› 1r6u

X-ray diffraction
2Å resolution

Crystal structure of an active fragment of human tryptophanyl-tRNA synthetase with cytokine activity

Released:
DOI: 10.2210/pdb1r6u/pdb
PDB 1r6u coloured by chain and viewed from the front.
PDB 1r6u coloured by chain and viewed from the side.
PDB 1r6u coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase.
Yang XL, Guo M, Kapoor M, Ewalt KL, Otero FJ, Skene RJ, McRee DE, Schimmel P
Structure 15 793-805 (2007)
PMID: 17637340

Function and Biology Details

Reaction catalysed: 
ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophyl-tRNA(Trp)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tryptophan--tRNA ligase, cytoplasmic Chains: A, B
Molecule details ›
Chains: A, B
Length: 437 amino acids
Theoretical weight: 50.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23381 (Residues: 48-471; Coverage: 90%)
Gene names: IFI53, WARS, WARS1, WRS
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand TYM 1 x TYM
Ligand GOL 2 x GOL
1 modified residue:
Ligand MSE 20 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2
Unit cell:
a: 134.658Å b: 96.46Å c: 97.132Å
α: 90° β: 129.9° γ: 90°
R-values:
R R work R free
0.255 0.254 0.298
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Unique roles of tryptophanyl-tRNA synthetase in immune control and its therapeutic implications.
Jin M. (2019)
4 more

3 mentions without citation

The structure of tryptophanyl-tRNA synthetase from Giardia lamblia reveals divergence from eukaryotic homologs.
Arakaki et al. (2010)
2 more