› 5f5w

X-ray diffraction
2.81Å resolution

Crystal structure of the alpha subunit of glycyl tRNA synthetase (GlyRS) from Aquifex aeolicus in complex with an analog of glycyl adenylate (Gly-SA)

Released:
DOI: 10.2210/pdb5f5w/pdb
PDB entry 5f5w coloured by chain, front view.
PDB entry 5f5w coloured by chain, side view.
PDB entry 5f5w coloured by chain, top view.
Source organism: Aquifex aeolicus VF5
Primary publication:
Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases.
Valencia-Sánchez MI, Rodríguez-Hernández A, Ferreira R, Santamaría-Suárez HA, Arciniega M, Dock-Bregeon AC, Moras D, Beinsteiner B, Mertens H, Svergun D, Brieba LG, Grøtli M, Torres-Larios A
J Biol Chem 291 14430-46 (2016)
PMID: 27226617

Function and Biology Details

Reaction catalysed: 
ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130428 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycine--tRNA ligase alpha subunit Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 299 amino acids
Theoretical weight: 35.55 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O67081 (Residues: 1-285; Coverage: 100%)
Gene names: aq_945, glyQ
Sequence domains: Glycyl-tRNA synthetase alpha subunit
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand G5A 5 x G5A
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Unit cell:
a: 101.829Å b: 130.01Å c: 145.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.239 0.252
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Aminoacyl-tRNA synthetases.
Rubio Gomez et al. (2020)
1 more

1 mention without citation

Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases.
Valencia-Sánchez et al. (2016)