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Information on EC 3.6.1.17 - bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) and Organism(s) Caenorhabditis elegans and UniProt Accession Q9U2M7

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EC Tree
IUBMB Comments
Also acts on bis(5'-xanthosyl)-tetraphosphate and, more slowly, on bis(5'-adenosyl)-tetraphosphate and bis(5'-uridyl)-tetraphosphate [cf. EC 3.6.1.41 bis(5'-nucleosyl)-tetraphosphatase (symmetrical)]
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Caenorhabditis elegans
UNIPROT: Q9U2M7
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The taxonomic range for the selected organisms is: Caenorhabditis elegans
The enzyme appears in selected viruses and cellular organisms
Synonyms
ap4a hydrolase, nudt2, diadenosine tetraphosphatase, enpp4, ap4aase, ndx-4, ct771, dinucleoside tetraphosphatase, ap4a-hydrolase, dipp1, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ap4A hydrolase
AP4AASE
-
-
-
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bis(5'-adenosyl)-tetraphosphatase
-
-
-
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bis(5'-guanosyl)-tetraphosphatase
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-
-
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bis(5-guanosyl)tetraphosphatase
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-
-
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Diadenosine 5',5'''-P1,P4-tetraphosphate asymmetrical hydrolase
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diadenosine 5',5'''-P1,P4-tetraphosphate pyrophosphohydrolase
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diadenosine P1,P4-tetraphosphatase
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-
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Diadenosine tetraphosphatase
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-
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diadenosine tetraphosphate pyrophosphohydrolase
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diguanosine tetraphosphatase
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-
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diguanosinetetraphosphatase (asymmetrical)
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diguanosinetetraphosphate guanosylhydrolase
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dinucleoside tetraphosphatase
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dinucleosidetetraphosphatase (asymmetrical)
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-
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-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphorous acid anhydride hydrolysis
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-
-
-
PATHWAY SOURCE
PATHWAYS
SYSTEMATIC NAME
IUBMB Comments
P1,P4-bis(5'-nucleosyl)-tetraphosphate nucleotidohydrolase
Also acts on bis(5'-xanthosyl)-tetraphosphate and, more slowly, on bis(5'-adenosyl)-tetraphosphate and bis(5'-uridyl)-tetraphosphate [cf. EC 3.6.1.41 bis(5'-nucleosyl)-tetraphosphatase (symmetrical)]
CAS REGISTRY NUMBER
COMMENTARY hide
37289-29-5
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-oxo-dATP + H2O
?
show the reaction diagram
less efficient hydrolysis compared to 8-oxo-dGTP
-
-
?
8-oxo-dGTP + H2O
8-oxo-dGMP + diphosphate
show the reaction diagram
the enzyme does not show a strong preference for 8-oxo-dGTP and is able to hydrolyze unmodified dATP and dGTP with comparable efficiency
-
-
?
dATP + H2O
?
show the reaction diagram
-
-
-
?
dGTP + H2O
?
show the reaction diagram
-
-
-
?
diadenosine 5',5''''-P1,P4-tetraphosphate + H2O
AMP + ATP
show the reaction diagram
-
-
-
?
Ap4A + H2O
?
show the reaction diagram
-
-
-
-
?
Ap6A + H2O
ATP + ATP
show the reaction diagram
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7% of the activity with Ap4A
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-
?
diadenosine 5',5''-P1,P4-tetraphosphate + H2O
ATP + AMP
show the reaction diagram
-
-
-
-
?
diadenosine 5',5''-P1,P5-pentaphosphate + H2O
ATP + ADP
show the reaction diagram
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19% of the activity with Ap4A
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-
?
p4A + H2O
ATP + phosphate
show the reaction diagram
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14% of the activity with Ap4A
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-
?
p5A + H2O
ATP + diphosphate
show the reaction diagram
-
29% of the activity with Ap4A
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-
?
additional information
?
-
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no activity with Ap3A
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
divalent cation required, 20% of maximal activity in presence of 1 mM Co2+
Mg2+
-
divalent cation required, maximal activity in presence of 3-5 mM Mg2+
Mn2+
-
divalent cation required, 20% of maximal activity in presence of 0.1 mM Mn2+
Zn2+
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divalent cation required, 20% of maximal activity in presence of 0.05 mM Mn2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
adenosine 5'-tetraphosphate
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competitive
F-
-
non-competitive
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.3846
2-oxo-dATP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.0986
8-oxo-dGTP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.1143
dATP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.182
dGTP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.007
diadenosine 5',5''''-P1,P4-tetraphosphate
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.0041 - 0.14
Ap4A
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.51
2-oxo-dATP
in 5 0mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.58
8-oxo-dGTP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.37
dATP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.53
dGTP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
27
diadenosine 5',5''''-P1,P4-tetraphosphate
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
0.00024 - 31
Ap4A
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.3
2-oxo-dATP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
5.9
8-oxo-dGTP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
3.3
dATP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
2.9
dGTP
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
3900
diadenosine 5',5''''-P1,P4-tetraphosphate
in 50 mM Tris-HCl (pH 8.0), 5 mM MgCl2, 20 mM NaCl, 1 mM dithiothreitol, 0.2 mg/ml bovine serum albumin, at 37°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00001
adenosine 5'-tetraphosphate
-
pH 7.8, 25°C
0.025
F-
-
pH 7.8, 25°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.3
-
hydrolysis pf Ap4A
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8
-
50% of maximal activity at pH 6.5 and at pH 8.0, hydrolysis of Ap4A
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
loss of NDX-4 leads to upregulation of key stress responsive genes that likely compensate for the in vivo role of NDX-4 in protection against deleterious consequences of oxidative stress. NDX-4 deficiency protects nematodes from acute heat shock
physiological function
the enzyme contributes to genomic stability in vivo in Caenorhabditis elegans
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
AP4A_CAEEL
138
0
15889
Swiss-Prot
Mitochondrion (Reliability: 5)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
19000
-
gel filtration
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting-drop vapour diffusion, crystals diffract to a minimum d-spacing of 2 A and belong to either space group C222 or C222(1)
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E103Q
-
turnover-number for hydrolysis of Ap4A is 3.2% of that of the wild-type enzyme, KM-value is 66% of the wild-type value
E52Q
-
turnover-number for hydrolysis of Ap4A is 0.02% of that of the wild-type enzyme, KM-value is 60% of the wild-type value
E56Q
-
turnover-number for hydrolysis of Ap4A is 0.001% of that of the wild-type enzyme, KM-value is 90% of the wild-type value
H31A
-
turnover-number for hydrolysis of Ap4A is 52% of that of the wild-type enzyme, KM-value is 8.3fold higher than the KM-value of the wild-type enzyme
H31V
-
turnover-number for hydrolysis of Ap4A is 61% of that of the wild-type enzyme, KM-value is 12.5fold higher than the KM-value of the wild-type enzyme
H38G
-
turnover-number for hydrolysis of Ap4A is 135% of that of the wild-type enzyme, KM-value is 66% of the wild-type value
H38K
-
turnover-number for hydrolysis of Ap4A is 135% of that of the wild-type enzyme, KM-value is 47% of the wild-type value
K36M
-
turnover-number for hydrolysis of Ap4A is 9% of that of the wild-type enzyme, KM-value is 1.5fold higher than the KM-value of the wild-type enzyme
K79M
-
turnover-number for hydrolysis of Ap4A is 0.7% of that of the wild-type enzyme, KM-value is 1.7fold higher than the KM-value of the wild-type enzyme
K81M
-
turnover-number for hydrolysis of Ap4A is 130% of that of the wild-type enzyme, KM-value is 2.3fold higher than the KM-value of the wild-type enzyme
K83M
-
turnover-number for hydrolysis of Ap4A is 2.6% of that of the wild-type enzyme, KM-value is 15.9fold higher than the KM-value of the wild-type enzyme
Y121A
-
turnover-number for hydrolysis of Ap4A is 61% of that of the wild-type enzyme, KM-value is 8.5fold higher than the KM-value of the wild-type enzyme
Y27A
-
turnover-number for hydrolysis of Ap4A is 113% of that of the wild-type enzyme, KM-value is 1.25fold higher than the KM-value of the wild-type enzyme
Y27D
-
turnover-number for hydrolysis of Ap4A is 126% of that of the wild-type enzyme, KM-value is 1.8fold higher than the KM-value of the wild-type enzyme
Y76A
-
turnover-number for hydrolysis of Ap4A is 8.7% of that of the wild-type enzyme, KM-value is 6.7fold higher than the KM-value of the wild-type enzyme
Y76A/Y121A
-
turnover-number for hydrolysis of Ap4A is 4.8% of that of the wild-type enzyme, KM-value is 3.75fold higher than the KM-value of the wild-type enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HisTrap FF column chromatography and Superdex 75 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3)T cells
expression in Escherichia coli
-
expression in Escherichia coli, mutant enzymes Y27A, Y27D, H31A, H31V, W32G, K36M, H38G, H38K, E52Q, E56Q, Y76A, Y76/Y121A, K79M, K81M, K83M, E103Q, Y121A
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Abdelghany, H.M.; Gasmi, L.; Cartwright, J.L.; Bailey, S.; Rafferty, J.B.; McLennan, A.G.
Cloning, characterisation and crystallization of a diadenosine 5',5'''-P1,P4-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans
Biochim. Biophys. Acta
1550
27-36
2001
Caenorhabditis elegans
Manually annotated by BRENDA team
Abdelghany, H.M.; Bailey, S.; Blackburn, G.M.; Rafferty, J.B.; McLennan, A.G.
Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis
J. Biol. Chem.
278
4435-4439
2003
Caenorhabditis elegans
Manually annotated by BRENDA team
Arczewska, K.D.; Baumeier, C.; Kassahun, H.; Sengupta, T.; Bjoras, M.; Kusmierek, J.T.; Nilsen, H.
Caenorhabditis elegans NDX-4 is a MutT-type enzyme that contributes to genomic stability
DNA Repair
10
176-187
2011
Caenorhabditis elegans (Q9U2M7), Caenorhabditis elegans, Caenorhabditis elegans Bristol N2 (Q9U2M7)
Manually annotated by BRENDA team