3A5Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.

Sumida, T.Ishii, R.Takemoto, C.Yokoyama, S.Yanagisawa, T.

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

  • DOI: 10.1038/nsmb.1889
  • Primary Citation of Related Structures:  

  • 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 s ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative lysyl-tRNA synthetase
A, B, C, D
345Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: epmA (genX, poxA, yjeA)
EC: 6.3.1.-
Find proteins for P0A8N7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8N7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAA
Query on KAA

Download SDF File 
Download CCD File 
A, B, C, D
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE
5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE
C16 H26 N8 O7 S
NARKTLKJPPMFJF-LEJQEAHTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KAAKd: 11 nM BINDINGMOAD
KAAKd: 11 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 54.800α = 95.47
b = 69.150β = 106.51
c = 94.080γ = 90.46
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-10-23
    Type: Database references