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: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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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: https://doi.org/10.1038/ncomms2421
  • Primary Citation of Related Structures:  
    3ZGZ

  • 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 strains of A ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEUCINE--TRNA LIGASEA,
C [auth D]		880Escherichia coliMutation(s): 0 
EC: 6.1.1.4
UniProt
Find proteins for P07813 (Escherichia coli (strain K12))
Explore P07813 
Go to UniProtKB:  P07813
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07813
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
TRNA-LEU UAA ISOACCEPTORB,
D [auth E]		88Escherichia coli K-12
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
84T
Query on 84T
Download Ideal Coordinates CCD File 
F [auth A],
M [auth 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
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
L [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
N [auth E],
O [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.58α = 90
b = 68.19β = 105.53
c = 226.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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