3C6O

Small molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling.

Hayashi, K.Tan, X.Zheng, N.Hatate, T.Kimura, Y.Kepinski, S.Nozaki, H.

(2008) Proc Natl Acad Sci U S A 105: 5632-5637

  • DOI: https://doi.org/10.1073/pnas.0711146105
  • Primary Citation of Related Structures:  
    3C6N, 3C6O, 3C6P

  • PubMed Abstract: 

    The regulation of gene expression by the hormone auxin is a crucial mechanism in plant development. We have shown that the Arabidopsis F-box protein TIR1 is a receptor for auxin, and our recent structural work has revealed the molecular mechanism of auxin perception. TIR1 is the substrate receptor of the ubiquitin-ligase complex SCF(TIR1). Auxin binding enhances the interaction between TIR1 and its substrates, the Aux/IAA repressors, thereby promoting the ubiquitination and degradation of Aux/IAAs, altering the expression of hundreds of genes. TIR1 is the prototype of a new class of hormone receptor and the first example of an SCF ubiquitin-ligase modulated by a small molecule. Here, we describe the design, synthesis, and characterization of a series of auxin agonists and antagonists. We show these molecules are specific to TIR1-mediated events in Arabidopsis, and their mode of action in binding to TIR1 is confirmed by x-ray crystallographic analysis. Further, we demonstrate the utility of these probes for the analysis of TIR1-mediated auxin signaling in the moss Physcomitrella patens. Our work not only provides a useful tool for plant chemical biology but also demonstrates an example of a specific small-molecule inhibitor of F-box protein-substrate recruitment. Substrate recognition and subsequent ubiquitination by SCF-type ubiquitin ligases are central to many cellular processes in eukaryotes, and ubiquitin-ligase function is affected in several human diseases. Our work supports the idea that it may be possible to design small-molecule agents to modulate ubiquitin-ligase function therapeutically.


  • Organizational Affiliation

    Department of Biochemistry, Okayama University of Science, Okayama 700-0005, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SKP1-like protein 1A160Arabidopsis thalianaMutation(s): 0 
Gene Names: SKP1AASK1SKP1UIP1
UniProt
Find proteins for Q39255 (Arabidopsis thaliana)
Explore Q39255 
Go to UniProtKB:  Q39255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39255
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TRANSPORT INHIBITOR RESPONSE 1594Arabidopsis thalianaMutation(s): 0 
Gene Names: TIR1FBL1WEI1
UniProt
Find proteins for Q570C0 (Arabidopsis thaliana)
Explore Q570C0 
Go to UniProtKB:  Q570C0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ570C0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
C [auth B]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
2S2
Query on 2S2

Download Ideal Coordinates CCD File 
D [auth B](2S)-2-(1H-indol-3-yl)hexanoic acid
C14 H17 N O2
RCBHCHBXRBYJGU-NSHDSACASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.264α = 90
b = 80.836β = 104.87
c = 124.748γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2008-04-22 
  • Deposition Author(s): Tan, X.

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-23
    Changes: Refinement description
  • Version 1.3: 2020-10-14
    Changes: Derived calculations, Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description