Information on EC 3.6.1.6 - nucleoside diphosphate phosphatase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.6.1.6
-
RECOMMENDED NAME
GeneOntology No.
nucleoside diphosphate phosphatase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a nucleoside diphosphate + H2O = a nucleoside phosphate + phosphate
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Purine metabolism
-
-
pyrimidine deoxyribonucleotides biosynthesis from CTP
-
-
Pyrimidine metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
nucleoside-diphosphate phosphohydrolase
The enzyme, which appears to be limited to metazoa, acts on multiple nucleoside diphosphates as well as on D-ribose 5-diphosphate. Specificity depends on species and isoform.
CAS REGISTRY NUMBER
COMMENTARY hide
9027-69-4
-
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
-
GS52 is a member of the NTPDase/apyrase family
malfunction
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ADP + H2O
AMP + phosphate
show the reaction diagram
ATP + 2 H2O
ADP + 2 phosphate
show the reaction diagram
ATP + 2 H2O
AMP + 2 phosphate
show the reaction diagram
ATP + H2O
ADP + phosphate
show the reaction diagram
CDP + H2O
CMP + phosphate
show the reaction diagram
CTP + 2 H2O
CMP + 2 phosphate
show the reaction diagram
-
-
-
-
?
CTP + H2O
CDP + phosphate
show the reaction diagram
3.8% of the specific activity with GDP
-
-
?
dTDP + H2O
dTMP + phosphate
show the reaction diagram
GDP + H2O
GMP + phosphate
show the reaction diagram
GTP + 2 H2O
GMP + 2 phosphate
show the reaction diagram
-
-
-
-
?
GTP + H2O
GDP + phosphate
show the reaction diagram
IDP + H2O
IMP + phosphate
show the reaction diagram
ITP + 2 H2O
IMP + 2 phosphate
show the reaction diagram
-
-
-
-
?
ITP + H2O
IDP + phosphate
show the reaction diagram
6% of the specific activity with GDP
-
-
?
TDP + H2O
TMP + H2O
show the reaction diagram
-
-
-
?
TPP + H2O
thiamine phosphate + phosphate
show the reaction diagram
UDP + H2O
UMP + phosphate
show the reaction diagram
UTP + 2 H2O
UMP + 2 phosphate
show the reaction diagram
-
-
-
-
?
UTP + H2O
UDP + phosphate
show the reaction diagram
additional information
?
-
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
ADP + H2O
AMP + phosphate
show the reaction diagram
ATP + 2 H2O
ADP + 2 phosphate
show the reaction diagram
ATP + 2 H2O
AMP + 2 phosphate
show the reaction diagram
ATP + H2O
ADP + phosphate
show the reaction diagram
GDP + H2O
GMP + phosphate
show the reaction diagram
UTP + H2O
UDP + phosphate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cd2+
-
Cd2+ can partially replace Mn2+, 16%, for TPPase activity. For GDPase activity Ca2+ can be partially replaced by Cd2+, 38%
Manganese
-
metalloenzyme contains 0.9 mol zinc and 0.1 mol manganese per mol of 65000 Da subunit
Ni2+
-
activates
Zinc
-
metalloenzyme contains 0.9 mol zinc and 0.1 mol manganese per mol of 65000 Da subunit
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
-
2 mM, 66% inhibition
1,2-bipyridyl
-
2 mM, 64% inhibition
-
ADP
-
1 mM, 27% inhibition of thiamin-diphosphatase activity, competitive
chlorpromazine
-
1 mM, 15% inhibition
diphosphate
IMP
-
slight competitive inhibition of thiamin-diphosphatase activity
iodoacetamide
-
NEM
-
1 mM, 16% inhibition
Promethazine
-
1 mM, 15% inhibition
pyridoxal 5'-phosphate
-
1 mM, 43% inhibition of thiamin-diphosphatase activity, competitive
additional information
-
no inhibition by 10 mM ascorbate, 80 mM molybdate, 20 mM KF or 10 mM vanadate
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
-
activation due to Schiff base formation with epsilon-amino groups of Lys residues of the enzyme, Km: 0.0052 mM, no further stimulation of the reaction which is maximally activated by pyridoxal 5'-phosphate
additional information
-
no enzymatic activity in the presence of EDTA
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.309 - 2.1
ADP
0.424
ATP
-
pH and temperature not specified in the publication
0.13 - 4
GDP
0.48 - 3.5
IDP
0.66
thiamine diphosphate
-
in presence of Mn2+
0.18 - 10
UDP
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
93 - 570
ADP
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.02 - 340
ADP
13
1.28
ATP
Glycine max
-
pH and temperature not specified in the publication
4
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.5
diphosphate
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4 - 6.5
ATP
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2.2
-
isoform 1
2.8
-
isoform 2
additional information
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-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9
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hydrolysis of GDP
6
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hydrolysis of IDP and TPP, enzyme type B
7
-
GDPase activity in presence of Mn2+ and Ca2+
7.5
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with GDP as substrate
8
-
with UDP as substrate
8 - 8.5
-
TTPase activity in presence of Ca2+
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
pH 6.0: about 80% of maximal activity, pH 8.0: about 70% of maximal activity
6.7 - 7.8
pH 6.7: about 50% of maximal activity with Mg2+ or Ca2+, about 80% of maximal activity with Ca2+, about 70% of maximal activity with Mg2+
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
assay at
38
-
free enzyme
50
-
immobilized enzyme
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
NTPDase3 in cells from the stratified esophageal and forestomach epithelia, and in some enteroendocrine cells of the gastric antrum. NTPDase3 and -2 are coexpressed within the myenteric and submucosal plexuses, as well as in the nerve terminals of the smooth muscle layer and mucosa
Manually annotated by BRENDA team
restricted to the canalicular membrane domain of hepatocytes
Manually annotated by BRENDA team
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ascites hepatoma AH-66 cells
Manually annotated by BRENDA team
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-
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
at the lumen side of the membrane
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Manually annotated by BRENDA team
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30000
-
4 * 30000, SDS-PAGE
43000
x * 43000, SDS-PAGE
45000
-
gel filtration
45700
x * 45700, calculation from nucleotide sequence
50000
-
gel filtration
52000
-
enzyme form A and B2, gel filtration
53000
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SDS-PAGE
60000
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enzyme form B, gel filtration
61580
-
x * 61580, calculated from amino acid sequence
63000
-
2 * 63000, SDS-PAGE
65000
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2 * 65000, SDS-PAGE
67000
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2 * 67000, SDS-PAGE
75000
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1 * 75000, SDS-PAGE
120000
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gel filtration
130000
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gel filtration
140000
155000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
tetramer
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4 * 30000, SDS-PAGE
additional information
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GS52 apyrase structure modeling of apo-form and tertiary complex with the nonhydrolyzable ATP analogue AMPPNP and cofactor Ca2+, overview
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glycoprotein
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
in complex with (alpha,beta)-imido-ADP and in the presence of Mg2+ ions, hanging drop vapor diffusion method, using Tris (pH 8.2-8.8, 100 mM), MgCl2 (50 mM), and pentaerythritol propoxylate (17/8 PO/OH, 23-25%, (v/v))
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
-
10 min, about 40% loss of activity of the native enzyme, about 30% loss of activity of the enzyme after treatment with pyridoxal phosphate and reduction with NaBH4
210211
6
-
10 min, native enzyme and enzyme after treatment with pyridoxal phosphate and reduction with NaBH4, stable
210211
9
-
10 min, about 25% loss of activity of the native enzyme, about 5% loss of activity of the enzyme after treatment with pyridoxal phosphate and reduction with NaBH4
210211
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0 - 40
-
stable, isoenzyme 1 and 2
40
-
about 70% loss of activity after 30 min
45
-
pH 7.4, 50 mM triethanolamine hydrochloride, about 80% loss of activity after 16 min, inactivation is decreased by 2 mM pyridoxal phosphate
55
-
5 min, about 50% loss of activity of the immobilized enzyme, complete loss of activity of the free enzyme
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
high resiststance against lipid peroxidation
-
mutant enzyme C139S lacking the single free sulfhydryl is more stable than the wild-type enzyme under refolding conditions, 10-15C, 2-3 days
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the mutant enzyme C139S is less susceptible to oxidative inactivation than the wild-type enzyme
654678
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-18C, stable for several months
-
-70C, stable for several weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
affinity purification
-
mitochondrial enzyme form A, B1 and B2
-
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli
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two isoforms
-
type L isoenzyme
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in a Saccharomyces cerevisiae gda1 null mutant
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expressed in Saccharomyces cerevisiae gda1-null mutant
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expression in Escherichia coli BL21(DE3), refolding of the enzyme from bacterial inclusion bodies
expression of NTPDase1, NTPDase2, and NTPDase3 in COS-7 cells
quantitative real-time RT-PCR expression analysis, recombinant expression of HA-tagged wild-type and mutant enzymes in transgenic soybean roots via Agrobacterium rhizogenes-mediated hairy root transformation, expression of His-tagged wild-type and mutant enzymes in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D209A
-
site-directed mutagenesis, the mutant enzyme shows reduced activity compared to the wild-type enzyme
E182A
-
site-directed mutagenesis, the mutant enzyme shows reduced activity compared to the wild-type enzyme
Q216A
-
site-directed mutagenesis, the mutant enzyme shows reduced activity compared to the wild-type enzyme
S214A
-
site-directed mutagenesis, the mutant enzyme shows reduced activity compared to the wild-type enzyme
C139S
mutant enzyme lacking the single free sulfhydryl is more stable than the wild-type enzyme under refolding conditions, 10-15C, 2-3 days. The mutant enzyme is less susceptible to oxidative inactivation than the wild-type enzyme
E493G
the mutant of isoform NTPDase1 shows conversion of ATP/ADP specificity compared to the wild type enzyme
R492G
the mutant of isoform NTPDase1 shows conversion of ATP/ADP specificity compared to the wild type enzyme
R492G/E493G
the mutant of isoform NTPDase1 shows conversion of ATP/ADP specificity compared to the wild type enzyme
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
refolding of the enzyme from bacterial inclusion bodies. For wild-type enzyme optimal refolding ocurs at 10-15C over 2-3 days
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
-
because of its resistance against lipid peroxidation nucleoside diphosphatase is a well-suited intrinsic parameter to estimate this effect of lipid peroxidation on the microsomal membrane