› 3nem

X-ray diffraction
1.89Å resolution

Aspartyl-tRNA synthetase complexed with aspartyl adenylate

Released:
DOI: 10.2210/pdb3nem/pdb
PDB entry 3nem coloured by chain, front view.
PDB entry 3nem coloured by chain, side view.
PDB entry 3nem coloured by chain, top view.
Source organism: Thermococcus kodakarensis
Primary publication:
Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.
Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D
EMBO J 17 5227-37 (1998)
PMID: 9724658

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176006 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aspartate--tRNA(Asp) ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 438 amino acids
Theoretical weight: 50.98 KDa
Source organism: Thermococcus kodakarensis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q52428 (Residues: 1-438; Coverage: 100%)
Gene names: TK0492, aspS
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand AMO 1 x AMO
Ligand ATP 1 x ATP
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LURE BEAMLINE DW32
Spacegroup: P21212
Unit cell:
a: 123.22Å b: 124.87Å c: 86.93Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.188 0.213
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Aminoacyl-tRNA synthesis.
Ibba et al. (2000)
9 more

5 mentions without citation

Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major.
Gowri et al. (2012)
4 more