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Literature summary for 3.6.1.5 extracted from

  • Zebisch, M.; Krauss, M.; Schaefer, P.; Straeter, N.
    Crystallographic evidence for a domain motion in rat nucleoside triphosphate diphosphohydrolase (NTPDase) 1 (2012), J. Mol. Biol., 415, 288-306.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli Rattus norvegicus
recombinant expression of the mutant NTPDase1 ECD DELTAMIL in Escherichia coli in soluble form and refolding to the active state Rattus norvegicus

Crystallization (Commentary)

Crystallization (Comment) Organism
NTPDase1 that lacks the two transmembrane helices and an additional putative membrane interaction loop, hanging drop vapor diffusion method, using 0.1 M sodium acetate (pH 4.5), 3.6 M sodium chloride Rattus norvegicus
purified recombinant wild-type enzyme, free or in complex with decavanadate or heptamolybdate, X-ray diffraction structure determination and analysis at 1.7-2.5 A resolution, modeling Rattus norvegicus

Protein Variants

Protein Variants Comment Organism
K257M site-directed mutagenesis Rattus norvegicus
additional information replacement of the extracellular domain of Rattus norvegicus NTPDase1, i.e. amino acid sequence 190TQEQSWLNFISDSQKQA206, with the shorter hydrophilic loop found in Homo sapiens NTPDase6, 240KTPGGS245. This NTPDase1 ECD DELTAMIL mutant variant is a soluble NTPDase1 that lacks a putative membrane interaction loop identified between the two lobes of the catalytic domain Rattus norvegicus
Y409F site-directed mutagenesis Rattus norvegicus
Y413F site-directed mutagenesis Rattus norvegicus

Inhibitors

Inhibitors Comment Organism Structure
ammonium heptamolybdate AHM, (NH4)6[Mo7O24] Rattus norvegicus
AMP
-
Rattus norvegicus
additional information inhibition mechanism of polyoxometallates, overview Rattus norvegicus
polytungstate salt POM-1 Na6[H2W12O40] Rattus norvegicus
Sodium vanadate Na3VO4 Rattus norvegicus
UMP
-
Rattus norvegicus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information kinetics, overview Rattus norvegicus
0.0025
-
ADP recombinant mutant EDC K257M, pH 7.4, 25°C Rattus norvegicus
0.0025
-
ADP recombinant mutant EDC Y314F, pH 7.4, 25°C Rattus norvegicus
0.0047
-
ADP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0051
-
ADP recombinant mutant EDC Y409F, pH 7.4, 25°C Rattus norvegicus
0.0059
-
ADP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus
0.009
-
GTP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.01
-
UTP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0105
-
IDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0108
-
ITP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0113
-
UDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0114
-
GDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0129
-
UTP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus
0.0131
-
GDP in presence of 0.1 mM UMP, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0175
-
UDP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus
0.0488
-
GDP in presence of 0.1 mM AMP, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.149
-
GDP in presence of 0.1 mM AHM, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.1712
-
AMPCPP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.7495
-
TDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus

Localization

Localization Comment Organism GeneOntology No. Textmining
extracellular
-
Rattus norvegicus
-
-

Metals/Ions

Metals/Ions Comment Organism Structure
Cl- the active-site clefts of NTPDase1 contain three chloride ions, one of which is bound to the second phosphate-binding loop, apyrase conserved region 4, ACR4 Rattus norvegicus
additional information complex structures with decavanadate and heptamolybdate show that both polyoxometallates bind electrostatically to a loop that is involved in binding of the nucleobase Rattus norvegicus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ATP + 2 H2O Rattus norvegicus
-
AMP + 2 phosphate
-
?

Organism

Organism UniProt Comment Textmining
Rattus norvegicus P97687
-
-

Source Tissue

Source Tissue Comment Organism Textmining
vascular system CD39 and NTPDase1 are the dominant NTPDases Rattus norvegicus
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
adenosine 5'-[(alpha,beta)-methyleno] triphosphate + H2O
-
Rattus norvegicus ?
-
?
ADP + H2O
-
Rattus norvegicus AMP + phosphate
-
?
AMPCPP + H2O low activity Rattus norvegicus ?
-
?
ATP + 2 H2O
-
Rattus norvegicus AMP + 2 phosphate
-
?
ATP + H2O
-
Rattus norvegicus ADP + phosphate
-
?
GDP + H2O
-
Rattus norvegicus GMP + phosphate
-
?
GTP + 2 H2O
-
Rattus norvegicus GMP + 2 phosphate
-
?
IDP + H2O
-
Rattus norvegicus IMP + phosphate
-
?
ITP + 2 H2O
-
Rattus norvegicus IMP + 2 phosphate
-
?
ITP + H2O
-
Rattus norvegicus IDP + phosphate
-
?
additional information establishment of a kinetic isothermal titration calorimetry assay. Substrate recognition by NTPDase1, overview Rattus norvegicus ?
-
?
additional information no hydrolysis of AMPCP Rattus norvegicus ?
-
?
TDP + H2O
-
Rattus norvegicus TMP + phosphate
-
?
TTP + 2 H2O weak substrate Rattus norvegicus TMP + 2 phosphate
-
?
UDP + H2O
-
Rattus norvegicus UMP + phosphate
-
?
UTP + 2 H2O
-
Rattus norvegicus UMP + 2 phosphate
-
?
UTP + H2O
-
Rattus norvegicus UDP + phosphate
-
?

Synonyms

Synonyms Comment Organism
CD39
-
Rattus norvegicus
NTPDase 1
-
Rattus norvegicus
NTPDase1
-
Rattus norvegicus
nucleoside triphosphate diphosphohydrolase 1
-
Rattus norvegicus

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Rattus norvegicus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
31.1
-
ADP recombinant mutant EDC Y409F, pH 7.4, 25°C Rattus norvegicus
40.5
-
AMPCPP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
50.4
-
ADP recombinant mutant EDC K257M, pH 7.4, 25°C Rattus norvegicus
77.3
-
ADP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
79.9
-
IDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
80.2
-
TDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
80.9
-
UDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
80.9
-
GTP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
82.6
-
GDP in presence of 0.1 mM AMP, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
83.2
-
GDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
83.2
-
GDP in presence of 0.1 mM UMP, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
86.1
-
ADP recombinant mutant EDC Y314F, pH 7.4, 25°C Rattus norvegicus
86.9
-
ADP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus
93
-
UDP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus
103.4
-
UTP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
103.7
-
GDP in presence of 0.1 mM AHM, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
105.3
-
ITP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
121.2
-
UTP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.4
-
assay at Rattus norvegicus

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.00859
-
ammonium heptamolybdate recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0268
-
AMP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.0268
-
AMP at pH 7.4 and 25°C Rattus norvegicus
0.3345
-
UMP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
0.3345
-
UMP at pH 7.4 and 25°C Rattus norvegicus

General Information

General Information Comment Organism
evolution the enzyme is a member of the eukaryotic NTPDase family Rattus norvegicus
additional information influence of transmembrane helix dynamics on activity is achieved by coupling to a domain motion. Active site structure of NTPDase1, overview, closure movement in NTPDases Rattus norvegicus
physiological function nucleoside triphosphate diphosphohydrolases are a physiologically important class of membrane-bound ectonucleotidases responsible for the regulation of extracellular levels of nucleotides Rattus norvegicus
physiological function the enzyme blocks platelet aggregation and supports blood flow Rattus norvegicus

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
110
-
TDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
230
-
AMPCPP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
700
-
GDP in presence of 0.1 mM AHM, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
1700
-
GDP in presence of 0.1 mM AMP, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
5300
-
UDP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus
6100
-
ADP recombinant mutant EDC Y409F, pH 7.4, 25°C Rattus norvegicus
6400
-
GDP in presence of 0.1 mM UMP, recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
7200
-
UDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
7300
-
GDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
7600
-
IDP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
9000
-
GTP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
9400
-
UTP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus
9800
-
ITP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
10300
-
UTP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
14700
-
ADP recombinant mutant EDC DELTA MIL, pH 7.4, 25°C Rattus norvegicus
16400
-
ADP recombinant wild-type enzyme, pH 7.4, 25°C Rattus norvegicus
20200
-
ADP recombinant mutant EDC K257M, pH 7.4, 25°C Rattus norvegicus
26900
-
ADP recombinant mutant EDC Y314F, pH 7.4, 25°C Rattus norvegicus