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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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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.

(2010) Nat Struct Mol Biol 17: 1136-1143

  • DOI: https://doi.org/10.1038/nsmb.1889
  • Primary Citation of Related Structures:  
    3A5Y, 3A5Z

  • 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.

  • Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative lysyl-tRNA synthetase
A, B, C, D
345Escherichia coliMutation(s): 0 
Gene Names: ECs5136GenX
Find proteins for P0A8N7 (Escherichia coli (strain K12))
Explore P0A8N7 
Go to UniProtKB:  P0A8N7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8N7
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
KAA Binding MOAD:  3A5Y Kd: 11 (nM) from 1 assay(s)
PDBBind:  3A5Y Kd: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.8α = 95.47
b = 69.15β = 106.51
c = 94.08γ = 90.46
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-10-23
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description