4TTV

Crystal structure of human ThrRS complexing with a bioengineered macrolide BC194


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Aminoacyl-tRNA synthetase dependent angiogenesis revealed by a bioengineered macrolide inhibitor.

Mirando, A.C.Fang, P.Williams, T.F.Baldor, L.C.Howe, A.K.Ebert, A.M.Wilkinson, B.Lounsbury, K.M.Guo, M.Francklyn, C.S.

(2015) Sci Rep 5: 13160-13160

  • DOI: 10.1038/srep13160

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases (AARSs) catalyze an early step in protein synthesis, but also regulate diverse physiological processes in animal cells. These include angiogenesis, and human threonyl-tRNA synthetase (TARS) represents a potent pro-angiogeni ...

    Aminoacyl-tRNA synthetases (AARSs) catalyze an early step in protein synthesis, but also regulate diverse physiological processes in animal cells. These include angiogenesis, and human threonyl-tRNA synthetase (TARS) represents a potent pro-angiogenic AARS. Angiogenesis stimulation can be blocked by the macrolide antibiotic borrelidin (BN), which exhibits a broad spectrum toxicity that has discouraged deeper investigation. Recently, a less toxic variant (BC194) was identified that potently inhibits angiogenesis. Employing biochemical, cell biological, and biophysical approaches, we demonstrate that the toxicity of BN and its derivatives is linked to its competition with the threonine substrate at the molecular level, which stimulates amino acid starvation and apoptosis. By separating toxicity from the inhibition of angiogenesis, a direct role for TARS in vascular development in the zebrafish could be demonstrated. Bioengineered natural products are thus useful tools in unmasking the cryptic functions of conventional enzymes in the regulation of complex processes in higher metazoans.


    Organizational Affiliation

    Isomerase Therapeutics Ltd, Science Village, Chesterford Research Park, Cambridge CB10 1XL, UK.,Department of Pharmacology, University of Vermont.,Department of Biochemistry, University of Vermont.,Department of Biology, University of Vermont.,Department of Cancer Biology, The Scripps Research Institute, Scripps Florida.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Threonine--tRNA ligase, cytoplasmic
A, B, C, D
414Homo 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
BC9
Query on BC9

Download SDF File 
Download CCD File 
A, B, C, D
(1R,2R)-2-[(2S,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadec-6-en-2-yl]cyclobutanecarboxylic acid
C27 H43 N O6
KHMHNBNVTBTHJD-IIZLMIOOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 92.020α = 90.00
b = 134.610β = 90.10
c = 128.670γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-06-23 
  • Released Date: 2015-09-30 
  • Deposition Author(s): Fang, P., Guo, M.

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: 2015-09-30
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations