› 2yxn

X-ray diffraction
1.8Å resolution

Structual basis of azido-tyrosine recognition by engineered bacterial Tyrosyl-tRNA synthetase

Released:
DOI: 10.2210/pdb2yxn/pdb
PDB entry 2yxn coloured by chain, front view.
PDB entry 2yxn coloured by chain, side view.
PDB entry 2yxn coloured by chain, top view.
Source organism: Escherichia coli str. K-12 substr. W3110
Primary publication:
Functional replacement of the endogenous tyrosyl-tRNA synthetase-tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion.
Iraha F, Oki K, Kobayashi T, Ohno S, Yokogawa T, Nishikawa K, Yokoyama S, Sakamoto K
Nucleic Acids Res 38 3682-91 (2010)
PMID: 20159998

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 Chain: A
Molecule details ›
Chain: A
Length: 322 amino acids
Theoretical weight: 35.98 KDa
Source organism: Escherichia coli str. K-12 substr. W3110
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AGJ9 (Residues: 1-322; Coverage: 76%)
Gene names: JW1629, b1637, tyrS
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P3121
Unit cell:
a: 83.155Å b: 83.155Å c: 93.668Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.199 0.247
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

Expanding and reprogramming the genetic code.
Chin JW. (2017)
8 more

4 mentions without citation

Biocontainment of genetically modified organisms by synthetic protein design.
Mandell et al. (2015)
3 more