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Information on EC 6.3.4.22 - tRNAIle2-agmatinylcytidine synthase and Organism(s) Archaeoglobus fulgidus and UniProt Accession O28025

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EC Tree
     6 Ligases
         6.3 Forming carbon-nitrogen bonds
             6.3.4 Other carbon-nitrogen ligases
                6.3.4.22 tRNAIle2-agmatinylcytidine synthase
IUBMB Comments
The enzyme from the archaeon Archaeoglobus fulgidus modifies the wobble base of the CAU anticodon of the archaeal tRNAIle2 at the oxo group in position 2 of cytidine34. This modification is crucial for accurate decoding of the genetic code. In bacteria EC 6.3.4.19, tRNAIle-lysidine synthase, catalyses the modification of [tRNAIle2]-cytidine34 to [tRNAIle2]-lysidine34 .
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Archaeoglobus fulgidus
UNIPROT: O28025
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The taxonomic range for the selected organisms is: Archaeoglobus fulgidus
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide
ATP
+
agmatine
+
[tRNAIle2]-cytidine34
+
H2O
=
[tRNAIle2]-2-agmatinylcytidine34
+
AMP
+
2
phosphate
+
+
+
=
[tRNAIle2]-2-agmatinylcytidine34
+
+
2
Synonyms
AF2259, TiaS, tRNAIle-2-agmatinylcytidine synthetase, tRNAIle-agm2C synthetase, tRNAIle-agmatidine synthetase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tRNAIle-2-agmatinylcytidine synthetase
-
tRNAIle-agm2C synthetase
-
tRNAIle-agmatidine synthetase
-
SYSTEMATIC NAME
IUBMB Comments
agmatine:[tRNAIle]-cytidine34 ligase
The enzyme from the archaeon Archaeoglobus fulgidus modifies the wobble base of the CAU anticodon of the archaeal tRNAIle2 at the oxo group in position 2 of cytidine34. This modification is crucial for accurate decoding of the genetic code. In bacteria EC 6.3.4.19, tRNAIle-lysidine synthase, catalyses the modification of [tRNAIle2]-cytidine34 to [tRNAIle2]-lysidine34 .
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + agmatine + [tRNAIle2]-cytidine34
[tRNAIle2]-2-agmatinylcytidine34 + ?
show the reaction diagram
-
-
-
?
ATP + agmatine + [tRNAIle2]-cytidine34
[tRNAIle2]-2-agmatinylcytidine34 + AMP + diphosphate
show the reaction diagram
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 + agmatine + [tRNAIle2]-cytidine34
[tRNAIle2]-2-agmatinylcytidine34 + ?
show the reaction diagram
-
-
-
?
ATP + agmatine + [tRNAIle2]-cytidine34
[tRNAIle2]-2-agmatinylcytidine34 + AMP + diphosphate
show the reaction diagram
the enzyme catalyzes the essential modification at the anticodon wobble position (position 34) of the AUA-codon of tRNAIle
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
optimal concentration: 100 mM
Mg2+
optimal concentration: 2-5 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
alpha,beta-methyleneadenosine 5'-triphosphate
-
beta,gamma-methyleneadenosine 5'-triphosphate
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00087
agmatine
pH 8.8, 70°C
0.006
ATP
pH 8.8, 70°C
0.00029
[tRNAIle2]-cytidine34
pH 8.8, 70°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.006
agmatine
pH 8.8, 70°C
0.0062
ATP
pH 8.8, 70°C
0.0065
[tRNAIle2]-cytidine34
pH 8.8, 70°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6.9
agmatine
pH 8.8, 70°C
1
ATP
pH 8.8, 70°C
22.41
[tRNAIle2]-cytidine34
pH 8.8, 70°C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00037
alpha,beta-methyleneadenosine 5'-triphosphate
Archaeoglobus fulgidus
pH 8.8, 70°C
0.00079
beta,gamma-methyleneadenosine 5'-triphosphate
Archaeoglobus fulgidus
pH 8.8, 70°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
modification at the anticodon wobble position of archaeal tRNAIle2. According to the chemical structure of agm2C, conjugation of an agmatine moiety at the C2 position of cytosine induces a tautomeric conversion with protonation of the N3 position and imino group formation at the C4 position. This modification completely alters the proton donor-acceptor pattern of cytosine in Watson-Click hydrogen bonding to that of uracil, enabling agm2C to base pair with adenine instead of guanine. tRNAIle2 acquires the ability to decode the AUA codon via formation 2-agmatinylcytidine
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
the Thr18-Cyt34 kinase domain autophosphorylates the Thr18 of the enzyme
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structures of the enzyme-tRNAIle complexed with ATP, or with alpha,beta-methyleneadenosine 5'-triphosphate and agmatine
the enzyme is cocrystallized with both tRNAIle2 and ATP by the vapour-diffusion method. The crystals of the TiaS–tRNAIle2–ATP complex diffract to 2.9 A resolution. The crystals belong to the hexagonal space group P3(2)21, with unit-cell parameters a = b = 131.1, c = 86.6 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C17A
complete loss of activity
C17S
complete loss of activity
C210S
complete loss of activity
C352A/C355A
almost no 2-agmatinylcytidine formation is observed
D11A
complete loss of activity
D8A
complete loss of activity
D9A
complete loss of activity
E159A
complete loss of activity
F286A
complete loss of activity
F301A
complete loss of activity
G218A
mutation reduces activity
I143A
reduced activity
I49A
reduced activity
K52A
complete loss of activity
N194A
reduced activity
N56A
complete loss of activity
R140/G141A
mutation completely abolishes activity
R164A
mutation reduces activity
R217A
R369A
complete loss of activity
R44A
complete loss of activity
R54A
complete loss of activity
T18A
complete loss of activity
T18D
complete loss of activity
T248A/D249A
mutation reduces activity
T53A
complete loss of activity
Y163A
mutation reduces activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
overexpressed in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ikeuchi, Y.; Kimura, S.; Numata, T.; Nakamura, D.; Yokogawa, T.; Ogata, T.; Wada, T.; Suzuki, T.; Suzuki, T.
Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea
Nat. Chem. Biol.
6
277-282
2010
Archaeoglobus fulgidus (O28025), Pyrococcus horikoshii (O59476)
Manually annotated by BRENDA team
Osawa, T.; Inanaga, H.; Kimura, S.; Terasaka, N.; Suzuki, T.; Numata, T.
Crystallization and preliminary X-ray diffraction analysis of an archaeal tRNA-modification enzyme, TiaS, complexed with tRNA(Ile2) and ATP
Acta Crystallogr. Sect. F
67
1414-1416
2011
Archaeoglobus fulgidus (O28025)
Manually annotated by BRENDA team
Terasaka, N.; Kimura, S.; Osawa, T.; Numata, T.; Suzuki, T.
Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS
Nat. Struct. Mol. Biol.
18
1268-1274
2011
Archaeoglobus fulgidus (O28025)
Manually annotated by BRENDA team
Osawa, T.; Kimura, S.; Terasaka, N.; Inanaga, H.; Suzuki, T.; Numata, T.
Structural basis of tRNA agmatinylation essential for AUA codon decoding
Nat. Struct. Mol. Biol.
18
1275-1280
2011
Archaeoglobus fulgidus (O28025)
Manually annotated by BRENDA team