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Information on EC 2.7.9.3 - selenide, water dikinase and Organism(s) Aquifex aeolicus and UniProt Accession O67139
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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
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deiodinases
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iodothyronine
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selenocysteine-containing
- trnasec
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secis
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2-selenouridine
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selenoproteome
- seryl-trna
- sepsecs
-
stadtman
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5-methylaminomethyl-2-selenouridine
- seryl-trnasec
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selenoenzymes
- txnrd3
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selenium-dependent
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trnasersec
- l-selenocysteine
- medicine
The taxonomic range for the selected organisms is: Aquifex aeolicus
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, sps 1, dsps2, sps-1, seld protein, selenophosphate synthase, selenophosphate synthetase-1, 
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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
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synthetase, selenophosphate
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + selenide + H2O = AMP + selenophosphate + phosphate
SPS catalyzes the exchange of the ATP gamma-phosphate group in the absence of selenide, suggesting that the beta-gamma-phosphate bond, but not the alpha-beta-phosphate bond, could be the initial cleavage site, formation of a phosphorylated enzyme intermediate, catalytic mechanism, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
ATP + selenide
AMP + selenophosphate + phosphate
selenophosphate synthetase catalyzes the activation of selenide with ATP to synthesize selenophosphate, the reactive selenium donor for biosyntheses of both the 21st amino acid selenocysteine and 2-selenouridine nucleotides in tRNA anticodons
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?
ATP + selenide
AMP + selenophosphate + phosphate
the phosphate moiety of selenophosphate is derived from the ATP gamma-phosphate, while the orthophosphate is from the beta-phosphate
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
Sec replaces the catalytically essential Cys residue, SPS is strictly conserved in the organisms that utilize Sec and/or selenouridine
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
the phosphate moiety of selenophosphate is derived from the ATP gamma-phosphate group, while the orthophosphate is from the beta-phosphate group. Although Thr221 is not essential for the reaction, it contributes to the enzyme activity, probably by interacting with the ATP gamma-phosphate group and a water molecule. Sec/Cys13 and Lys16 are essential for the SPS catalysis. Thr221 and Gly222 interact with the gamma-phosphate group of ATP
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?
additional information
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SPS orthologs, SPS1 and SPS2, exist, and SPS2 is the one that synthesizes selenophosphate, while SPS1 does not
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?
additional information
?
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SPS orthologs, SPS1 and SPS2, exist, and SPS2 is the one that synthesizes selenophosphate, while SPS1 does not
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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
AMP + selenophosphate + phosphate
selenophosphate synthetase catalyzes the activation of selenide with ATP to synthesize selenophosphate, the reactive selenium donor for biosyntheses of both the 21st amino acid selenocysteine and 2-selenouridine nucleotides in tRNA anticodons
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?
ATP + selenide + H2O
AMP + selenophosphate + phosphate
Sec replaces the catalytically essential Cys residue, SPS is strictly conserved in the organisms that utilize Sec and/or selenouridine
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?
additional information
?
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SPS orthologs, SPS1 and SPS2, exist, and SPS2 is the one that synthesizes selenophosphate, while SPS1 does not
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?
additional information
?
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SPS orthologs, SPS1 and SPS2, exist, and SPS2 is the one that synthesizes selenophosphate, while SPS1 does not
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
the ATP-binding site is formed at the subunit interface of the homodimer. Four Asp residues coordinate four metal ions to bind the phosphate groups of AMPCPP. In the free SPS structure, the two loop regions in the ATP-binding site are not ordered, and no enzyme-associated metal is observed. This suggests that ATP binding, metal binding, and the formation of their binding sites are interdependent, Thr221 and Gly222 interact with the gamma-phosphate group of ATP
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
ATP binding, metal binding, and the formation of their binding sites are interdependent, Thr221 and Gly222 are involved in metal binding
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
2 * 31000-34000, about, sequence calculation and analytical ultracentrifugation
additional information
additional information
SPS is a two-domain alpha/beta protein, with domain folds that are homologous to those of PurM superfamily proteins
additional information
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SPS is a two-domain alpha/beta protein, with domain folds that are homologous to those of PurM superfamily proteins
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 20°C, 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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
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
N79A
site-directed mutagenesis, the mutation enhances the ATP consumption by about 3fold compared to the wild-type enzyme
additional information
additional information
construction of an N-terminally truncated SPS mutant lacking 25 amino acid residues, i.e SPS-DELTAN
additional information
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construction of an N-terminally truncated SPS mutant lacking 25 amino acid residues, i.e SPS-DELTAN
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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 70°C for 30 min, anion exchange and hydrophobic interaction chromatography, followed by another step of anion exchange chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Matsumoto, E.; Sekine, S.; Akasaka, R.; Otta, Y.; Katsura, K.; Inoue, M.; Kaminishi, T.; Terada, T.; Shirouzu, M.; Yokoyama, S.
Structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus
Acta Crystallogr. Sect. F
F64
453-458
2008
Aquifex aeolicus (O67139), Aquifex aeolicus
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