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Information on EC 3.1.5.B1 - dNTPase and Organism(s) Homo sapiens

for references in articles please use BRENDA:EC3.1.5.B1
preliminary BRENDA-supplied EC number
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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.5 Triphosphoric-monoester hydrolases
                3.1.5.B1 dNTPase
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This record set is specific for:
Homo sapiens
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Word Map
The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
samhd1, dntpase, deoxynucleoside triphosphate triphosphohydrolase, hd domain protein, dntp triphosphorylase, deoxyribonucleotide triphosphohydrolase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
deoxynucleoside triphosphate triphosphohydrolase
-
-
deoxyribonucleotide triphosphohydrolase
-
SAMHD1
SYSTEMATIC NAME
IUBMB Comments
dNTP triphosphorylase
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
bis(4-nitrophenyl) phosphate + H2O
4-nitrophenyl phosphate + 4-nitrophenol
show the reaction diagram
-
-
-
?
dATP + H2O
deoxyadenosine + triphosphate
show the reaction diagram
dATP + H2O
deoxyadeonsine + triphosphate
show the reaction diagram
-
-
-
-
?
dCTP + H2O
deoxycytidine + triphosphate
show the reaction diagram
dGTP + H2O
deoxyguanosine + triphosphate
show the reaction diagram
dTTP + H2O
deoxythymidine + triphosphate
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
with substrate bis(4-nitrophenyl) phosphate, enzyme is able to tetramerize in presence of Mn2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acycloguanosine
-
amrinone
IC50 value below 250 microM, Hill coefficient between 0.5 and 1.5
cephalosporin C
zinc salt, inhibition is largely attributable to zinc
dimedone
oxidization in the presence of dimedone results in multiple cysteine residues displaying formation of sulfenic acid. Cys341-Cys350 is the predominant intrachain disulfide bond formed
ergotamine
IC50 value below 250 microM, Hill coefficient between 0.5 and 1.5
H2O2
90% inhibition at 0.1 mM. dNTPase activity of SAMHD1 is reversibly inhibited by oxidation, addition of dithiothreitol restores the activity. Oxidation prevents subunit oligomerization
Hexestrol
IC50 value below 250 microM, Hill coefficient between 0.5 and 1.5
L-thyroxine
IC50 value below 250 microM, Hill coefficient between 0.5 and 1.5
lomofungin
IC50 value below 250 microM, Hill coefficient between 0.5 and 1.5
montelukast
IC50 value below 250 microM, Hill coefficient between 0.5 and 1.5
retinoic acid
IC50 value below 250 microM, Hill coefficient between 0.5 and 1.5
sulindac
IC50 value below 250 microM, Hill coefficient between 0.5 and 1.5
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
dNTP
both GTP and dNTP are required for tetramer activation of the enzyme. SAMHD1 activation is regulated by the concentration of dNTP
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0016 - 0.34
dATP
0.0016 - 0.29
dCTP
0.0021 - 0.24
dGTP
0.002 - 0.3
dTTP
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1
dATP
pH 7.5, 37°C, presence of 0.02 mM GTP
0.9
dCTP
pH 7.5, 37°C, presence of 0.02 mM GTP plus 0.02 mM dATP
0.9
dGTP
pH 7.5, 37°C
1
dTTP
pH 7.5, 37°C, presence of 0.02 mM GTP plus 0.02 mM dATP
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.764
acycloguanosine
Homo sapiens
pH 7.5, temperature not specified in the publication
0.0011
cephalosporin C
Homo sapiens
pH 7.5, temperature not specified in the publication
0.0021
Zn2+
Homo sapiens
pH 7.5, temperature not specified in the publication
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
oxidation of the protein occurs in the cytoplasm
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
SAMHD1 and R451A/L453A mutant proteins are degraded by virion-associated protein Vpx from HIV-2 but are not spontaneously ubiquitinated in the absence of Vpx. Their protein levels are enhanced only when both proteasomal and autophagy degradation pathways are inhibited
physiological function
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
SAMH1_HUMAN
626
0
72201
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
142000
dynamic light scattering, oxidized enzyme, presence of activating nucleotides
280000
-
and 72000, gel filtration
292000
dynamic light scattering, presence of activating nucleotides
72000
-
and 280000, gel filtration
72200
dynamic light scattering, absence of activating nucleotides
72600
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
2 * 72200, calculated from sequence, presence of activating nucleotides, oxidized enzyme
monomer
tetramer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
acetylation
SAMHD1 is acetylated at residue K405 in vitro and in vivo by acetylatransferase arrest defective protein ARD1. Acetylated SAMHD1 wildtype proteins have enhanced dNTPase activity in vitro. SAMHD1 acetylation levels are strongest during the G1 phase
phosphoprotein
S-phase kinase CDK2-cyclin A phosphorylates SAMHD1 at residue Thr-592. Thr-592 phosphorylation occurs first at the G1/S border and is removed during mitotic exit. Thr-592 phosphorylation does not cause rapid protein degradation
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with the allosteric activator and substrate dGTP/dATP, to 1.8 A resolution
-
structures of the catalytic core of SAMHD1 in complex with different combinations of GTP and dNTPs. SAMHD1 contains two activator-binding sites in the allosteric pocket. The primary activator GTP binds to one site and the substrate dNTP (dATP, dCTP, dUTP or dTTP) occupies the other. Both GTP and dNTP are required for tetramer activation of the enzyme. In the absence of substrate binding, SAMHD1 adopts an inactive dimer conformation even when complexed with GTP
structures of variants T592E and T592V. Mutation T592E induces large conformational changes, likely triggered by electrostatic repulsion from a distinct negatively charged environment surrounding residue Thr-592
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C320A
mutant shows the formation of disulfide bonds similar to wild type
C341A
mutant shows no disulfide species
C350A
mutant shows no disulfide species
C522A
mutant shows no significant inhibition by oxidation
D137A
-
reduced ability to form tetramers, reduced dNTPase activity
D311A
mutation which removes one of the metal coordination residues in the active site and results in the loss of dNTPase activity
K405R
mutant cannot be acetylated, reduced activity compared to acetylated wild-type protein. K405R mutant expressing cancer cells show reduced G1/S transition and slower proliferation compared to wildtype
Q142E/R145K
-
reduced ability to form tetramers, reduced dNTPase activity
R333E
-
reduced ability to form tetramers, reduced dNTPase activity
R333E/R451E
-
reduced ability to form tetramers, reduced dNTPase activity
R451A/L453A
mutation in the RXL motif, disrupts SAMHD1 tetramer formation and abolishes its dNTPase activity in vitro and in cells. The mutant fails to restrict HIV-1 infection and has reduced binding to cyclin A2
R451E
-
reduced ability to form tetramers, reduced dNTPase activity
T592D
T592E
phosphomimetic mutation, reduces the stability of the SAMHD1 tetramer. about 3fold decrease in activity
T592V
neutral substitution, does not perturb the structure
Y146S/Y154S
dimerization-defective mutant, displays a severe dNTPase defect in vitro, but is indistinguishable from wild-type in its ability to deplete cellular dNTP pools and to restrict HIV replication
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in U2OS cell
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
enzyme is variably expressed during the cell cycle, maximally during quiescence and minimally during S-phase
maximum expressionin quescent cells
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
medicine
in fibroblasts of patients with genetic mutations of deoxyguanosine kinase, SAMHD1 leads to manifestation of dNTP pool imbalance and DNA depletion. When SAMHD1 is silenced by siRNA transfection the composition of the mitochondrial dNTP pool approaches that of the controls, and DNA copy number increases
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Miazzi, C.; Ferraro, P.; Pontarin, G.; Rampazzo, C.; Reichard, P.; Bianchi, V.
Allosteric regulation of the human and mouse deoxyribonucleotide triphosphohydrolase sterile alpha-motif/histidine-aspartate domain-containing protein 1 (SAMHD1)
J. Biol. Chem.
289
18339-18346
2014
Mus musculus (Q60710), Mus musculus, Homo sapiens (Q9Y3Z3), Homo sapiens
Manually annotated by BRENDA team
Zhu, C.; Gao, W.; Zhao, K.; Qin, X.; Zhang, Y.; Peng, X.; Zhang, L.; Dong, Y.; Zhang, W.; Li, P.; Wei, W.; Gong, Y.; Yu, X.
Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase
Nat. Commun.
4
2722
2013
Homo sapiens
Manually annotated by BRENDA team
Franzolin, E.; Pontarin, G.; Rampazzo, C.; Miazzi, C.; Ferraro, P.; Palumbo, E.; Reichard, P.; Bianchi, V.
The deoxynucleotide triphosphohydrolase SAMHD1 is a major regulator of DNA precursor pools in mammalian cells
Proc. Natl. Acad. Sci. USA
110
14272-14277
2013
Homo sapiens (Q9Y3Z3), Homo sapiens
Manually annotated by BRENDA team
Zhu, C.F.; Wei, W.; Peng, X.; Dong, Y.H.; Gong, Y.; Yu, X.F.
The mechanism of substrate-controlled allosteric regulation of SAMHD1 activated by GTP
Acta Crystallogr. Sect. D
71
516-524
2015
Homo sapiens (Q9Y3Z3), Homo sapiens
Manually annotated by BRENDA team
Mauney, C.H.; Rogers, L.C.; Harris, R.S.; Daniel, L.W.; Devarie-Baez, N.O.; Wu, H.; Furdui, C.M.; Poole, L.B.; Perrino, F.W.; Hollis, T.
The SAMHD1 dNTP triphosphohydrolase is controlled by a redox switch
Antioxid. Redox Signal.
27
1317-1331
2017
Homo sapiens (Q9Y3Z3)
Manually annotated by BRENDA team
Jang, S.; Zhou, X.; Ahn, J.
Substrate specificity of SAMHD1 triphosphohydrolase activity is controlled by deoxyribonucleoside triphosphates and phosphorylation at Thr592
Biochemistry
55
5635-5646
2016
Homo sapiens
Manually annotated by BRENDA team
Mauney, C.H.; Perrino, F.W.; Hollis, T.
Identification of inhibitors of the dNTP triphosphohydrolase SAMHD1 using a novel and direct high-throughput assay
Biochemistry
57
6624-6636
2018
Homo sapiens (Q9Y3Z3)
Manually annotated by BRENDA team
Tramentozzi, E.; Ferraro, P.; Hossain, M.; Stillman, B.; Bianchi, V.; Pontarin, G.
The dNTP triphosphohydrolase activity of SAMHD1 persists during S-phase when the enzyme is phosphorylated at T592
Cell Cycle
17
1102-1114
2018
Homo sapiens (Q9Y3Z3)
Manually annotated by BRENDA team
Franzolin, E.; Salata, C.; Bianchi, V.; Rampazzo, C.
The deoxynucleoside triphosphate triphosphohydrolase activity of SAMHD1 protein contributes to the mitochondrial DNA depletion associated with genetic deficiency of deoxyguanosine kinase
J. Biol. Chem.
290
25986-25996
2015
Homo sapiens (Q9Y3Z3), Homo sapiens
Manually annotated by BRENDA team
Tang, C.; Ji, X.; Wu, L.; Xiong, Y.
Impaired dNTPase activity of SAMHD1 by phosphomimetic mutation of Thr-592
J. Biol. Chem.
290
26352-26359
2015
Homo sapiens (Q9Y3Z3)
Manually annotated by BRENDA team
Seamon, K.J.; Stivers, J.T.
A high-throughput enzyme-coupled assay for SAMHD1 dNTPase
J. Biomol. Screen.
20
801-809
2015
Homo sapiens (Q9Y3Z3)
Manually annotated by BRENDA team
Gelais, C.; Kim, S.; Maksimova, V.; Buzovetsky, O.; Knecht, K.; Shepard, C.; Kim, B.; Xiong, Y.; Wu, L.
A cyclin-binding motif in human SAMHD1 is required for its HIV-1 restriction, dNTPase activity, tetramer formation, and efficient phosphorylation
J. Virol.
92
e01787
2018
Homo sapiens (Q9Y3Z3), Homo sapiens
Manually annotated by BRENDA team
Lee, E.J.; Seo, J.H.; Park, J.H.; Vo, T.T.L.; An, S.; Bae, S.J.; Le, H.; Lee, H.S.; Wee, H.J.; Lee, D.; Chung, Y.H.; Kim, J.A.; Jang, M.K.; Ryu, S.H.; Yu, E.; Jang, S.H.; Park, Z.Y.; Kim, K.W.
SAMHD1 acetylation enhances its deoxynucleotide triphosphohydrolase activity and promotes cancer cell proliferation
Oncotarget
8
68517-68529
2017
Homo sapiens (Q9Y3Z3), Homo sapiens
Manually annotated by BRENDA team
Choi, J.; Ryoo, J.; Oh, C.; Hwang, S.; Ahn, K.
SAMHD1 specifically restricts retroviruses through its RNase activity
Retrovirology
12
46
2015
Homo sapiens (Q9Y3Z3), Homo sapiens
Manually annotated by BRENDA team
Bhattacharya, A.; Wang, Z.; White, T.; Buffone, C.; Nguyen, L.A.; Shepard, C.N.; Kim, B.; Demeler, B.; Diaz-Griffero, F.; Ivanov, D.N.
Effects of T592 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 can not explain the retroviral restriction defect
Sci. Rep.
6
31353
2016
Homo sapiens (Q9Y3Z3)
Manually annotated by BRENDA team