2P1N

Mechanism of Auxin Perception by the TIR1 Ubiqutin Ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of auxin perception by the TIR1 ubiquitin ligase

Tan, X.Calderon-Villalobos, L.I.A.Sharon, M.Zheng, C.Robinson, C.V.Estelle, M.Zheng, N.

(2007) Nature 446: 640-645

  • DOI: 10.1038/nature05731
  • Primary Citation of Related Structures:  
    2P1M, 2P1Q, 2P1P, 2P1O, 2P1N

  • PubMed Abstract: 
  • Auxin is a pivotal plant hormone that controls many aspects of plant growth and development. Perceived by a small family of F-box proteins including transport inhibitor response 1 (TIR1), auxin regulates gene expression by promoting SCF ubiquitin-ligase-catalysed degradation of the Aux/IAA transcription repressors, but how the TIR1 F-box protein senses and becomes activated by auxin remains unclear ...

    Auxin is a pivotal plant hormone that controls many aspects of plant growth and development. Perceived by a small family of F-box proteins including transport inhibitor response 1 (TIR1), auxin regulates gene expression by promoting SCF ubiquitin-ligase-catalysed degradation of the Aux/IAA transcription repressors, but how the TIR1 F-box protein senses and becomes activated by auxin remains unclear. Here we present the crystal structures of the Arabidopsis TIR1-ASK1 complex, free and in complexes with three different auxin compounds and an Aux/IAA substrate peptide. These structures show that the leucine-rich repeat domain of TIR1 contains an unexpected inositol hexakisphosphate co-factor and recognizes auxin and the Aux/IAA polypeptide substrate through a single surface pocket. Anchored to the base of the TIR1 pocket, auxin binds to a partially promiscuous site, which can also accommodate various auxin analogues. Docked on top of auxin, the Aux/IAA substrate peptide occupies the rest of the TIR1 pocket and completely encloses the hormone-binding site. By filling in a hydrophobic cavity at the protein interface, auxin enhances the TIR1-substrate interactions by acting as a 'molecular glue'. Our results establish the first structural model of a plant hormone receptor.


    Organizational Affiliation

    Department of Pharmacology, University of Washington, School of Medicine, Box 357280, Seattle, Washington 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SKP1-like protein 1AA, D160Arabidopsis thalianaMutation(s): 0 
Gene Names: SKP1AASK1SKP1UIP1At1g75950T4O12.17
UniProt
Find proteins for Q39255 (Arabidopsis thaliana)
Explore Q39255 
Go to UniProtKB:  Q39255
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSPORT INHIBITOR RESPONSE 1 proteinB, E594Arabidopsis thalianaMutation(s): 0 
Gene Names: TIR1FBL1WEI1At3g62980T20O10.80
UniProt
Find proteins for Q570C0 (Arabidopsis thaliana)
Explore Q570C0 
Go to UniProtKB:  Q570C0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Auxin-responsive protein IAA7C, F13N/AMutation(s): 0 
UniProt
Find proteins for Q38825 (Arabidopsis thaliana)
Explore Q38825 
Go to UniProtKB:  Q38825
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
G [auth B], I [auth E]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
CFA
Query on CFA

Download Ideal Coordinates CCD File 
H [auth B], J [auth E](2,4-DICHLOROPHENOXY)ACETIC ACID
C8 H6 Cl2 O3
OVSKIKFHRZPJSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.665α = 90
b = 82.745β = 100.4
c = 125.791γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-10-14
    Changes: Derived calculations, Structure summary