› 1efw

X-ray diffraction
3Å resolution

Crystal structure of aspartyl-tRNA synthetase from Thermus thermophilus complexed to tRNAasp from Escherichia coli

Released:
DOI: 10.2210/pdb1efw/pdb
PDB entry 1efw coloured by chain, front view.
PDB entry 1efw coloured by chain, side view.
PDB entry 1efw coloured by chain, top view.
Source organisms:
Primary publication:
An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase.
Briand C, Poterszman A, Eiler S, Webster G, Thierry J, Moras D
J Mol Biol 299 1051-60 (2000)
PMID: 10843857

Function and Biology Details

Reaction catalysed: 
ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153185 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Aspartate--tRNA(Asp) ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 580 amino acids
Theoretical weight: 66.12 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P36419 (Residues: 1-580; Coverage: 100%)
Gene name: aspS
Sequence domains:
Structure domains:
ASPARTYL-TRNA Chains: C, D
Molecule details ›
Chains: C, D
Length: 73 nucleotides
Theoretical weight: 23.72 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
Sequence domains: tRNA

Ligands and Environments

No bound ligands
7 modified residues:
Ligand 4SU 2 x 4SU
Ligand H2U 6 x H2U
Ligand QUO 2 x QUO
Ligand 2MA 2 x 2MA
Ligand G7M 2 x G7M
Ligand 5MU 2 x 5MU
Ligand PSU 4 x PSU

Experiments and Validation Details

Entry percentile scores
X-ray source: LURE BEAMLINE DW32
Spacegroup: P63
Unit cell:
a: 251.45Å b: 251.45Å c: 88.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.248 0.248 0.293
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition.
Vasil'eva et al. (2007)
20 other articles

17 mentions without citation

Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs.
Tragni et al. (2022)
16 more