3ZGZ

Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Plant Tumour Biocontrol Agent Employs a tRNA-Dependent Mechanism to Inhibit Leucyl-tRNA Synthetase

Chopra, S.Palencia, A.Virus, C.Tripathy, A.Temple, B.R.Velazquez-Campoy, A.Cusack, S.Reader, J.S.

(2013) Nat.Commun. 4: 1417

  • DOI: 10.1038/ncomms2421

  • PubMed Abstract: 
  • Leucyl-tRNA synthetases (LeuRSs) have an essential role in translation and are promising targets for antibiotic development. Agrocin 84 is a LeuRS inhibitor produced by the biocontrol agent Agrobacterium radiobacter K84 that targets pathogenic strain ...

    Leucyl-tRNA synthetases (LeuRSs) have an essential role in translation and are promising targets for antibiotic development. Agrocin 84 is a LeuRS inhibitor produced by the biocontrol agent Agrobacterium radiobacter K84 that targets pathogenic strains of A. tumefaciens, the causative agent of plant tumours. Agrocin 84 acts as a molecular Trojan horse and is processed inside the pathogen into a toxic moiety (TM84). Here we show using crystal structure, thermodynamic and kinetic analyses, that this natural antibiotic employs a unique and previously undescribed mechanism to inhibit LeuRS. TM84 requires tRNA(Leu) for tight binding to the LeuRS synthetic active site, unlike any previously reported inhibitors. TM84 traps the enzyme-tRNA complex in a novel 'aminoacylation-like' conformation, forming novel interactions with the KMSKS loop and the tRNA 3'-end. Our findings reveal an intriguing tRNA-dependent inhibition mechanism that may confer a distinct evolutionary advantage in vivo and inform future rational antibiotic design.


    Organizational Affiliation

    Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, 536 Taylor Hall, CB# 7090, Chapel Hill, North Carolina 27599-7090, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCINE--TRNA LIGASE
A, D
880Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: leuS
EC: 6.1.1.4
Find proteins for P07813 (Escherichia coli (strain K12))
Go to UniProtKB:  P07813
Entity ID: 2
MoleculeChainsLengthOrganism
TRNA-LEU UAA ISOACCEPTORB,E88Escherichia coli K-12
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
84T
Query on 84T

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Download CCD File 
A, D
[(2S,4S,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-N-[(2S,3R)-4-methyl-2,3-bis(oxidanyl)pentanoyl]phosphonamidic acid
C16 H25 N6 O8 P
KHSKVNAFZAVNFC-UVIICUSPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 158.580α = 90.00
b = 68.190β = 105.53
c = 226.220γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-02-13
    Type: Database references