3A5Y

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

Summary for 3A5Y

• Entry DOI: 10.2210/pdb3a5y/pdb
• Descriptor: Putative lysyl-tRNA synthetase, 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE (3 entities in total)
• Functional Keywords: aminoacyl-trna synthetase paralog, translation, trna, lysyl-trna synthetase, lysyladenylate analog, aminoacyl-trna synthetase, ligase, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 158651.42

Authors

Sumida, T.,Yanagisawa, T.,Ishii, R.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2009-08-17, release date: 2010-08-25, Last modification date: 2023-11-01)

Primary citation

Yanagisawa, T.,Sumida, T.,Ishii, R.,Takemoto, C.,Yokoyama, S.
A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.
Nat.Struct.Mol.Biol., 17:1136-1143, 2010

PubMed Abstract: 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.

PubMed: 20729861
DOI: 10.1038/nsmb.1889

Experimental method

X-RAY DIFFRACTION (1.9 Å)