› 4rr9

X-ray diffraction
1.67Å resolution

N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 4)

Released:
DOI: 10.2210/pdb4rr9/pdb
PDB entry 4rr9 coloured by chain, front view.
PDB entry 4rr9 coloured by chain, side view.
PDB entry 4rr9 coloured by chain, top view.
Source organism: Aeropyrum pernix K1
Primary publication:
Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Ahmad S, Muthukumar S, Kuncha SK, Routh SB, Yerabham AS, Hussain T, Kamarthapu V, Kruparani SP, Sankaranarayanan R
OpenAccess logo Nat Commun 6 7552 (2015)
PMID: 26113036

Function and Biology Details

Reaction catalysed: 
ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-579087 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Threonine--tRNA ligase editing subunit Chain: A
Molecule details ›
Chain: A
Length: 136 amino acids
Theoretical weight: 15.14 KDa
Source organism: Aeropyrum pernix K1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YFY3 (Residues: 1-136; Coverage: 32%)
Gene names: APE_0117.1, thrS2
Sequence domains: Archaea-specific editing domain of threonyl-tRNA synthetase
Structure domains: D-tyrosyl-tRNA(Tyr) deacylase

Ligands and Environments

2 bound ligands:
Ligand A3S 1 x A3S
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P41212
Unit cell:
a: 47.871Å b: 47.871Å c: 113.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.196 0.225
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification.
Fang et al. (2015)
3 more

1 mention without citation

Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Ahmad et al. (2015)