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Information on EC 2.7.9.3 - selenide, water dikinase and Organism(s) Escherichia coli and UniProt Accession P16456
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2.7.9.3 selenide, water dikinaseIUBMB Comments
Mg2+-dependent enzyme identified in Escherichia coli
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Word Map
- 2.7.9.3
-
selenoproteins
- monoselenophosphate
-
deiodinases
-
iodothyronine
-
selenocysteine-containing
- trnasec
-
secis
-
2-selenouridine
-
selenoproteome
- seryl-trna
- sepsecs
-
stadtman
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5-methylaminomethyl-2-selenouridine
- seryl-trnasec
-
selenoenzymes
- txnrd3
-
selenium-dependent
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trnasersec
- l-selenocysteine
- medicine
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
selenophosphate synthetase, sephs2, selenophosphate synthetase 2, selenophosphate synthetase 1, dsps2, sps 1, sps-1, seld protein, selenophosphate synthase, selenophosphate synthetase-1, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
GenBank AE000719-derived protein GI 2983519
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gene selD proteins
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kinase (phosphorylating), pyruvate-water di-
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Patufet protein
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proteins , gene selD (specific proteins and subclasses)
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proteins, gene selD
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pyruvate-water di-kinase (phosphorylating)
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SELD protein
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selenium donor protein
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selenophosphate synthase
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selenophosphate synthase (Aquifex aeolicus gene selD)
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selenophosphate synthetase
synthetase, selenophosphate
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selenophosphate synthetase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + selenide + H2O = AMP + selenophosphate + phosphate
no pyrophosphorylated enzyme intermediate detectable
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ATP + selenide + H2O = AMP + selenophosphate + phosphate
the existence of a pyrophosphorylated enzyme intermediate can be excluded
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phospho group transfer
phospho group transfer
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SYSTEMATIC NAME
IUBMB Comments
ATP:selenide, water phosphotransferase
Mg2+-dependent enzyme identified in Escherichia coli
CAS REGISTRY NUMBER
COMMENTARY
151125-25-6
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204795-23-3
selenophosphate synthase (Aquifex aeolicus gene selD), genBank AE000719-derived protein GI 2983519
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
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
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the compound is used as a synthetic analogue of the substrate ATP for the monitoring and quantitative analysis of the functional activity of SPS
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?
additional information
?
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no activity by selenophosphate synthetase 1
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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specific for ATP
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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in the absence of selenide, ATP is converted completely to AMP and phosphate
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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in the absence of selenide, ATP is converted completely to AMP and phosphate
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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in the absence of selenide, ATP is converted completely to AMP and phosphate
selenophosphate is derived from the gamma phosphoryl group and phosphate from the beta phosphoryl group of ATP
?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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the gamma-phosphoryl group of the substrate ATP is cleaved in a kinetically competent reaction to form a phosphoryl-enzyme intermediate in the absence of the second substrate, selenide
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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the enzyme provides the biologically active selenium donor compound monoseleniumphosphate
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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-
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
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the enzyme provides the biologically active selenium donor compound monoseleniumphosphate
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2'(3')-O-(2,4,6-trinitrophenyl)adenosine-5'-triphosphate
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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
additional information
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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
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K+
Mg2+
Mn2+
Mn2+
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MnATP2-, although not able to replace MgATP2- for catalytic activity, binding to the enzyme in presence of K+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
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the enzyme is involved in selenocysteine biosynthesis. The interaction between selenocysteine lyase and selenophosphate synthetase occurs with a stoichiometry of 1:1
physiological function
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selenophosphate synthetase is a key enzyme of the selenium pathway in the cell
additional information
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the non-linear regression analysis of the saturation curve of TNP-ATP binding to D197 SPS fits to a model with 2 distinct binding sites with KDs different in order. Enzyme SPS exists in a form of tetramer in given reaction conditions, in accordance with the concentration stoichiometry of 4 mol of 2'(3')-O-(2,4,6-trinitrophenyl)adenosine-5'-triphosphate to 1 mole of recombinant protein
evolution
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selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme selenophosphate synthetase, conserved in all prokaryotic and eukaryotic genomes encoding selenoproteins. SPS1 genes originated through a number of independent gene duplications from an ancestral metazoan selenoprotein SPS2 gene that most likely already carried the SPS1 function. In SPS genes, parallel duplications and subsequent convergent subfunctionalization have resulted in the segregation to different loci of functions initially carried by a single gene. Evolutionary history of SPS genes, mapping of selenoprotein function spanning the whole tree of life. SPS is itself a selenoprotein in many species, although functionally equivalent homologues that replace the Sec site with cysteine (Cys) are common. Phylogenetic profile of SPS and selenium utilization traits in prokaryotes, overview
evolution
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SEPHS1 and SEPHS2 most likely segregate from their common ancestor prior to speciation
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
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4 * 37500, SDS-PAGE, in solution, the recombinant SPS exists as a dimer with two active sites capable of ATP binding in each subunit
tetramer
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4 * 37500, SDS-PAGE, the enzyme SPS seems to exist in a form of tetramer in given reaction conditions, in accordance with the concentration stoichiometry of 4 mol of TNP-ATP to 1 mole of recombinant protein, molecular structure modelling
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C17S
C19S
G18V
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70% reduced activity, 4fold-increase in the Km-value for ATP compared to that of the wild type enzyme
H13N
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unaltered activity level, no substantially altered Km-value for ATP compared to that of the wild type enzyme
SPS238
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C-terminally truncated mutant containing the N-terminal 238 amino acids of the 348-amino-acid protein
SPS262
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C-terminally truncated mutant containing the N-terminal 262 amino acids of the 348-amino-acid protein
SPS332
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C-terminally truncated mutant containing the N-terminal 332 amino acids of the 348-amino-acid protein
C17S
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in mutants C17S and C19S the binding of MnATP2- is unaffected by Zn2+
C19S
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in mutants C17S and C19S the binding of MnATP2- is unaffected by Zn2+
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
DEAE-Sepharose chromatography is used after an ammonium sulfate fractionation step followed by phenyl-Sepharose and butyl-Sepharose chromatography
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recombinant wild-type and mutant enzymes from Escherichia coli strain BL21-Gold (DE3) by ammonium sulfate fractionation, dialysis, and anion exchange chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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)
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gene selD, DNA and amino acid sequence determination and analysis, phylogenetic profiling
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gene sps2, DNA and amino acid sequence determination and analysis, phylogenetic analysis, sequence comparison, expression in Escherichia coli strain BL21(DE3)
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into the vector pCR2.1 and subsequently into pKK233.2 for expression in Escherichia coli MB08 cells
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Veres, Z.; Kim, I.Y.; Scholz, T.D.; Stadtman, T.C.
Selenophosphate synthetase. Enzyme properties and catalytic reaction
J. Biol. Chem.
269
10597-10603
1994
Escherichia coli
Walker, H.; Ferretti, J.A.; Stadtman, T.C.
Isotope exchange studies on the Escherichia coli selenophosphate synthetase mechanism
Proc. Natl. Acad. Sci. USA
95
2180-2185
1998
Escherichia coli
Kim, I.Y.; Stadtman, T.C.
Effects of monovalent cations and divalent metal ions on Escherichia coli selenophosphate synthetase
Proc. Natl. Acad. Sci. USA
91:
7326-7329
1994
Escherichia coli
Kim, I.Y.; Stadtman, T.C.
Selenophosphate synthetase: detection in extracts of rat tissues by immunoblot assay and partial purification of the enzyme from the archaeon Methanococcus vannielii
Proc. Natl. Acad. Sci. USA
92
7710-7713
1995
Escherichia coli, Methanococcus vannielii, Rattus norvegicus
Kim, I.Y.; Veres, Z.; Stadtman, T.C.
Biochemical analysis of Escherichia coli selenophosphate synthetase mutants
J. Biol. Chem.
268
27020-27025
1993
Escherichia coli
Liu, S.Y.; Stadtman, T.C.
Selenophosphate synthetase: enzyme labeling studies with [gamma-32P]ATP, [beta-32P]ATP, [8-14C]ATP, and [75Se]selenide
Arch. Biochem. Biophys.
341
353-359
1997
Escherichia coli
Liu, S.Y.; Stadtman, T.C.
A non-r4adioactive and two radioactive assays for selenophosphate synthetase activity
BioFactors
6
305-309
1997
Escherichia coli
Lacourciere, G.M.; Stadtman, T.C.
Catalytic properties of selenophosphate synthetases: comparison of the selenocysteine-containing enzyme from Haemophilus influenzae with the corresponding cysteine-containing enzyme from Escherichia coli
Proc. Natl. Acad. Sci. USA
96
44-48
1999
Escherichia coli, Haemophilus influenzae
Mullins, L.S.; Hong, S.B.; Gibson, G.E.; Walker, H.; Stadtman, T.C.; Raushel, F.M.
Identification of a phosphorylated enzyme intermediate in the catalytic mechanism for selenophosphate synthetase
J. Am. Chem. Soc.
119
6684-6685
1997
Escherichia coli
-
Wolfe, M.D.
Mechanistic insights revealed through characterization of a novel chromophore in selenophosphate synthetase from Escherichia coli
IUBMB Life
55
689-693
2003
Escherichia coli
Haft, D.H.; Self, W.T.
Orphan SelD proteins and selenium-dependent molybdenum hydroxylases
Biol. Direct
3
4
2008
Escherichia coli, Enterococcus faecalis, Clostridioides difficile (Q182I1), Haloarcula marismortui (Q5V6B2), Haloarcula marismortui
Xu, X.; Carlson, B.A.; Mix, H.; Zhang, Y.; Saira, K.; Glass, R.S.; Berry, M.J.; Gladyshev, V.N.; Hatfield, D.L.
Biosynthesis of selenocysteine on its tRNA in eukaryotes
PLoS Biol.
5
96-105
2007
Caenorhabditis elegans, Escherichia coli, Mus musculus (P97364), Drosophila melanogaster (Q9VKY8)
-
Preabrazhenskaya, Y.V.; Kim, I.Y.; Stadtman, T.C.
Binding of ATP and its derivatives to selenophosphate synthetase from Escherichia coli
Biochemistry (Moscow)
74
910-916
2009
Escherichia coli
Noinaj, N.; Wattanasak, R.; Lee, D.Y.; Wally, J.L.; Piszczek, G.; Chock, P.B.; Stadtman, T.C.; Buchanan, S.K.
Structural insights into the catalytic mechanism of Escherichia coli selenophosphate synthetase
J. Bacteriol.
194
499-508
2012
Escherichia coli (P16456), Escherichia coli
Mariotti, M.; Santesmasses, D.; Capella-Gutierrez, S.; Mateo, A.; Arnan, C.; Johnson, R.; D'Aniello, S.; Yim, S.H.; Gladyshev, V.N.; Serras, F.; Corominas, M.; Gabaldon, T.; Guigo, R.
Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
Genome Res.
25
1256-1267
2015
Ciona intestinalis, Escherichia coli, no activity in Hymenoptera, Oikopleura dioica, Molgula tectiformis, Botryllus schlosseri, no activity in Lepidoptera, no activity in Coleoptera, no activity in Endopterygota, no activity in Acyrthosiphon pisum, no activity in Drosophila willistoni, Drosophila melanogaster (O18373), Caenorhabditis elegans (O62461), Homo sapiens (Q99611)
Preobrazhenskaya, Y.V.; Stenko, A.I.; Shvarts, M.V.; Lugovtsev, V.Y.
Binding stoichiometry of a recombinant selenophosphate synthetase with one synonymic substitution E197D to a fluorescent nucleotide analog of ATP, TNP-ATP
J. Amino Acids
2013
983565
2013
Escherichia coli, Escherichia coli DH5alpha-T1 and BL21-Gold(DE3)
Na, J.; Jung, J.; Bang, J.; Lu, Q.; Carlson, B.A.; Guo, X.; Gladyshev, V.N.; Kim, J.; Hatfield, D.L.; Lee, B.J.
Selenophosphate synthetase 1 and its role in redox homeostasis, defense and proliferation
Free Radic. Biol. Med.
127
190-197
2018
Escherichia coli, Homo sapiens (Q99611), Homo sapiens
Scortecci, J.F.; Serrao, V.H.B.; Fernandes, A.F.; Basso, L.G.M.; Gutierrez, R.F.; Araujo, A.P.U.; Neto, M.O.; Thiemann, O.H.
Initial steps in selenocysteine biosynthesis The interaction between selenocysteine lyase and selenophosphate synthetase
Int. J. Biol. Macromol.
156
18-26
2020
Escherichia coli
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