› 5on3

X-ray diffraction
3.1Å resolution

Quaternary complex of mutant T252A of E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of leucine in the aminoacylation conformation

Released:
DOI: 10.2210/pdb5on3/pdb
PDB entry 5on3 coloured by chain, front view.
PDB entry 5on3 coloured by chain, side view.
PDB entry 5on3 coloured by chain, top view.
Source organisms:
Primary publication:
Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.
Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I
J Mol Biol 430 1-16 (2018)
PMID: 29111343

Function and Biology Details

Reaction catalysed: 
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139770 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Leucine--tRNA ligase Chains: A, D
Molecule details ›
Chains: A, D
Length: 880 amino acids
Theoretical weight: 99.49 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P07813 (Residues: 1-860; Coverage: 100%)
Gene names: JW0637, b0642, leuS
Sequence domains:
tRNA(leu) Chains: B, E
Molecule details ›
Chains: B, E
Length: 87 nucleotides
Theoretical weight: 28.05 KDa
Source organism: Escherichia coli
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand LSS 2 x LSS
Ligand 9YN 2 x 9YN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Spacegroup: C2
Unit cell:
a: 159Å b: 68.7Å c: 227.2Å
α: 90° β: 102.8° γ: 90°
R-values:
R R work R free
0.243 0.241 0.278
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

3 review citations

Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications.
Jin et al. (2019)
2 more