3A5Y: Crystal Structure Of Genx From Escherichia Coli In Complex With Lysyladenylate Analog

Aminoacyl-tRNA synthetase (aaRS) paralogs with unknown functions exist in various species. We now report novel 'protein lysylation' by an Escherichia coli lysyl-tRNA synthetase paralog, GenX/PoxA/YjeA. X-ray crystallographic analysis shows that the structure of the GenX protein resembles that of a class II aaRS. Further in vitro studies reveal that it specifically aminoacylates EF-P with lysine. The shape of the protein substrate mimics that of the L-shaped tRNA, and its lysylation site corresponds to the tRNA 3' end. Thus, we show how the aaRS architecture can be adapted to achieve aminoacylation of a specific protein. Moreover, in vivo analyses reveal that the translation elongation factor P (EF-P) lysylation by GenX is enhanced by YjeK (lysine 2,3-aminomutase paralog), which is encoded next to the EF-P gene, and might convert alpha-lysyl-EF-P to beta-lysyl-EF-P. In vivo analyses indicate that the EF-P modification by GenX and YjeK is essential for cell survival.
PDB ID: 3A5YDownload
MMDB ID: 84324
PDB Deposition Date: 2009/8/17
Updated in MMDB: 2013/10
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Source Organism:
Similar Structures:
Biological Unit for 3A5Y: dimeric; determined by author and by software (PISA)
Molecular Components in 3A5Y
Label Count Molecule
Proteins (2 molecules)
Putative Lysyl-trna Synthetase
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

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