› 5thh

X-ray diffraction
1.96Å resolution

Crystal structure of a human tyrosyl-tRNA synthetase mutant

Released:
DOI: 10.2210/pdb5thh/pdb
PDB entry 5thh coloured by chain, front view.
PDB entry 5thh coloured by chain, side view.
PDB entry 5thh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy.
Blocquel D, Li S, Wei N, Daub H, Sajish M, Erfurth ML, Kooi G, Zhou J, Bai G, Schimmel P, Jordanova A, Yang XL
Nucleic Acids Res 45 8091-8104 (2017)
PMID: 28531329

Function and Biology Details

Reaction catalysed: 
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157047 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed Chain: A
Molecule details ›
Chain: A
Length: 339 amino acids
Theoretical weight: 38.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P54577 (Residues: 4-342; Coverage: 64%)
Gene names: YARS, YARS1
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Unit cell:
a: 35.238Å b: 75.705Å c: 163.51Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.219
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

12 review citations

Translation deregulation in human disease.
Tahmasebi et al. (2018)
11 more

3 mentions without citation

Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy.
Blocquel et al. (2017)
2 more