Information on EC 2.7.9.3 - selenide, water dikinase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY hide
2.7.9.3
-
RECOMMENDED NAME
GeneOntology No.
selenide, water dikinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + selenide + H2O = AMP + selenophosphate + phosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-selenocysteine biosynthesis I (bacteria)
-
-
L-selenocysteine biosynthesis II (archaea and eukaryotes)
-
-
Metabolic pathways
-
-
Selenocompound metabolism
-
-
selenocysteine biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:selenide, water phosphotransferase
Mg2+-dependent enzyme identified in Escherichia coli
CAS REGISTRY NUMBER
COMMENTARY hide
151125-25-6
-
204795-23-3
selenophosphate synthase (Aquifex aeolicus gene selD), genBank AE000719-derived protein GI 2983519
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Bortryllus schlosseri
contains an active SPS2-Sec and an inactive SPS1-Gly isozyme
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
gene selD
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain ATCC 43049, gene selD
UniProt
Manually annotated by BRENDA team
DNA sequence comparison
-
-
Manually annotated by BRENDA team
contains an active SPS-Sec and an inactive SPS-Gly isozyme
-
-
Manually annotated by BRENDA team
gene SPS1
UniProt
Manually annotated by BRENDA team
no activity in Acyrthosiphon pisum
selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared
-
-
Manually annotated by BRENDA team
no activity in Bombyx mori
the organism lacks any selenocysteine-containing proteins, but contains SPS1, which functions in a pathway unrelated to selenocysteine biosynthesis in selenoproteinless animals, overview
-
-
Manually annotated by BRENDA team
no activity in Coleoptera
selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared
-
-
Manually annotated by BRENDA team
no activity in Drosophila willistoni
-
-
-
Manually annotated by BRENDA team
no activity in Endopterygota
selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared
-
-
Manually annotated by BRENDA team
no activity in Hymenoptera
selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared
-
-
Manually annotated by BRENDA team
no activity in Lepidoptera
selenoprotein genes are converted to Cys homologues or lost, and the Sec machinery degenerated and/or disappeared
-
-
Manually annotated by BRENDA team
no activity in Methanosarcina acetivorans
-
-
-
Manually annotated by BRENDA team
no activity in Methanosarcina mazei
-
-
-
Manually annotated by BRENDA team
no activity in Pyrobaculum aerophilum
-
-
-
Manually annotated by BRENDA team
no activity in Pyrobaculum calidifontis
-
-
-
Manually annotated by BRENDA team
no activity in Thermotoga maritima
-
-
-
Manually annotated by BRENDA team
no activity in Tribolium castaneum
the organism lacks any selenocysteine-containing proteins, but contains SPS1, which functions in a pathway unrelated to selenocysteine biosynthesis in selenoproteinless animals, overview
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
tiger shrimp
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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
2'(3')-O-(2,4,6-trinitrophenyl)adenosine-5'-triphosphate + selenide + H2O
2'(3')-O-(2,4,6-trinitrophenyl)adenosine-5'-monophosphate + selenophosphate + phosphate
show the reaction diagram
ATP + dithiothreitol + H2O
?
show the reaction diagram
-
as effective as selenide
-
-
?
ATP + selenide
AMP + selenophosphate + phosphate
show the reaction diagram
ATP + selenide + H2O
AMP + selenophosphate + 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
ATP + selenide
AMP + selenophosphate + phosphate
show the reaction diagram
ATP + selenide + H2O
AMP + selenophosphate + phosphate
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2'(3')-O-(2,4,6-trinitrophenyl)adenosine-5'-triphosphate
-
i.e. TNP-ATP, binding analysis of recombinant wild-type and mutant E197D to TNP-ATP, a synthetic fluorescent nucleotide analogue of ATP. The compound is used as a synthetic analogue of the substrate ATP for the monitoring and quantitative analysis of the functional activity of SPS. A non-linear regression analysis of the saturation curve of TNP-ATP binding to D197 SPS fitting to a model with 2 distinct binding sites with KDs different in order. Kinetics, overview
-
alpha,beta-methylene ATP
i.e. MPCPP, binding structure, overview
additional information
-
initial characterization of an unknown chromophore. Either the chromophore is directly involved in phosphoryl transfer or indirectly reflects a phosphorylation-dependent conformational change in selenophosphate synthetase
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ammonium sulfate
-
slightly stimulating
NH4+
-
monovalent cation required. K+, NH4+ or Rb+
Rb+
-
monovalent cation required. K+, NH4+ or Rb+
selenium
selenoprotein
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8-azido-ATP
alpha,beta-methylene-ATP
-
-
gamma-Thio-ATP
-
-
Li+
-
in presence of K+
phosphate
-
weak
Selenophosphate
-
weak
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
selenium-binding protein
-
3-mercaptopyruvate sulfurtransferase and GAPDH have more suitable potentials as a physiological selenium-delivery protein than rhodanese. In the presence of a selenium-binding protein, a low level of selenodiglutathione formed from SeO32- and glutathione could effectively replace the high concentrations of selenide routinely used as substrate in the selenophosphate synthetase in vitro assays
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.026 - 10.3
ATP
0.02 - 0.046
selenide
additional information
additional information
steady-state kinetics for the C-terminally His6-tagged enzyme mutant Sephs2-U60C
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0058
ATP
Homo sapiens
Q99611
pH 7.0, temperature not specified in the publication, recombinant His6-tagged enzyme mutant Sephs2-U60C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.95
8-azido-ATP
-
pH 7.2, 37C
0.17
AMP
-
pH 7.2, 37C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
-
2'(3')-O-(2,4,6-trinitrophenyl)-ATP binding to wild-type and mutant SPS
7.2 - 9
-
-
8
-
activity assay
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.9
calculated from amino acid sequence
5.2
-
wild-type enzyme
5.78
-
mutant SPS262
5.83
isoelectric focusing, recombinant His6-tagged enzyme
5.98
isoelectric focusing, recombinant His6-tagged enzyme
6.05
isoelectric focusing, recombinant enzyme
6.34
-
isoelectric focusing, recombinant enzyme
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
low expression level
Manually annotated by BRENDA team
very low expression level
Manually annotated by BRENDA team
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25000
-
mutant SPS238
29000
-
mutant SPS262
34000
-
mutant SPS332
35589
-
x * 33000, SPS2, SDS-PAGE, x * 35589, SPS2 isozyme 1, sequence calculation, x * 41768, SPS2 isozyme 2, sequence calculation
35590
-
calculated from amino acid sequence
36000
-
x * 36000, Sel1
36152
x * 36152, calculated from sequence
41768
-
x * 33000, SPS2, SDS-PAGE, x * 35589, SPS2 isozyme 1, sequence calculation, x * 41768, SPS2 isozyme 2, sequence calculation
42700
2 * 42700, about, sequence calculation, 2 * 45000, recombinant SelD, SDS-PAGE
43000
-
2 * 43000, about, sequence calculation, 2 * 45000, recombinant SelD, SDS-PAGE
45500
x * 45500, calculated from amino acid sequence
63000
about, analytical ultracentrifugation
68200
about, sequence calculation
100000
204000
crystal structure
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
6 * 31000-34000, about, crystal structure
homodimer
-
monomer
-
application of immunoblot assay to extracts after SDS-PAGE
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant truncated mutant enzyme SPS-DELTAN, mixing of 0.001 ml of protein solution, containing 9.9 mg/ml protein in 20 mM Tris-HCl, pH 8.0, 2 mM dithiothreitol, and 150 mM NaCl, with 0.001 ml of a reservoir solution containing 100 mM Na HEPES, pH 7.1, 50% 2-methyl-2,4-pentanediol, 200 mM ammonium phosphate, and 50 mM ammonium sulfate and equilibrating this mixture against 0.5 ml reservoir solution at 20C, X-ray diffraction structure determination and analysis at 2.0 A resolution, hexameric crystal structure
SPS2 free or with bound alpha/beta-methylene ATP, X-ray diffraction structure determination and analysis at 1.98-2.1 A resolution, molecular replacement
mutant enzyme C17S in apo form, hanging drop vapor diffusion method, using 50 mM Tris-HCl (pH 8.25), 50 mM MgCl2, and 32% (w/v) PEG MME 550
the crystal structures of selenophosphate synthetase 1 and of selenophosphate synthetase 1 complexed with AMPCP and K+ are solved to a resolution of 2.0 and 1.9 A, respectively
the recombinant full-length enzyme cannot be crystallized, but the DELTAN-LmSPS2, which lacks residues 1-69, is efficiently crystallized, from 0.2 M ammonium sulfate, 0.1 M trisodium citrate, pH 5.2, and 21% w/v PEG 4000, 3 days, X-ray diffraction structure determination and analysis at 1.88 A resolution
recombinant His6-tagged enzyme, from 0.1 M trisodium citrate, pH 5.6, 17% w/v, PEG 3350 using the microbatch method, 2 months, X-ray diffraction structure determination and analysis at 3.40 A resolution
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
-
22C, 10 min, stable
645479
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
pH 5, 10 min, stable
60
-
pH 7.2, aerobic conditions, 5 min, stable
70
-
pH 7.2, aerobic conditions, 5 min, complete inactivation
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
3 mM H2O2, pH 7.2, in absence of DTT and EDTA, 50% loss of activity
-
concentration-dependent inactivation
labile in 0.12% sucrose monolaurate, 1% sodium cholate, and 0.2 M sodium thiocyanate, slightly stable in 2% MEGA-9, 1% sodium deoxycholate, 1% nonidet P-40 and 1% polyoxyethylene 9 lauryl ether
-
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Triton X-100
-
slightly stable in 1% (v/v) Triton X-100
urea
-
labile in 2 M urea
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80C, in 0.2 M Hepes buffer at pH 6.8, less than one year, stable
-
-80C, stable for 1 year
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DEAE-cellulose column chromatography, Sephacryl S-300 gel filtration, Heparin Toyopearl column chromatography, and hydroxylapatite column chromatography
-
DEAE-Sepharose chromatography is used after an ammonium sulfate fractionation step followed by phenyl-Sepharose and butyl-Sepharose chromatography
-
native enzyme from liver, by anion exchange chromatography, gel filtration, heparin affinity and hydroxyapatite chromatography
-
Ni-agarose column chromatography
on a Ni-chelating column, the His-tag is removed by thrombin digestion, further purification by gel-filtration
recombinant C-terminally His6-tagged enzyme mutant Sephs2U60C from Escherichia coli Rosetta (DE3) pLysS by nickel affinity chromatography
recombinant from COS-7 cells as FLAG tagged enzyme
recombinant from Escherichia coli, to homogeneity
-
recombinant from Sf9 insect cells as N-FLAG tagged protein
-
recombinant His-tagged SPS1 and His-tagged SPS2 mutant Sec69Cys from Escherichia coli strain Rosetta (DE3) to homogeneity by affinity chromatography on a His-binding resin
-
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, and gel filtration
recombinant SelD from Escherichia coli strain BL21(DE3) to homogeneity
recombinant trigger factor-fused SPS2 from Escherichia coli, during purification, the N-terminal trigger factor portion is removed by proteolysis with thrombin, and the final SPS protein comprises the full-length SPS region, residues 1-336, and nine extra N-terminal residues, GSGGIEGRH, which are derived from the linker
recombinant truncated mutant enzyme SPS-DELTAN from Escherichia coli by heat treatment at 70C for 30 min, anion exchange and hydrophobic interaction chromatography, followed by another step of anion exchange chromatography and gel filtration
recombinant wild-type and mutant enzymes from Escherichia coli strain BL21-Gold (DE3) by ammonium sulfate fractionation, dialysis, and anion exchange chromatography
-
recombinant wild-type enzyme from strain BL21(DE3)
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a single SPS gene, phylogenetic analysis
-
DNA and amino acid sequence determination and analysis of SPS1; DNA and amino acid sequence determination and analysis of SPS2, complementation of SPS2 knockout NIH3T3 cells by expression of SPS2
DNA sequence determination and analysis
DNA sequence determination and analysis, chromosomal mapping, expression in COS-7 cells as FLAG tagged enzyme
expressed in CHO-K1 cells
-
expressed in Escherichia coli BL21(DE3) cells
expression analysis for SPS2 and selenoproteins, overview
expression in Spodoptera frugiperda Sf9 insect cells via baculovirus infection, expression as N-FLAG tagged protein
-
expression in strain BL21(DE3)
-
expression of His-tagged SPS1 and of His-tagged SPS2 mutant Sec69Cys in Escherichia coli strain Rosetta (DE3)
-
expression of trigger factor-fused SPS2 in Escherichia coli
expression of truncated mutant enzyme SPS-DELTAN in Escherichia coli
gene ptuf/SelD or SPS1, genetic structure analysis, SPS1-UGA might perhaps be translated by a readthrough mechanism not involving Sec insertion. In this respect, there is growing evidence for abundant stop codon readthrough in insects, with UGA being the most frequently observed readthrough codon in Drosophila
gene selD, DNA and amino acid sequence determination and analysis of enzymes from Escherichia coli strains DH5alpha-T1 AND BL21-Gold (DE3), that differ in position 14 and 197, and compared to the DNA sequence from Escherichia coli strain K-12, recombinant overexpression of wild-type and mutant enzymes in Escherichia coli strain BL21-Gold (DE3)
-
gene selD, DNA and amino acid sequence determination and analysis, genomic location, phylogenetic analysis and multiple sequence alignment, genes involved in selenium utilization, overview
gene selD, DNA and amino acid sequence determination and analysis, overexpression in Escherichia coli strain BL21(DE3), and functional complementation of Escherichia coli SelD deletion strain WL400
gene selD, DNA and amino acid sequence determination and analysis, phylogenetic profiling
gene selD, DNA sequence determination and analysis, subcloning and transient expression in enzyme deficient Escherichia coli resulting in poor complemetation of the bacteria by the human gene, and expression in mammalian HtTA cells together with human type I iodothyronine 5'-deiodinase and Xenopus tRNASeC
gene selD, expression of SelD1 alone in Escherichia coli results in low selenophosphate synthetase activity in the wild-type strain XL1-Blue, an Escherichia coli SelB mutant strain WL81300 does not show any selenophosphate synthetase activity. Co-expression of SelB, SelC, and SelD from Eubacterium acidaminophilum leads to production of selenocystein containing proteins, selenoprotein synthesis in Escherichia coli requires the products of the genes selA, selB, selC, and selD
-
gene seld-1, genetic structure analysis
gene selD/sps1, DNA and amino acid sequence determination and analysis, the gene is actually translated in male accessory glands of the selenoprotein-less ant Cardiocondyla obscurior
-
gene Sephs2, recombinant expression of C-terminally His6-tagged enzyme mutant Sephs2U60C in Escherichia coli Rosetta (DE3) pLysS
gene SPS, phylogenetic analysis
gene Sps1, located on chromosome 2, expression anaysis
gene sps2, DNA and amino acid sequence determination and analysis, phylogenetic analysis, sequence comparison, expression in Escherichia coli strain BL21(DE3)
gene SPS2, gene expression profiles of the knockdown of SPS2 in larval and adult stages, quantitative real-time PCR enzyme exxpression analysis in wild-type and mutant strains, detailed overview
-
gene SPS2, phylogenetic analysis
Bortryllus schlosseri
-
into the vector pCR2.1 and subsequently into pKK233.2 for expression in Escherichia coli MB08 cells
-
into the vector pET28a for expression in Escherichia coli Rosetta DE3 cells
NIH3T3 cells are stably transfected with the Tet-on U6 control construct or the Tet-siSPS2 construct and grown in the presence or absence of doxycycline for 3 d to induce SPS2 knockdown, then transiently transfected with pTriEX expression vector or the expression vector encoding SPS2 wild-type gene or SPS2 knock-in gene, SPS2 overexpression and functional restoration
-
overexpression in Escherichia coli strain BL21
-
overexpression of the wild-type enzyme in motoneurons does not extend longevity
-
recombinant expression of His6-tagged enzyme with a thrombin-cleavage site in Escherichia coli strain BL21(DE3)
the mutated sps2 gene, which contains cysteine in the place of the TGA encoded selenocysteine in the wild-type, is expressed in Escherichia coli selD deficient mutant, MB08. Like the Escherichia coli wild-type selD gene, the mutant spos2 gene complements the selD mutation. Replacement of Cys with either Ala, Ser, or Thr results in a loss of ability to complement the selD mutation
-
the open reading frame of Dsps2 mRNA is interrupted by a UGA stop codon. The 3'-UTR contains a mammalian-like Sec insertion sequence which causes translation readthrough in both transfected Drosophila cells and transgenic embryos
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
enzyme expression by hemocytes significantly increases in stage C, and then gradually decreases until stage A. The relative enzyme expression (compared to enzyme expression in shrimp injected with saline) of shrimp injected with white spot syndrome virus after 3, 6, 12, 24 and 48 h increases by 7.0, 4.4, 2.0, 1.6, and 1.8fold, respectively
SPS mRNA expression in hemocytes of shrimp injected with white spot syndrome virus significantly decreases from 3 to 48 h
the enzyme, among other proteins in apregulated in winged males compared to unwinged males of Cardiocondyla obscurior, analysis of the protein profile of male accessory glands from winged and unwinged male ants
-
the levels of the major type and DELTAE8 splice variants of selenophosphate synthetase 1 are gradually increased until G2/M phase and then gradually decreases. Splice variant DELTAE2 expression peaks at mid-S phase and then gradually decreases
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C13S
site-directed mutagenesis, inactive mutant, the activity cannot be recovered by the NifS-like protein
C17S
site-directed mutagenesis, inactive mutant, the activity can be recovered by the NifS-like protein
K16A
site-directed mutagenesis, inactive mutant
N79A
site-directed mutagenesis, the mutation enhances the ATP consumption by about 3fold compared to the wild-type enzyme
C17S/C19S
-
no catalytic activity
D227A
inactive
E197D
-
site-directed mutagenesis
G18V
-
70% reduced activity, 4fold-increase in the Km-value for ATP compared to that of the wild type enzyme
H13N
-
unaltered activity level, no substantially altered Km-value for ATP compared to that of the wild type enzyme
K20Q
-
no catalytic activity
K20R
-
nearly no remaining activity
SPS238
-
C-terminally truncated mutant containing the N-terminal 238 amino acids of the 348-amino-acid protein
SPS262
-
C-terminally truncated mutant containing the N-terminal 262 amino acids of the 348-amino-acid protein
SPS332
-
C-terminally truncated mutant containing the N-terminal 332 amino acids of the 348-amino-acid protein
E197D
-
site-directed mutagenesis
-
G269C
site-directed mutagenesis, reduced activity, slightly reduced ATP binding
G271R
site-directed mutagenesis, reduced activity, slightly reduced ATP binding
G274A
site-directed mutagenesis, reduced activity and ATP binding
G274D
site-directed mutagenesis, reduced activity, no ATP binding
G274V
site-directed mutagenesis, no activity and ATP binding
H275N
site-directed mutagenesis, reduced activity, no ATP binding
H275Y
site-directed mutagenesis, increased catalytic activity and ATP binding
Sec60C
site-directed mutagenesis, the in-frame opal codon for Sec60 is altered to Cys-coding TGT in mutant Sephs2U60C, the substitution of active site Sec with Cys does not significantly perturb the catalytic function of the His6-tagged human Sephs2
C46A
site-directed mutagenesis
Sec63C
-
site-directed mutagenesis, SPS2 mutant Sec63Cys catalyzes the selenide-dependent synthesis of selenophosphate
T29C
-
site-directed mutagenesis, the Thr29Cys mutant of SPS1 exhibits SPS activity
C42A
-
site-directed mutagenesis
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
-
Sps1 and its reaction product selenophosphate might play a role in cancer prevention and therapy when a modulation of the enzyme activity is combined with cancer therapies
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