› 3a5y

X-ray diffraction
1.9Å resolution

Crystal structure of GenX from Escherichia coli in complex with lysyladenylate analog

Released:
DOI: 10.2210/pdb3a5y/pdb
PDB entry 3a5y coloured by chain, front view.
PDB entry 3a5y coloured by chain, side view.
PDB entry 3a5y coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.
Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S
Nat Struct Mol Biol 17 1136-43 (2010)
PMID: 20729861

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141718 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Elongation factor P--(R)-beta-lysine ligase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 345 amino acids
Theoretical weight: 39.19 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8N7 (Residues: 1-325; Coverage: 100%)
Gene names: JW4116, b4155, epmA, genX, poxA, yjeA
Sequence domains: tRNA synthetases class II (D, K and N)
Structure domains: Bira Bifunctional Protein; Domain 2

Ligands and Environments

1 bound ligand:
Ligand KAA 4 x KAA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P1
Unit cell:
a: 54.8Å b: 69.15Å c: 94.08Å
α: 95.47° β: 106.51° γ: 90.46°
R-values:
R R work R free
0.171 0.171 0.219
Expression system: Escherichia coli

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Citations

18 review citations

The elongation, termination, and recycling phases of translation in eukaryotes.
Dever et al. (2012)
17 more