› 2e89

X-ray diffraction
2.5Å resolution

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

Released:
DOI: 10.2210/pdb2e89/pdb
PDB 2e89 coloured by chain and viewed from the front.
PDB 2e89 coloured by chain and viewed from the side.
PDB 2e89 coloured by chain and viewed from the top.
Source organism: Aquifex aeolicus
Primary publication:
Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine.
Kuratani M, Yoshikawa Y, Bessho Y, Higashijima K, Ishii T, Shibata R, Takahashi S, Yutani K, Yokoyama S
Structure 15 1642-53 (2007)
PMID: 18073113

Function and Biology Details

Reaction catalysed: 
(tRNA(Ile2))-cytidine(34) + L-lysine + ATP = (tRNA(Ile2))-lysidine(34) + AMP + diphosphate + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA(Ile)-lysidine synthase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 317 amino acids
Theoretical weight: 37.39 KDa
Source organism: Aquifex aeolicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O67728 (Residues: 1-317; Coverage: 100%)
Gene names: aq_1887, tilS
Sequence domains: PP-loop family
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ATP 4 x ATP
Ligand LYS 1 x LYS
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 97.42Å b: 81.57Å c: 109.11Å
α: 90° β: 105.98° γ: 90°
R-values:
R R work R free
0.229 0.229 0.274
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA.
Hori et al. (2018)
5 more

2 mentions without citation

Convergent evolution of AUA decoding in bacteria and archaea.
Suzuki et al. (2014)
1 more