Information on EC 2.7.1.164 - O-phosphoseryl-tRNASec kinase

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

EC NUMBER
COMMENTARY hide
2.7.1.164
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RECOMMENDED NAME
GeneOntology No.
O-phosphoseryl-tRNASec kinase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + L-seryl-tRNASec = ADP + O-phospho-L-seryl-tRNASec
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-selenocysteine biosynthesis II (archaea and eukaryotes)
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selenocysteine biosynthesis
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Selenocompound metabolism
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Aminoacyl-tRNA biosynthesis
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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
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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
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?
ATP + seryl-tRNASec
ADP + O-phospho-L-seryl-tRNASec
show the reaction diagram
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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)
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?
CTP + L-seryl-tRNASec
CDP + O-phospho-L-seryl-tRNASec
show the reaction diagram
dATP + L-seryl-tRNASec
dADP + O-phospho-L-seryl-tRNASec
show the reaction diagram
GTP + L-seryl-tRNASec
GDP + O-phospho-L-seryl-tRNASec
show the reaction diagram
phosphorylation at about 40% the activity of ATP
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?
ITP + L-seryl-tRNASec
IDP + O-phospho-L-seryl-tRNASec
show the reaction diagram
phosphorylation at about 85% the activity of ATP
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?
L-threonyl-tRNASec + ATP
O-phospho-L-threonyl-tRNASec + ADP
show the reaction diagram
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?
UTP + L-seryl-tRNASec
UDP + O-phospho-L-seryl-tRNASec
show the reaction diagram
phosphorylation at about 40% the activity of ATP
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?
additional information
?
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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 + 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
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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)
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
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required, maximal activity at 1.0 mM
Mn2+
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Mn2+ can replace Mg2+ as a divalent metal cation, but it is not as efficient as Mg2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
tRNASec
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potent inhibitor
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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
0.069
ATP
Methanocaldococcus jannaschii
Q58933
37°C
0.098
L-seryl-tRNASec
Methanocaldococcus jannaschii
Q58933
37°C
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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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
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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
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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expression in Escherichia coli BL21
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D146A
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mutant is active in vivo
D41A
strongly reduced activity
G14W
strongly reduced activity
K142A
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mutant is active in vivo
K142A/Y143A
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mutant shows severely reduced activity with the Methanopyrus kandleri tRNASec substrate
K30A
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mutant is defective in phosphorylation activity
N161A
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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
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mutant is active in vivo
D146A
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mutant is active in vivo
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K142A
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mutant is active in vivo
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K30A
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mutant is defective in phosphorylation activity
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S18A
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mutation abolishes catalytic activity and and inhibits tRNASec recognition
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G14W
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strongly reduced activity
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K17A
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strongly reduced activity
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R116A
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mutant enzyme is 23.5fold less active than wild-type enzyme
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S18A
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strongly reduced activity
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T19W
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mutant enzyme is 2.8fold less active than wild-type enzyme
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additional information