› 4rrr

X-ray diffraction
1.86Å resolution

K121M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi with L-Thr3AA

Released:
DOI: 10.2210/pdb4rrr/pdb
PDB entry 4rrr coloured by chain, front view.
PDB entry 4rrr coloured by chain, side view.
PDB entry 4rrr coloured by chain, top view.
Source organism: Pyrococcus abyssi GE5
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-577822 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Threonine--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 147 amino acids
Theoretical weight: 16.74 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UZ14 (Residues: 1-147; Coverage: 24%)
Gene names: PAB1490, PYRAB13430, thrS
Sequence domains: Archaea-specific editing domain of threonyl-tRNA synthetase
Structure domains: D-tyrosyl-tRNA(Tyr) deacylase

Ligands and Environments

1 bound ligand:
Ligand A3T 2 x A3T
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P212121
Unit cell:
a: 38.586Å b: 66.312Å c: 93.688Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.2 0.23
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

3 mentions without citation

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