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Information on EC 2.7.1.164 - O-phosphoseryl-tRNASec kinase and Organism(s) Methanocaldococcus jannaschii and UniProt Accession Q58933

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IUBMB Comments
In archaea and eukarya selenocysteine formation is achieved by a two-step process: O-phosphoseryl-tRNASec kinase (PSTK) phosphorylates the endogenous L-seryl-tRNASec to O-phospho-L-seryl-tRNASec, and then this misacylated amino acid-tRNA species is converted to L-selenocysteinyl-tRNASec by EC 2.9.1.2 (Sep-tRNA:Sec-tRNA synthase).
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Methanocaldococcus jannaschii
UNIPROT: Q58933
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The taxonomic range for the selected organisms is: Methanocaldococcus jannaschii
The expected taxonomic range for this enzyme is: Archaea, Eukaryota
Synonyms
o-phosphoseryl-trna(sec) kinase, o-phosphoseryl-trna kinase, phosphoseryl-trna[ser]sec kinase, phosphoseryl-trnasec kinase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
O-phosphoseryl-tRNA(Sec) kinase
-
O-phosphoseryl-tRNASec kinase
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SYSTEMATIC NAME
IUBMB Comments
ATP:L-seryl-tRNASec O-phosphotransferase
In archaea and eukarya selenocysteine formation is achieved by a two-step process: O-phosphoseryl-tRNASec kinase (PSTK) phosphorylates the endogenous L-seryl-tRNASec to O-phospho-L-seryl-tRNASec, and then this misacylated amino acid-tRNA species is converted to L-selenocysteinyl-tRNASec by EC 2.9.1.2 (Sep-tRNA:Sec-tRNA synthase).
CAS REGISTRY NUMBER
COMMENTARY hide
91273-83-5
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + L-seryl-tRNASec
ADP + O-phospho-L-seryl-tRNASec
show the reaction diagram
ATP + L-seryl-tRNASec
O-phospho-L-seryl-tRNASec + ADP
show the reaction diagram
PSTK distinguishes tRNASec from tRNASer. Unlike eukaryotic PSTK, the archaeal enzyme recognizes the acceptor stem rather than the length and secondary structure of the D-stem. The seryl moiety of L-seryl-tRNASec is not required for enzyme recognition, as PSTK efficiently phosphorylates L-threonyl-tRNASec
-
-
?
ATP + seryl-tRNASec
ADP + O-phospho-L-seryl-tRNASec
show the reaction diagram
L-phosphoseryl-tRNA is the crucial precursor for L-selenocysteinyl-tRNA formation in archaea and eukarya. Selenocysteine formation is achieved by a two-step process: O-phosphoseryl-tRNASec kinase (PSTK) phosphorylates the endogenous Ser-tRNASec to O-phosphoseryl-tRNASec, and then this misacylated amino acid-tRNA species is converted to L-selenocysteinyl-tRNASec by Sep-tRNA:Sec-tRNA synthase (SepSecS)
-
-
?
CTP + L-seryl-tRNASec
CDP + O-phospho-L-seryl-tRNASec
show the reaction diagram
phosphorylation at about 60% the activity of ATP
-
-
?
dATP + L-seryl-tRNASec
dADP + O-phospho-L-seryl-tRNASec
show the reaction diagram
phosphorylation at about 65% the activity of ATP
-
-
?
GTP + L-seryl-tRNASec
GDP + O-phospho-L-seryl-tRNASec
show the reaction diagram
phosphorylation at about 40% the activity of ATP
-
-
?
ITP + L-seryl-tRNASec
IDP + O-phospho-L-seryl-tRNASec
show the reaction diagram
phosphorylation at about 85% the activity of ATP
-
-
?
L-threonyl-tRNASec + ATP
O-phospho-L-threonyl-tRNASec + ADP
show the reaction diagram
-
-
-
?
UTP + L-seryl-tRNASec
UDP + O-phospho-L-seryl-tRNASec
show the reaction diagram
phosphorylation at about 40% the activity of ATP
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + L-seryl-tRNASec
ADP + O-phospho-L-seryl-tRNASec
show the reaction diagram
ATP + seryl-tRNASec
ADP + O-phospho-L-seryl-tRNASec
show the reaction diagram
L-phosphoseryl-tRNA is the crucial precursor for L-selenocysteinyl-tRNA formation in archaea and eukarya. Selenocysteine formation is achieved by a two-step process: O-phosphoseryl-tRNASec kinase (PSTK) phosphorylates the endogenous Ser-tRNASec to O-phosphoseryl-tRNASec, and then this misacylated amino acid-tRNA species is converted to L-selenocysteinyl-tRNASec by Sep-tRNA:Sec-tRNA synthase (SepSecS)
-
-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00004
L-seryl-tRNASec
37°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.098
L-seryl-tRNASec
37°C
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
the enzyme is involved in the biosynthesis of selenocysteine
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
29500
x * 29500, calculated
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 29500, calculated
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with an anticodon-stem/loop truncated tRNASec, to 2.4 A resolution. Truncated tRNASec is bound between the enzyme's C-terminal domain CTD and N-terminal kinase domain NTD that are connected by a flexible 11 amino acid linker. Upon tRNASec recognition, the CTD undergoes a 62-A movement to allow proper binding of the 7-bp D-stem. This large reorganization of the quaternary structure likely provides a means by which the unique tRNASec species can be accurately recognized with high affinity by the translation machinery
in complex with Methanopyrus tRNASec and with 5'-adenylyl imidodiphosphate, to 2.5-2.9 A resolution. The enzyme consists of two independent linker-connected domains, the N-terminal catalytic domain NTD and the C-terminal domain CTD. The D-arm-CTD binding occurs independently of and much more strongly than the acceptor-arm-NTD binding. The enzyme thereby distinguishes the characteristic D arm with the maximal stem and the minimal loop of tRNASec from the canonical D arm of tRNASer, without interacting with the anticodon
sitting drop vapor diffusion method at 20°C, the structures of MjPSTK complexed with ADP and AMPPNP revealed that this enzyme belongs to the P-loop kinase class, and that the kinase domain is closely related to gluconate kinase and adenylate kinase. ATP is bound by the P-loop domain (residues 11-18). Formed by antiparallel dimerization of two O-phosphoseryl-tRNASec kinase monomers, the enzyme structure shows a deep groove with positive electrostatic potential. Located in this groove is the active site of the enzyme, which biochemical and genetic data suggest is composed of Asp-41, Arg-44, Glu-55, Tyr-82, Tyr-83, Met-86, and Met-132
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D146A
mutant is active in vivo
D41A
strongly reduced activity
G14W
strongly reduced activity
K142A
mutant is active in vivo
K142A/Y143A
mutant shows severely reduced activity with the Methanopyrus kandleri tRNASec substrate
K30A
mutant is defective in phosphorylation activity
N161A
mutant is defective in phosphorylation activity
R116A
mutant enzyme is 23.5fold less active than wild-type enzyme
R120A
strongly reduced activity
T19W
mutant enzyme is 2.8fold less active than wild-type enzyme
W145A
mutant is active in vivo
additional information
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression in Escherichia coli BL21
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kaiser, J.T.; Gromadski, K.; Rother, M.; Engelhardt, H.; Rodnina, M.V.; Wahl, M.C.
Structural and functional investigation of a putative archaeal selenocysteine synthase
Biochemistry
44
13315-13327
2005
Methanocaldococcus jannaschii (Q58933), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661 (Q58933)
Manually annotated by BRENDA team
Sherrer, R.L.; O'Donoghue, P.; Sll D.
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation
Nucleic Acids Res.
36
1247-1259
2008
Methanocaldococcus jannaschii (Q58933), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661 (Q58933)
Manually annotated by BRENDA team
Sherrer, R.L.; Ho, J.M.; Sll, D.
Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase
Nucleic Acids Res.
36
1871-1880
2008
Methanocaldococcus jannaschii (Q58933), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661 (Q58933)
Manually annotated by BRENDA team
Yuan, J.; Palioura, S.; Salazar, J.C.; Su, D.; O'Donoghue, P.; Hohn, M.J.; Cardoso, A.M.; Whitman, W.B.; Sll, D.
RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea
Proc. Natl. Acad. Sci. USA
103
18923-18927
2006
Methanocaldococcus jannaschii (Q58933), Methanocaldococcus jannaschii DSM 2661 (Q58933)
Manually annotated by BRENDA team
Chiba, S.; Itoh, Y.; Sekine, S.; Yokoyama, S.
Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine
Mol. Cell
39
410-420
2010
Methanocaldococcus jannaschii (Q58933), Methanocaldococcus jannaschii DSM 2661 (Q58933)
Manually annotated by BRENDA team
Sherrer, R.L.; Araiso, Y.; Aldag, C.; Ishitani, R.; Ho, J.M.; Soell, D.; Nureki, O.
C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec)
Nucleic Acids Res.
39
1034-1041
2011
Methanocaldococcus jannaschii (Q58933), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661 (Q58933)
Manually annotated by BRENDA team
Araiso, Y.; Sherrer, R.L.; Ishitani, R.; Ho, J.M.; Sll, D.; Nureki, O.
Structure of a tRNA-dependent kinase essential for selenocysteine decoding
Proc. Natl. Acad. Sci. USA
106
16215-16220
2009
Methanocaldococcus jannaschii (Q58933), Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661 (Q58933)
Manually annotated by BRENDA team