4P3N

Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for full-spectrum inhibition of translational functions on a tRNA synthetase.

Fang, P.Yu, X.Jeong, S.J.Mirando, A.Chen, K.Chen, X.Kim, S.Francklyn, C.S.Guo, M.

(2015) Nat Commun 6: 6402-6402

  • DOI: 10.1038/ncomms7402
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The polyketide natural product borrelidin displays antibacterial, antifungal, antimalarial, anticancer, insecticidal and herbicidal activities through the selective inhibition of threonyl-tRNA synthetase (ThrRS). How borrelidin simultaneously attenua ...

    The polyketide natural product borrelidin displays antibacterial, antifungal, antimalarial, anticancer, insecticidal and herbicidal activities through the selective inhibition of threonyl-tRNA synthetase (ThrRS). How borrelidin simultaneously attenuates bacterial growth and suppresses a variety of infections in plants and animals is not known. Here we show, using X-ray crystal structures and functional analyses, that a single molecule of borrelidin simultaneously occupies four distinct subsites within the catalytic domain of bacterial and human ThrRSs. These include the three substrate-binding sites for amino acid, ATP and tRNA associated with aminoacylation, and a fourth 'orthogonal' subsite created as a consequence of binding. Thus, borrelidin competes with all three aminoacylation substrates, providing a potent and redundant mechanism to inhibit ThrRS during protein synthesis. These results highlight a surprising natural design to achieve the quadrivalent inhibition of translation through a highly conserved family of enzymes.


    Organizational Affiliation

    Medicinal Bioconvergence Research Center, Seoul National University, Seoul 151-742, Korea.,Department of Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.,Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont 05405, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Threonine--tRNA ligase, cytoplasmic
A, B, C, D
415Homo sapiensMutation(s): 0 
Gene Names: TARS
EC: 6.1.1.3
Find proteins for P26639 (Homo sapiens)
Go to Gene View: TARS
Go to UniProtKB:  P26639
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
2CR
Query on 2CR

Download SDF File 
Download CCD File 
A, B, C, D
(1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid
Borrelidin
C28 H43 N O6
OJCKRNPLOZHAOU-RSXXJMTFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.228 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 63.870α = 86.99
b = 78.000β = 83.32
c = 118.050γ = 84.39
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM100136
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM106134

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy