› 3kt8

X-ray diffraction
3Å resolution

Crystal structure of S. cerevisiae tryptophanyl-tRNA synthetase in complex with L-tryptophanamide

Released:
DOI: 10.2210/pdb3kt8/pdb
Model geometry
Fit model/data
PDB entry 3kt8 coloured by chain, front view.
PDB entry 3kt8 coloured by chain, side view.
PDB entry 3kt8 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design.
Zhou M, Dong X, Shen N, Zhong C, Ding J
OpenAccess logo Nucleic Acids Res 38 3399-413 (2010)
PMID: 20123733

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171295 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tryptophan--tRNA ligase, cytoplasmic Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 438 amino acids
Theoretical weight: 50.25 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12109 (Residues: 1-432; Coverage: 100%)
Gene names: HRE432, WRS1, YOL097C
Sequence domains: tRNA synthetases class I (W and Y)
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand LTN 4 x LTN
Ligand SO4 10 x SO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P61
Unit cell:
a: 252.26Å b: 252.26Å c: 111.376Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.248 0.247 0.273
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

The nonribosomal synthesis of diketopiperazines in tRNA-dependent cyclodipeptide synthase pathways.
Belin et al. (2012)
3 more

2 mentions without citation

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