Information on EC 6.3.4.19 - tRNAIle-lysidine synthase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
6.3.4.19
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RECOMMENDED NAME
GeneOntology No.
tRNAIle-lysidine synthase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
[tRNAIle2]-cytidine34 + L-lysine + ATP = [tRNAIle2]-lysidine34 + AMP + diphosphate + H2O
show the reaction diagram
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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 hide
635304-92-6
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SwissProt
Manually annotated by BRENDA team
no activity in Mycoplasma mobile
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
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
mature [tRNAIle2]-cytidine34 + L-lysine + ATP
mature [tRNAIle2]-2-lysylcytidine34 + AMP + diphosphate
show the reaction diagram
TilS can modify both types of tRNA, pre-tRNAIle2 and mature tRNAIle2, with comparable efficiencies. TilS specifically recognizes the entire L-shape structure in pre-tRNAIle2 through extensive interactions coupled with sequential domain movements. TilS prevents the recognition of tRNAIle2 by methionyl-tRNA synthetase and achieves high specificity for its substrate
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?
precursor [tRNAIle2]-cytidine34 + L-lysine + ATP
precursor [tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
show the reaction diagram
TilS can modify both types of tRNA, pre-tRNAIle2 and mature tRNAIle2, with comparable efficiencies. TilS specifically recognizes the entire L-shape structure in pre-tRNAIle2 through extensive interactions coupled with sequential domain movements. TilS prevents the recognition of tRNAIle2 by methionyl-tRNA synthetase and achieves high specificity for its substrate
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?
[tRNAIle2]-cytidine34 + L-lysine + 7-deazaadenosine 5'-triphosphate
[tRNAIle2]-2-L-lysylcytidine34 + 7-deazaadenosine 5'-phosphate + diphosphate
show the reaction diagram
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Vmax/Km is 8.6% of Vmax/Km for ATP
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?
[tRNAIle2]-cytidine34 + L-lysine + 8-azidoadenosine 5'-triphosphate
[tRNAIle2]-2-L-lysylcytidine34 + 8-azidoadenosine 5'-phosphate + diphosphate
show the reaction diagram
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Vmax/Km is 2.3% of Vmax/Km for ATP
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?
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
show the reaction diagram
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-lysidine34 + AMP + diphosphate + H2O
show the reaction diagram
[tRNAIle2]-cytidine34 + L-lysine + N6-methyladenosine-5'-triphosphate
[tRNAIle2]-2-L-lysylcytidine34 + N6-methyladenosine-5'-phosphate + diphosphate
show the reaction diagram
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Vmax/Km is 4.7% of Vmax/Km for ATP
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?
additional information
?
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no substrate: N1-methyladenosine-5'-triphosphate, 2-aminoadenosine-5'-triphosphate, 2-amino-6-chloropurineriboside-5'-triphosphate, and 6-chloropurineriboside-5'-triphosphate
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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
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
show the reaction diagram
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-lysidine34 + AMP + diphosphate + H2O
show the reaction diagram
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(5R)-5-hydroxy-L-lysine
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4,5-trans-dehydro-L-lysine
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8-azaadenosine 5-triphosphate
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adenosine 5-O-(1-thiotriphosphate)
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alpha,beta-methyleneadenosine 5-triphosphate
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aminoethylcysteine
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aminoethylserine
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benzimidazoleriboside 5-triphosphate
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beta,gamma-methyleneadenosine 5-triphosphate
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cadaverine
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ethanolamine
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histamine
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L-lysinamide
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L-ornithine
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mutated tRNAIle2
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C34G-tRNAILe2
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N-acetylethylenediamine
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N-alpha-methyl-L-lysine
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0018
7-deazaadenosine-5-triphosphate
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pH 8.5, 21C
0.01
8-azidoadenosine-5-triphosphate
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pH 8.5, 21C
0.0016 - 0.287
ATP
0.38 - 3.05
L-lysine
0.00014
mature [tRNAIle2]-cytidine34
pH 7.8, 60C
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0.0217
N6-methyladenosine-5-triphosphate
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pH 8.5, 21C
0.00008
precursor [tRNAIle2]-cytidine34
pH 7.8, 60C
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0.00038 - 0.0202
[tRNAIle2]-cytidine34
additional information
additional information
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kinetic parameters of Escherichia coli TilS with various tRNAIle2 mutants and with tRNAMet mutants
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.015
ATP
Escherichia coli
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pH 7.8, 37C
0.07
L-lysine
Escherichia coli
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pH 7.8, 37C
0.03
mature [tRNAIle2]-cytidine34
Geobacillus kaustophilus
Q5L3T3
pH 7.8, 60C
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0.025
precursor [tRNAIle2]-cytidine34
Geobacillus kaustophilus
Q5L3T3
pH 7.8, 60C
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0.012
[tRNAIle2]-cytidine34
Escherichia coli
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unmodified tRNAIle2, pH 7.8, 37C
additional information
additional information
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
21.4
mature [tRNAIle2]-cytidine34
Geobacillus kaustophilus
Q5L3T3
pH 7.8, 60C
40023
31.2
precursor [tRNAIle2]-cytidine34
Geobacillus kaustophilus
Q5L3T3
pH 7.8, 60C
40024
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0176
(5R)-5-hydroxylysine
Escherichia coli
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pH 8.5, 21C
0.0025
4,5-trans-dehydrolysine
Escherichia coli
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pH 8.5, 21C
0.255
8-azaadenosine-5-triphosphate
Escherichia coli
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pH 8.5, 21C
0.000016
adenosine-5-O-(1-thiotriphosphate)
Escherichia coli
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pH 8.5, 21C
0.000035
alpha,beta-methyleneadenosine-5-triphosphate
Escherichia coli
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pH 8.5, 21C
0.000045
aminoethylcysteine
Escherichia coli
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pH 8.5, 21C
0.0004
aminoethylserine
Escherichia coli
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pH 8.5, 21C
0.105
benzimidazoleriboside-5-triphosphate
Escherichia coli
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pH 8.5, 21C
0.000082
beta,gamma-methyleneadenosine-5-triphosphate
Escherichia coli
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pH 8.5, 21C
0.91
cadaverine
Escherichia coli
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pH 8.5, 21C
1.77
ethanolamine
Escherichia coli
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pH 8.5, 21C
0.33
histamine
Escherichia coli
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pH 8.5, 21C
0.62
lysinamide
Escherichia coli
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pH 8.5, 21C
0.000085
mutated tRNAIle2
Escherichia coli
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pH 8.5, 21C, C34G-tRNAILe2
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0.0068
N-acetylethylenediamine
Escherichia coli
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pH 8.5, 21C
1.3
N-alpha-methyl-lysine
Escherichia coli
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pH 8.5, 21C
0.7
ornithine
Escherichia coli
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pH 8.5, 21C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.5 - 9.5
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Aquifex aeolicus (strain VF5)
Aquifex aeolicus (strain VF5)
Aquifex aeolicus (strain VF5)
Geobacillus kaustophilus (strain HTA426)
Geobacillus kaustophilus (strain HTA426)
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure of Aquifex aeolicus TilS, complexed with ATP, Mg2+, and L-lysine, at 2.5 A resolution. The presence of the TilS-specific subdomain causes the active site to have two separate gateways, a large hole and a narrow tunnel on the opposite side. ATP is bound inside the hole, and L-lysine is bound at the entrance of the tunnel. The conserved Asp36 in the PP-motif coordinates Mg2+. In these initial binding modes, the ATP, Mg2+, and L-lysine are held far apart from each other, but they seem to be brought together for the reaction upon cytidine binding, with putative structural changes of the complex
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crystal structure of TilS at 2.42 A resolution. Structural and functional comparisons with Escherichia coli TilS reveals that the two TilS enzymes discriminate premodified tRNAIle2 from premodified tRNAMet by strategies similar to that used by IleRS, but in distinct manners
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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
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crystal structure of Geobacillus kaustophilus TilS complexed with Bacillus subtilis tRNAIle CAU at 3.65 A resolution, by the multiwavelength anomalous dispersion method. The asymmetric unit contains one TilS homodimer and two tRNAs, each tightly embedded in one monomer of TilS, with an overall interface of 2998 A. Each monomer consists of an amino-terminal catalytic domain, and two carboxy-terminal domains, connected by a long a-helical linker and a loop linker, respectively
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
overepression in Escherichia coli
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D137A
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no activity detectable
D191A
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no activity detectable
D36A
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no activity detectable
E140A
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Km-value for L-lysine is 2.2fold higher than wild-type value, Km-value for ATP is about 7fold higher than wild-type value, Km-value for [tRNAIle2]-cytidine34 is 4.7fold higher than wild-type value
H133A
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Km-value for L-lysine is 1.6 fold higher than wild-type value, Km-value for ATP is 2.5fold lower than wild-type value, Km-value for [tRNAIle2]-cytidine34 is similar to wild-type value
N194A
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no activity detectable
R113A
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no activity detectable
R174A
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Km-value for L-lysine is 1.8fold higher than wild-type value, Km-value for ATP is 2.1fold higher than wild-type value, Km-value for [tRNAIle2]-cytidine34 is 6fold higher than wild-type value
R201A
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no activity detectable
R205A
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Km-value for L-lysine is 1.6fold higher than wild-type value, Km-value for ATP is 14.8fold higher than wild-type value, Km-value for [tRNAIle2]-cytidine34 is 3.6fold higher than wild-type value
S37A
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Km-value for ATP is 13fold higher than wild-type value
W188A
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Km-value for ATP is 5fold higher than wild-type value
Y114A
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Km-value for L-lysine is about 5fold higher than wild-type value, Km-value for ATP is about 8fold higher than wild-type value, Km-value for [tRNAIle2]-cytidine34 is 2.2fold higher than wild-type value
additional information
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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
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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lysidine/TilS is a eubacterial-specific system of AUA decoding. Therefore, TilS is an ideal target for a broad-spectrum antibacterial agent
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