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Crystal structure of Aquifex aeolicus TilS in a complex with ATP, Magnesium ion, and L-lysine

Source organism: Aquifex aeolicus
Biochemical function: tRNA(Ile)-lysidine synthase activity
Biological process: tRNA processing
Cellular component: cytoplasm

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EC 6.3.4.19: tRNA(Ile)-lysidine synthetase

Reaction catalysed:
(tRNA(Ile2))-cytidine(34) + L-lysine + ATP = (tRNA(Ile2))-lysidine(34) + AMP + diphosphate + H(2)O
Systematic name:
L-lysine:(tRNA(Ile2))-cytidine(34) ligase (AMP-forming)
Alternative Name(s):
  • Isoleucine-specific transfer ribonucleate lysidine synthetase
  • MesJ (gene name)
  • TilS
  • YacA (gene name)

GO terms

Sequence families

Pfam Protein families (Pfam)
PF22132
Domain description: TilS-like substrate binding domain
Occurring in:
  1. tRNA(Ile)-lysidine synthase
The deposited structure of PDB entry 2e89 contains 4 copies of Pfam domain PF22132 (TilS-like substrate binding domain) in tRNA(Ile)-lysidine synthase. Showing 1 copy in chain A.

PF01171
Domain description: PP-loop family
Occurring in:
  1. tRNA(Ile)-lysidine synthase
The deposited structure of PDB entry 2e89 contains 4 copies of Pfam domain PF01171 (PP-loop family) in tRNA(Ile)-lysidine synthase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR012094
Domain description: tRNA(Ile)-lysidine synthase
Occurring in:
  1. tRNA(Ile)-lysidine synthase
IPR011063
Domain description: tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal
Occurring in:
  1. tRNA(Ile)-lysidine synthase
IPR012795
Domain description: tRNA(Ile)-lysidine synthase, N-terminal
Occurring in:
  1. tRNA(Ile)-lysidine synthase
IPR014729
Domain description: Rossmann-like alpha/beta/alpha sandwich fold
Occurring in:
  1. tRNA(Ile)-lysidine synthase

Structure domains

CATH CATH domains
1.20.59.20
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Chorismate Mutase Domain, subunit A
Homology: Chorismate Mutase Domain, subunit A
Occurring in:
  1. tRNA(Ile)-lysidine synthase
The deposited structure of PDB entry 2e89 contains 4 copies of CATH domain 1.20.59.20 (Chorismate Mutase Domain, subunit A) in tRNA(Ile)-lysidine synthase. Showing 1 copy in chain A.
3.40.50.620
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: HUPs
Occurring in:
  1. tRNA(Ile)-lysidine synthase
The deposited structure of PDB entry 2e89 contains 4 copies of CATH domain 3.40.50.620 (Rossmann fold) in tRNA(Ile)-lysidine synthase. Showing 1 copy in chain A.
SCOP SCOP annotations
82830
Class: Alpha and beta proteins (a+b)
Fold: MesJ substrate recognition domain-like
Superfamily: MesJ substrate recognition domain-like
Occurring in:
  1. tRNA(Ile)-lysidine synthase
The deposited structure of PDB entry 2e89 contains 4 copies of SCOP domain 82830 (MesJ substrate recognition domain-like) in tRNA(Ile)-lysidine synthase. Showing 1 copy in chain A.
82359
Class: Alpha and beta proteins (a/b)
Fold: Adenine nucleotide alpha hydrolase-like
Superfamily: Adenine nucleotide alpha hydrolases-like
Occurring in:
  1. tRNA(Ile)-lysidine synthase
The deposited structure of PDB entry 2e89 contains 4 copies of SCOP domain 82359 (PP-loop ATPase) in tRNA(Ile)-lysidine synthase. Showing 1 copy in chain A.

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