› 1yi8

X-ray diffraction
2.1Å resolution

Crystal structure of tryptophanyl trRNA synthetase II from Deinococcus radiodurans in complex with L-Trp

Released:
DOI: 10.2210/pdb1yi8/pdb
PDB entry 1yi8 coloured by chain, front view.
PDB entry 1yi8 coloured by chain, side view.
PDB entry 1yi8 coloured by chain, top view.
Source organism: Deinococcus radiodurans R1
Primary publication:
Structure and activity of an aminoacyl-tRNA synthetase that charges tRNA with nitro-tryptophan.
Buddha MR, Crane BR
Nat Struct Mol Biol 12 274-5 (2005)
PMID: 15723076

Function and Biology Details

Reaction catalysed: 
ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophyl-tRNA(Trp)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193298 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tryptophan--tRNA ligase 2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 351 amino acids
Theoretical weight: 38.23 KDa
Source organism: Deinococcus radiodurans R1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9RVD6 (Residues: 1-351; Coverage: 100%)
Gene names: DR_1093, trpS2, trpSII
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25, CHESS BEAMLINE F2
Spacegroup: C2
Unit cell:
a: 211.8Å b: 58.5Å c: 88.9Å
α: 90° β: 100.725° γ: 90°
R-values:
R R work R free
0.26 0.26 0.28
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 review citations

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

3 mentions without citation

An appended domain results in an unusual architecture for malaria parasite tryptophanyl-tRNA synthetase.
Khan et al. (2013)
2 more