› 1wk9

X-ray diffraction
1.75Å resolution

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain

Released:
DOI: 10.2210/pdb1wk9/pdb
PDB entry 1wk9 coloured by chain, front view.
PDB entry 1wk9 coloured by chain, side view.
PDB entry 1wk9 coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain.
Fukunaga R, Yokoyama S
J Biol Chem 280 29937-45 (2005)
PMID: 15970591

Function and Biology Details

Reaction catalysed: 
ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161204 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Valine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 146 amino acids
Theoretical weight: 16.54 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P96142 (Residues: 193-337; Coverage: 17%)
Gene name: valS
Structure domains: Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain

Ligands and Environments

1 bound ligand:
Ligand TSB 1 x TSB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P6522
Unit cell:
a: 95.49Å b: 95.49Å c: 72.3Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.205 0.247
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Development of tRNA synthetases and connection to genetic code and disease.
Schimmel P. (2008)
2 more

2 mentions without citation

Caenorhabditis elegans glp-4 Encodes a Valyl Aminoacyl tRNA Synthetase.
Rastogi et al. (2015)
1 more