› 4q93

X-ray diffraction
2.1Å resolution

Crystal structure of resveratrol bound human tyrosyl tRNA synthetase

Released:
DOI: 10.2210/pdb4q93/pdb
PDB entry 4q93 coloured by chain, front view.
PDB entry 4q93 coloured by chain, side view.
PDB entry 4q93 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A human tRNA synthetase is a potent PARP1-activating effector target for resveratrol.
Sajish M, Schimmel P
Nature 519 370-3 (2015)
PMID: 25533949

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: 372 amino acids
Theoretical weight: 42.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P54577 (Residues: 1-364; Coverage: 69%)
Gene names: YARS, YARS1
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand STL 1 x STL
Ligand SO4 6 x SO4
Ligand CL 1 x CL
Ligand GOL 2 x GOL
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21212
Unit cell:
a: 73.966Å b: 162.55Å c: 35.014Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.174 0.231
Expression system: Escherichia coli

Quick links

Citations

22 review citations

NAD(+) Metabolism and the Control of Energy Homeostasis: A Balancing Act between Mitochondria and the Nucleus.
Cantó et al. (2015)
21 more

6 mentions without citation

Polypharmacology or Promiscuity? Structural Interactions of Resveratrol With Its Bandwagon of Targets.
Saqib et al. (2018)
5 more