› 1j1u

X-ray diffraction
1.95Å resolution

Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine

Released:
DOI: 10.2210/pdb1j1u/pdb
PDB entry 1j1u coloured by chain, front view.
PDB entry 1j1u coloured by chain, side view.
PDB entry 1j1u coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.
Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S
Nat Struct Biol 10 425-32 (2003)
PMID: 12754495

Function and Biology Details

Reaction catalysed: 
ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176483 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Tyrosine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 35.1 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q57834 (Residues: 1-306; Coverage: 100%)
Gene names: MJ0389, tyrS
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:
tRNA(Tyr) Chain: B
Molecule details ›
Chain: B
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand TYR 1 x TYR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P3121
Unit cell:
a: 86.805Å b: 86.805Å c: 156.075Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.188 0.239
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

22 review citations

Adding new chemistries to the genetic code.
Liu et al. (2010)
21 more

62 mentions without citation

Designing logical codon reassignment - Expanding the chemistry in biology.
Dumas et al. (2015)
61 more