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show all sequences of 2.9.1.2

The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation

Palioura, S.; Sherrer, R.L.; Steitz, T.A.; Söll, D.; Simonovic, M.; Science 325, 321-325 (2009)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
crystal structure of the quaternary complex between human SepSecS, unacylated tRNASec, and a mixture of O-phosphoserine and thiophosphate to 2.8 A resolution
Homo sapiens
Engineering
Amino acid exchange
Commentary
Organism
K173A
in vivo activity of the mutant is indistinguishable from that of the wild-type enzyme
Homo sapiens
K173M
in vivo activity of the mutant is indistinguishable from that of the wild-type enzyme
Homo sapiens
Q105A
mutant is inactive in vivo
Homo sapiens
R313A
mutant is inactive in vivo
Homo sapiens
R75A
mutant is inactive in vivo
Homo sapiens
R97A
in vivo activity of the mutant is indistinguishable from that of the wild-type enzyme
Homo sapiens
R97Q
in vivo activity of the mutant is indistinguishable from that of the wild-type enzyme
Homo sapiens
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-phosphoseryl-tRNASec + selenophosphate
Homo sapiens
selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase catalyzes the final step of selenocysteine formation by a tRNA-dependent mechanism
L-selenocysteinyl-tRNASec + phosphate
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Homo sapiens
Q9HD40
-
-
Reaction
Reaction
Commentary
Organism
O-phospho-L-seryl-tRNASec + selenophosphate + H2O = L-selenocysteinyl-tRNASec + 2 phosphate
proposed pyridoxal 5'-phosphate mechanism of L-phosphoseryl-tRNA to L-selenocysteinyl-tRNA conversion: the reaction begins by the covalently attached O-phospho-L-serine being brought into the proximity of the Schiff base when L-phosphoseryl-tRNASec binds to the enzyme. The amino group of O-phospho-L-serine can then attack the Schiff base formed between Lys284 and pyridoxal 5'-phosphate, which yields an external aldimine. The reoriented side chain of Lys284 abstracts the Calpha proton from O-phospho-L-serine, and the electron delocalization by the pyridine ring assists in rapid beta-elimination of the phosphate group, which produces an intermediate dehydroalanyl-tRNASec. After phosphate dissociation and binding of selenophosphate, the concomitant attack of water on the selenophosphate group and of the nucleophilic selenium onto the highly reactive dehydroalanyl moiety yield an oxidized form of L-phosphoseryl-tRNASec. The protonated Lys284, returns the proton to the Calpha carbon and then attacks pyridoxal 5'-phosphate to form an internal aldimine. Finally, Sec-tRNASec is released from the active site
Homo sapiens
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-phosphoseryl-tRNASec + selenophosphate
selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase catalyzes the final step of selenocysteine formation by a tRNA-dependent mechanism
695136
Homo sapiens
L-selenocysteinyl-tRNASec + phosphate
-
-
-
?
O-phospho-L-seryl-tRNASec + selenophosphate
proposed pyridoxal 5'-phosphate mechanism of L-phosphoseryl-tRNA to L-selenocysteinyl-tRNA conversion: the reaction begins by the covalently attached O-phospho-L-serine being brought into the proximity of the Schiff base when L-phosphoseryl-tRNASec binds to the enzyme. The amino group of O-phospho-L-serine can then attack the Schiff base formed between Lys284 and pyridoxal 5'-phosphate, which yields an external aldimine. The reoriented side chain of Lys284 abstracts the Calpha proton from O-phospho-L-serine, and the electron delocalization by the pyridine ring assists in rapid beta-elimination of the phosphate group, which produces an intermediate dehydroalanyl-tRNASec. After phosphate dissociation and binding of selenophosphate, the concomitant attack of water on the selenophosphate group and of the nucleophilic selenium onto the highly reactive dehydroalanyl moiety yield an oxidized form of L-phosphoseryl-tRNASec. The protonated Lys284, returns the proton to the Calpha carbon and then attacks pyridoxal 5'-phosphate to form an internal aldimine. Finally, Sec-tRNASec is released from the active site
695136
Homo sapiens
L-selenocysteinyl-tRNASec + phosphate
-
-
-
?
Subunits
Subunits
Commentary
Organism
tetramer
two SepSecS monomers form a homodimer, and two active sites are formed at the dimer interface. The two homodimers associate into a tetramer through interactions between the N-terminal alpha1-loop-alpha2 motifs
Homo sapiens
Cofactor
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
pyridoxal 5'-phosphate–dependent mechanism of Sec-tRNASec formation. Each SepSecS monomer has a pyridoxal 5'-phosphate cofactor covalently linked to the Nepsilon-amino group of the conserved Lys284 by means of formation of a Schiff base
Homo sapiens
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
pyridoxal 5'-phosphate–dependent mechanism of Sec-tRNASec formation. Each SepSecS monomer has a pyridoxal 5'-phosphate cofactor covalently linked to the Nepsilon-amino group of the conserved Lys284 by means of formation of a Schiff base
Homo sapiens
Crystallization (Commentary) (protein specific)
Crystallization
Organism
crystal structure of the quaternary complex between human SepSecS, unacylated tRNASec, and a mixture of O-phosphoserine and thiophosphate to 2.8 A resolution
Homo sapiens
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
K173A
in vivo activity of the mutant is indistinguishable from that of the wild-type enzyme
Homo sapiens
K173M
in vivo activity of the mutant is indistinguishable from that of the wild-type enzyme
Homo sapiens
Q105A
mutant is inactive in vivo
Homo sapiens
R313A
mutant is inactive in vivo
Homo sapiens
R75A
mutant is inactive in vivo
Homo sapiens
R97A
in vivo activity of the mutant is indistinguishable from that of the wild-type enzyme
Homo sapiens
R97Q
in vivo activity of the mutant is indistinguishable from that of the wild-type enzyme
Homo sapiens
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-phosphoseryl-tRNASec + selenophosphate
Homo sapiens
selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase catalyzes the final step of selenocysteine formation by a tRNA-dependent mechanism
L-selenocysteinyl-tRNASec + phosphate
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-phosphoseryl-tRNASec + selenophosphate
selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase catalyzes the final step of selenocysteine formation by a tRNA-dependent mechanism
695136
Homo sapiens
L-selenocysteinyl-tRNASec + phosphate
-
-
-
?
O-phospho-L-seryl-tRNASec + selenophosphate
proposed pyridoxal 5'-phosphate mechanism of L-phosphoseryl-tRNA to L-selenocysteinyl-tRNA conversion: the reaction begins by the covalently attached O-phospho-L-serine being brought into the proximity of the Schiff base when L-phosphoseryl-tRNASec binds to the enzyme. The amino group of O-phospho-L-serine can then attack the Schiff base formed between Lys284 and pyridoxal 5'-phosphate, which yields an external aldimine. The reoriented side chain of Lys284 abstracts the Calpha proton from O-phospho-L-serine, and the electron delocalization by the pyridine ring assists in rapid beta-elimination of the phosphate group, which produces an intermediate dehydroalanyl-tRNASec. After phosphate dissociation and binding of selenophosphate, the concomitant attack of water on the selenophosphate group and of the nucleophilic selenium onto the highly reactive dehydroalanyl moiety yield an oxidized form of L-phosphoseryl-tRNASec. The protonated Lys284, returns the proton to the Calpha carbon and then attacks pyridoxal 5'-phosphate to form an internal aldimine. Finally, Sec-tRNASec is released from the active site
695136
Homo sapiens
L-selenocysteinyl-tRNASec + phosphate
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
tetramer
two SepSecS monomers form a homodimer, and two active sites are formed at the dimer interface. The two homodimers associate into a tetramer through interactions between the N-terminal alpha1-loop-alpha2 motifs
Homo sapiens
Other publictions for EC 2.9.1.2
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
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Homo sapiens
Placenta
34
967-972
2013
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Gallus gallus
PLoS ONE
7
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2012
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723214
Hohn
Genetic analysis of selenocyst ...
Methanococcus maripaludis
Mol. Microbiol.
81
249-258
2011
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1
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694074
Aeby
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Trypanosoma brucei
Mol. Biochem. Parasitol.
168
191-193
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694917
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Trypanosoma brucei
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106
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695136
Palioura
The human SepSecS-tRNASec comp ...
Homo sapiens
Science
325
321-325
2009
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7
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694428
Araiso
Structural insights into RNA-d ...
Methanococcus maripaludis
Nucleic Acids Res.
36
1187-1199
2008
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1
1
5
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5
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694847
Yuan
RNA-dependent conversion of ph ...
Homo sapiens, Methanocaldococcus jannaschii, Methanococcus maripaludis
Proc. Natl. Acad. Sci. USA
103
18923-18927
2006
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