6AP8

Crystal Structure of rice D14 bound to 2-(2-methyl-3-nitroanilino)benzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibition of strigolactone receptors byN-phenylanthranilic acid derivatives: Structural and functional insights.

Hamiaux, C.Drummond, R.S.M.Luo, Z.Lee, H.W.Sharma, P.Janssen, B.J.Perry, N.B.Denny, W.A.Snowden, K.C.

(2018) J Biol Chem 293: 6530-6543

  • DOI: https://doi.org/10.1074/jbc.RA117.001154
  • Primary Citation of Related Structures:  
    6AP6, 6AP7, 6AP8

  • PubMed Abstract: 

    The strigolactone (SL) family of plant hormones regulates a broad range of physiological processes affecting plant growth and development and also plays essential roles in controlling interactions with parasitic weeds and symbiotic fungi. Recent progress elucidating details of SL biosynthesis, signaling, and transport offers many opportunities for discovering new plant-growth regulators via chemical interference. Here, using high-throughput screening and downstream biochemical assays, we identified N -phenylanthranilic acid derivatives as potent inhibitors of the SL receptors from petunia (DAD2), rice (OsD14), and Arabidopsis (AtD14). Crystal structures of DAD2 and OsD14 in complex with inhibitors further provided detailed insights into the inhibition mechanism, and in silico modeling of 19 other plant strigolactone receptors suggested that these compounds are active across a large range of plant species. Altogether, these results provide chemical tools for investigating SL signaling and further define a framework for structure-based approaches to design and validate optimized inhibitors of SL receptors for specific plant targets.


  • Organizational Affiliation

    From the New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand, [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Strigolactone esterase D14
A, B
269Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: D14D88HTD2Os03g0203200LOC_Os03g10620
EC: 3.1
UniProt
Find proteins for Q10QA5 (Oryza sativa subsp. japonica)
Explore Q10QA5 
Go to UniProtKB:  Q10QA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10QA5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.005α = 90
b = 88.433β = 90
c = 119.026γ = 90
Software Package:
Software NamePurpose
XDSdata processing
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2018-03-21 
  • Deposition Author(s): Hamiaux, C.

Funding OrganizationLocationGrant Number
AGMARDTNew Zealand1323
MarsdenNew ZealandPAF1301

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description