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Information on EC 6.3.4.19 - tRNAIle-lysidine synthase and Organism(s) Escherichia coli and UniProt Accession P52097
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6.3.4.19 tRNAIle-lysidine synthaseIUBMB Comments
The bacterial enzyme modifies the wobble base of the CAU anticodon of tRNAIle at the oxo group in position 2 of cytidine34. This modification determines both codon and amino acid specificities of tRNAIle.
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Word Map
- 6.3.4.19
- isoleucine
-
anticodons
-
wobble
-
decode
- aminoacylation
-
aquifex
- ilers
- analysis
- aeolicus
-
hole
- pyrophosphatase
- trnamet
-
isoleucyl-trna
- methionyl-trna
- medicine
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
lysidine synthetase, tils protein, trnaile-lysidine synthetase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
TilS
SYSTEMATIC NAME
IUBMB Comments
L-lysine:[tRNAIle2]-cytidine34 ligase (AMP-forming)
The bacterial enzyme modifies the wobble base of the CAU anticodon of tRNAIle at the oxo group in position 2 of cytidine34. This modification determines both codon and amino acid specificities of tRNAIle.
CAS REGISTRY NUMBER
COMMENTARY
635304-92-6
-
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
[tRNAIle2]-cytidine34 + L-lysine + 7-deazaadenosine 5'-triphosphate
[tRNAIle2]-2-L-lysylcytidine34 + 7-deazaadenosine 5'-phosphate + diphosphate
Vmax/Km is 8.6% of Vmax/Km for ATP
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + 8-azidoadenosine 5'-triphosphate
[tRNAIle2]-2-L-lysylcytidine34 + 8-azidoadenosine 5'-phosphate + diphosphate
Vmax/Km is 2.3% of Vmax/Km for ATP
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + N6-methyladenosine-5'-triphosphate
[tRNAIle2]-2-L-lysylcytidine34 + N6-methyladenosine-5'-phosphate + diphosphate
Vmax/Km is 4.7% of Vmax/Km for ATP
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
-
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
bacteria decode the isoleucine codon AUA using a tRNA species that is posttranscriptionally modified at the wobble position of the anticodon with a lysine-containing cytidine derivative called lysidine. The lysidine modification of tRNAIle2 is an essential identity determinant for proper aminoacylation by isoleucyl tRNA synthetase and codon recognition on the ribosome. The ATP- and lysine-dependent formation of lysidine is catalyzed by tRNAIle-lysidine synthetase
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
TilS specifically interacts with the isolated Escherichia coli tRNAIle2. Molecular mechanism of lysidine formation consists of two consecutive reactions involving the adenylated tRNA intermediate. TilS activates the C-2 position of C34 by forming an adenylate intermediate. Second, nucleophilic attack of the C-2 position of the intermediate by the epsilon-amino group of lysine completes the reaction
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
-
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
enzyme catalyzes the lysylation of C34 (wobble position) in the precursor tRNAIle(CAU), thereby leading to the formation of tRNAIle(lysidineAU). The formation of lysidine by this essential enzyme allows recognition of tRNAIle(lysidineCAU) by Ile-tRNA synthetase and switches the base pairing of the tRNA from AUG (Met) to AUA (Ile)
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
the enzyme generates lysidine at the wobble position of tRNAIle. The enzyme is essential for the decoding of AUA codons in the cell
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
lysidine synthesis consists of two consecutive reactions that involve an adenylated tRNA intermediate. A mutation study reveals that Escherichia coli TilS discriminates tRNAIle from the structurally similar tRNAMet having the same anticodon loop by recognizing the anticodon loop, the anticodon stem, and the acceptor stem. TilS binds to the anticodon region and 3' side of the acceptor stem, which cover the recognition sites. A dedicated mechanism is embedded in tRNAIle that controls its recognition and discrimination by TilS
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
lysidine synthesis TilS directly converts the amino acid specificity from methionine to isoleucine in vitro
-
-
?
additional information
?
-
no substrate: N1-methyladenosine-5'-triphosphate, 2-aminoadenosine-5'-triphosphate, 2-amino-6-chloropurineriboside-5'-triphosphate, and 6-chloropurineriboside-5'-triphosphate
-
-
?
additional information
?
-
-
no substrate: N1-methyladenosine-5'-triphosphate, 2-aminoadenosine-5'-triphosphate, 2-amino-6-chloropurineriboside-5'-triphosphate, and 6-chloropurineriboside-5'-triphosphate
-
-
?
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
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
bacteria decode the isoleucine codon AUA using a tRNA species that is posttranscriptionally modified at the wobble position of the anticodon with a lysine-containing cytidine derivative called lysidine. The lysidine modification of tRNAIle2 is an essential identity determinant for proper aminoacylation by isoleucyl tRNA synthetase and codon recognition on the ribosome. The ATP- and lysine-dependent formation of lysidine is catalyzed by tRNAIle-lysidine synthetase
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
-
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
enzyme catalyzes the lysylation of C34 (wobble position) in the precursor tRNAIle(CAU), thereby leading to the formation of tRNAIle(lysidineAU). The formation of lysidine by this essential enzyme allows recognition of tRNAIle(lysidineCAU) by Ile-tRNA synthetase and switches the base pairing of the tRNA from AUG (Met) to AUA (Ile)
-
-
?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
-
the enzyme generates lysidine at the wobble position of tRNAIle. The enzyme is essential for the decoding of AUA codons in the cell
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3-bromo-N-(3-methoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
-
competitive with respect to ATP
4-(2-fluoro-5-methoxyanilino)-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one
-
competitive with respect to ATP
N-(3-methoxyphenyl)-5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine
-
competitive with respect to ATP
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
kinetic parameters of Escherichia coli TilS with various tRNAIle2 mutants and with tRNAMet mutants
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
kinetic parameters of Escherichia coli TilS with various tRNAIle2 mutants and with tRNAMet mutants
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0016
3-bromo-N-(3-methoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
Escherichia coli
-
pH 8.5, temperature not specified in the publication
0.0016
4-(2-fluoro-5-methoxyanilino)-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one
Escherichia coli
-
pH 8.5, temperature not specified in the publication
0.0042
N-(3-methoxyphenyl)-5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine
Escherichia coli
-
pH 8.5, temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
malfunction
-
partial inactivation of tilS in vivo results in an AUA codon-dependent translational defect
physiological function
physiological function
bacteria decode the isoleucine codon AUA using a tRNA species that is posttranscriptionally modified at the wobble position of the anticodon with a lysine-containing cytidine derivative called lysidine. The lysidine modification of tRNAIle2 is an essential identity determinant for proper aminoacylation by isoleucyl tRNA synthetase and codon recognition on the ribosome. The ATP- and lysine-dependent formation of lysidine is catalyzed by tRNAIle-lysidine synthetase
physiological function
the single 2-lysylcytidine modification converts the codon-specificity from AUG to AUA, and the amino acid specificity from Met to Ile
physiological function
-
2-lysyl cytidine is a lysine-containing cytidine derivative commonly found at the wobble position of bacterial AUA codon-specific tRNAIle. This modification determines both codon and amino acid specificities of tRNAIle
physiological function
-
enzyme catalyzes the lysylation of C34 in the precursor tRNAIle(CAU), thereby leading to the formation of tRNAIle(lysidineAU). The formation of lysidine by this essential enzyme allows recognition of tRNAIle(lysidineCAU) by Ile-tRNA synthetase and switches the base pairing of the tRNA from AUG (Met) to AUA (Ile). TilS is essential and plays a crucial role in accurate decoding and hence viability of cells
physiological function
-
the enzyme generates lysidine at the wobble position of tRNAIle. The enzyme is essential for the decoding of AUA codons in the cell
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structural and functional comparisons of Escherichia coli TilS and Axifex aeolicus TilS reveal that the two TilS enzymes discriminate premodified tRNAIle2 from premodified tRNAMet bystrategies similar to that used by IleRS, but in distinct manners
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
a mutation study reveals that Escherichia coli TilS discriminates tRNAIle from the structurally similar tRNAMet having the same anticodon loop by recognizing the anticodon loop, the anticodon stem, and the acceptor stem
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
lysidine/TilS is a eubacterial-specific system of AUA decoding. Therefore, TilS is an ideal target for a broad-spectrum antibacterial agent
analysis
-
development of a ultrahigh-throughput, fluorescence anisotropy-based assay for the incorporation of lysine into Ile2 tRNA
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Suzuki, T.; Miyauchi, K.
Discovery and characterization of tRNAIle lysidine synthetase (TilS)
FEBS Lett.
584
272-277
2010
Escherichia coli (P52097), Escherichia coli
Salowe, S.P.; Wiltsie, J.; Hawkins, J.C.; Sonatore, L.M.
The catalytic flexibility of tRNAIle-lysidine synthetase can generate alternative tRNA substrates for isoleucyl-tRNA synthetase
J. Biol. Chem.
284
9656-9662
2009
Escherichia coli (P52097), Escherichia coli
Soma, A.; Ikeuchi, Y.; Kanemasa, S.; Kobayashi, K.; Ogasawara, N.; Ote, T.; Kato, J.; Watanabe, K.; Sekine, Y.; Suzuki, T.
An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA
Mol. Cell
12
689-698
2003
Escherichia coli, Bacillus subtilis (P37563)
Ikeuchi, Y.; Soma, A.; Ote, T.; Kato, J.; Sekine, Y.; Suzuki, T.
Molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition
Mol. Cell
19
235-246
2005
Escherichia coli
Nakanishi, K.; Fukai, S.; Ikeuchi, Y.; Soma, A.; Sekine, Y.; Suzuki, T.; Nureki, O.
Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain.
Proc. Natl. Acad. Sci. USA
102
7487-7492
2005
Aquifex aeolicus (O67728), Aquifex aeolicus, Escherichia coli
Grosjean, H.; Bjrk, G.R.
Enzymatic conversion of cytidine to lysidine in anticodon of bacterial isoleucyl-tRNA - an alternative way of RNA editing
Trends Biochem. Sci.
29
165-168
2004
Escherichia coli
Shapiro, A.B.; Plant, H.; Walsh, J.; Sylvester, M.; Hu, J.; Gao, N.; Livchak, S.; Tentarelli, S.; Thresher, J.
Discovery of ATP-competitive inhibitors of tRNAIle lysidine synthetase (TilS) by high-throughput screening
J. Biomol. Screen.
19
1137-1146
2014
Escherichia coli, Pseudomonas aeruginosa
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