› 1vbm

X-ray diffraction
2.7Å resolution

Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS

Released:
DOI: 10.2210/pdb1vbm/pdb
PDB entry 1vbm coloured by chain, front view.
PDB entry 1vbm coloured by chain, side view.
PDB entry 1vbm coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.
Kobayashi T, Takimura T, Sekine R, Kelly VP, Vincent K, Kamata K, Sakamoto K, Nishimura S, Yokoyama S
J Mol Biol 346 105-17 (2005)
PMID: 15663931

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-142838 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosine--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 318 amino acids
Theoretical weight: 35.7 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AGJ9 (Residues: 5-322; Coverage: 75%)
Gene names: JW1629, b1637, tyrS
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SO4 4 x SO4
Ligand YSA 2 x YSA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P3221
Unit cell:
a: 83.189Å b: 83.189Å c: 182.424Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.246 0.246 0.284
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Expanding the genetic code.
Wang et al. (2006)
4 more

7 mentions without citation

Biochemical Characterization of the Lysine Acetylation of Tyrosyl-tRNA Synthetase in Escherichia coli.
Venkat et al. (2017)
6 more