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Information on EC 6.3.4.19 - tRNAIle-lysidine synthase and Organism(s) Aquifex aeolicus and UniProt Accession O67728

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     6 Ligases
         6.3 Forming carbon-nitrogen bonds
             6.3.4 Other carbon-nitrogen ligases
                6.3.4.19 tRNAIle-lysidine synthase
IUBMB 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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This record set is specific for:
Aquifex aeolicus
UNIPROT: O67728
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The taxonomic range for the selected organisms is: Aquifex aeolicus
The enzyme appears in selected viruses and cellular organisms
Synonyms
lysidine synthetase, tils protein, trnaile-lysidine synthetase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
lysidine synthetase
-
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
-
SUBSTRATE
PRODUCT                       
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
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
[tRNAIle2]-cytidine34 + L-lysine + ATP
[tRNAIle2]-2-L-lysylcytidine34 + AMP + diphosphate
show the reaction diagram
-
-
-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0077 - 0.287
ATP
0.629 - 3.05
L-lysine
0.0019 - 0.0202
[tRNAIle2]-cytidine34
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
each subunit consists of the N-terminal dinucleotide-binding fold domain, with a characteristic central hole, and the C-terminal globular domain connected by a long alpha-helical linker
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
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D137A
no activity detectable
D191A
no activity detectable
D36A
no activity detectable
E140A
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
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
no activity detectable
R113A
no activity detectable
R174A
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
no activity detectable
R205A
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
Km-value for ATP is 13fold higher than wild-type value
W188A
Km-value for ATP is 5fold higher than wild-type value
Y114A
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Manually annotated by BRENDA team
Kuratani, M.; Yoshikawa, Y.; Bessho, Y.; Higashijima, K.; Ishii, T.; Shibata, R.; Takahashi, S.; Yutani, K.; Yokoyama, S.
Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine
Structure
15
1642-1653
2007
Aquifex aeolicus (O67728), Aquifex aeolicus
Manually annotated by BRENDA team