› 2zue

X-ray diffraction
2Å resolution

Crystal structure of Pyrococcus horikoshii arginyl-tRNA synthetase complexed with tRNA(Arg) and an ATP analog (ANP)

Released:
DOI: 10.2210/pdb2zue/pdb
PDB entry 2zue coloured by chain, front view.
PDB entry 2zue coloured by chain, side view.
PDB entry 2zue coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
Konno M, Sumida T, Uchikawa E, Mori Y, Yanagisawa T, Sekine S, Yokoyama S, Yokoyama S
FEBS J 276 4763-79 (2009)
PMID: 19656186

Function and Biology Details

Reaction catalysed: 
ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129811 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Arginine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 629 amino acids
Theoretical weight: 72.44 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O59147 (Residues: 1-629; Coverage: 100%)
Gene names: PH1478, argS
Sequence domains:
Structure domains:
tRNA-Arg Chain: B
Molecule details ›
Chain: B
Length: 78 nucleotides
Theoretical weight: 25.16 KDa
Source organism: Pyrococcus horikoshii
Expression system: Not provided
Sequence domains: tRNA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 76.27Å b: 60Å c: 110.66Å
α: 90° β: 106.94° γ: 90°
R-values:
R R work R free
0.219 0.213 0.253
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Emergence and evolution.
Bullwinkle et al. (2014)
8 other articles

8 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)
7 more