Biol. Chem.
271
24010-24016
1996
Escherichia coli
Takacs, E.; Grolmusz, V.K.; Vertessy, B.G.
A tradeoff between protein stability and conformational mobility in homotrimeric dUTPases
FEBS Lett.
566
48-54
2004
Drosophila melanogaster, Escherichia coli
Barabas, O.; Pongracz, V.; Kovari, J.; Wilmanns, M.; Vertessy, B.G.
Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase
J. Biol. Chem.
279
42907-42915
2004
Escherichia coli (P06968)
Mustafi, D.; Bekesi, A.; Vertessy, B.G.; Makinen, M.W.
Catalytic and structural role of the metal ion in dUTP pyrophosphatase
Proc. Natl. Acad. Sci. USA
100
5670-5675
2003
Escherichia coli
Galperin, M.Y.; Moroz, O.V.; Wilson, K.S.; Murzin, A.G.
House cleaning, a part of good housekeeping
Mol. Microbiol.
59
5-19
2006
Saccharomyces cerevisiae, Campylobacter jejuni, Escherichia coli, Leishmania major, Staphylococcus aureus, Trypanosoma cruzi, Mycobacterium tuberculosis (P9WNS5), Mycobacterium tuberculosis H37Rv (P9WNS5)
Kovari, J.; Imre, T.; Szabo, P.; Vertessy, B.G.
Mechanistic studies of dUTPases
Nucleosides Nucleotides Nucleic Acids
23
1475-1479
2004
Drosophila melanogaster, Escherichia coli
Kovari, J.; Barabas, O.; Varga, B.; Bekesi, A.; Toelgyesi, F.; Fidy, J.; Nagy, J.; Vertessy, B.G.
Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site
Proteins
71
308-319
2008
Escherichia coli (P06968), Escherichia coli
Palmen, L.G.; Becker, K.; Buelow, L.; Kvassman, J.O.
A double role for a strictly conserved serine: further insights into the dUTPase catalytic mechanism
Biochemistry
47
7863-7874
2008
Escherichia coli (P06968), Escherichia coli
Takacs, E.; Barabas, O.; Petoukhov, M.V.; Svergun, D.I.; Vertessy, B.G.
Molecular shape and prominent role of beta-strand swapping in organization of dUTPase oligomers
FEBS Lett.
583
865-871
2009
Escherichia coli (P06968), Escherichia coli, Homo sapiens (P33316), Homo sapiens, Drosophila melanogaster (Q9V3I1)
Palmen, L.G.; Kvassman, J.O.
Differential inhibition of homotrimeric dUTPases by the 3-azido derivative of dideoxy-UTP
J. Enzyme Inhib. Med. Chem.
25
146-150
2010
Escherichia coli, equine infectious anemia virus, Homo sapiens
Benedek, A.; Temesvary-Kis, F.; Khatanbaatar, T.; Leveles, I.; Suranyi, E.V.; Szabo, J.E.; Wunderlich, L.; Vertessy, B.G.
The role of a key amino acid position in species-specific proteinaceous dUTPase inhibition
Biomolecules
9
221
2019
Escherichia coli (P06968), Escherichia coli
Kerepesi, C.; Szabo, J.E.; Papp-Kadar, V.; Dobay, O.; Szabo, D.; Grolmusz, V.; Vertessy, B.G.
Life without dUTPase
Front. Microbiol.
7
1768
2016
Aeromonas hydrophila, Campylobacter jejuni, Escherichia coli, no activity in Staphylococcus aureus strain RN450, Aeromonas hydrophila ATCC 7966, Escherichia coli ATCC 25922
Zang, K.; Li, F.; Ma, Q.
The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner
J. Biol. Chem.
293
1088-1099
2018
Escherichia coli, white spot syndrome virus (Q77J78), white spot syndrome virus
Hizi, A.; Herzig, E.
dUTPase the frequently overlooked enzyme encoded by many retroviruses
Retrovirology
12
70
2015
bovine immunodeficiency virus, Caenorhabditis elegans, Caprine arthritis encephalitis virus, equine infectious anemia virus, Escherichia coli (P06968), feline immunodeficiency virus, Homo sapiens (P33316), Homo sapiens, Human endogenous retrovirus K, Human gammaherpesvirus 4, Human gammaherpesvirus 8, Jembrana disease virus, Mason-Pfizer monkey virus, mouse mammary tumor virus, Murid gammaherpesvirus 4, Mycobacterium tuberculosis, Plasmodium falciparum, Saccharomyces cerevisiae, Visna-maedi virus
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