5ZHS

Crystal structure of OsD14 in complex with covalently bound KK052


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Triazole Ureas Covalently Bind to Strigolactone Receptor and Antagonize Strigolactone Responses.

Nakamura, H.Hirabayashi, K.Miyakawa, T.Kikuzato, K.Hu, W.Xu, Y.Jiang, K.Takahashi, I.Niiyama, R.Dohmae, N.Tanokura, M.Asami, T.

(2019) Mol Plant 12: 44-58

  • DOI: https://doi.org/10.1016/j.molp.2018.10.006
  • Primary Citation of Related Structures:  
    5ZHR, 5ZHS, 5ZHT

  • PubMed Abstract: 

    Strigolactones, a class of plant hormones with multiple functions, mediate plant-plant and plant-microorganism communications in the rhizosphere. In this study, we developed potent strigolactone antagonists, which covalently bind to the strigolactone receptor D14, by preparing an array of triazole urea compounds. Using yeast two-hybrid and rice-tillering assays, we identified a triazole urea compound KK094 as a potent inhibitor of strigolactone receptors. Liquid chromatography-tandem mass spectrometry analysis and X-ray crystallography revealed that KK094 was hydrolyzed by D14, and that a reaction product of this degradation covalently binds to the Ser residue of the catalytic triad of D14. Furthermore, we identified two triazole urea compounds KK052 and KK073, whose effects on D14-D53/D14-SLR1 complex formation were opposite due to the absence (KK052) or presence (KK073) of a trifluoromethyl group on their phenyl ring. These results demonstrate that triazole urea compounds are potentially powerful tools for agricultural application and may be useful for the elucidation of the complicated mechanism underlying strigolactone perception.


  • Organizational Affiliation

    Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Strigolactone esterase D14274Oryza 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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KAT (Subject of Investigation/LOI)
Query on KAT

Download Ideal Coordinates CCD File 
B [auth A](4-phenylpiperazin-1-yl)(1H-1,2,3-triazol-1-yl)methanone
C13 H15 N5 O
ILKSIXGCKDCMDG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.97α = 90
b = 48.97β = 90
c = 192.199γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan16H06736
Japan Society for the Promotion of Science (JSPS)Japan17J04676
Japan Society for the Promotion of Science (JSPS)Japan17K15258

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description