3A5Z

Crystal structure of Escherichia coli GenX in complex with elongation factor P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

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.

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

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

  • DOI: 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative lysyl-tRNA synthetaseA, C, E, G328Escherichia coliMutation(s): 0 
Gene Names: genXECs5136
EC: 6.1.1.6 (PDB Primary Data), 6.3.1 (UniProt)
Find proteins for P0A8N7 (Escherichia coli (strain K12))
Explore P0A8N7 
Go to UniProtKB:  P0A8N7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor PB, D, F, H191Escherichia coliMutation(s): 0 
Gene Names: efpECs5128
Find proteins for P0A6N4 (Escherichia coli (strain K12))
Explore P0A6N4 
Go to UniProtKB:  P0A6N4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAA
Query on KAA

Download Ideal Coordinates CCD File 
I [auth A], J [auth C], K [auth E], L [auth G]5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE
C16 H26 N8 O7 S
NARKTLKJPPMFJF-LEJQEAHTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.93α = 90
b = 102.96β = 99.4
c = 119.94γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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