4P3N | pdb_00004p3n

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4P3N

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/ncomms7402
  • Primary Citation Related Structures: 
    4P3N, 4P3O, 4P3P

  • 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 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
    • Department of Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.

Macromolecule Content 

  • Total Structure Weight: 196.09 kDa 
  • Atom Count: 13,506 
  • Modeled Residue Count: 1,608 
  • Deposited Residue Count: 1,660 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Threonine--tRNA ligase, cytoplasmic
A, B, C, D
415Homo sapiensMutation(s): 0 
Gene Names: TARS
EC: 6.1.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P26639 (Homo sapiens)
Explore P26639 
Go to UniProtKB:  P26639
PHAROS:  P26639
GTEx:  ENSG00000113407 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26639
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2CR

Query on 2CR



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth 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
C28 H43 N O6
OJCKRNPLOZHAOU-RSXXJMTFSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.87α = 86.99
b = 78β = 83.32
c = 118.05γ = 84.39
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100136
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106134

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Refinement description