Crystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L)

Experimental Data Snapshot

  • Resolution: 1.15 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

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Structures of D14 and D14L in the strigolactone and karrikin signaling pathways

Kagiyama, M.Hirano, Y.Mori, T.Kim, S.Y.Kyozuka, J.Seto, Y.Yamaguchi, S.Hakoshima, T.

(2013) Genes Cells 18: 147-160

  • DOI: https://doi.org/10.1111/gtc.12025
  • Primary Citation of Related Structures:  
    3W04, 3W05, 3W06

  • PubMed Abstract: 

    Strigolactones (SLs) are plant hormones that inhibit shoot branching. DWARF14 (D14) inhibits rice tillering and is an SL receptor candidate in the branching inhibition pathway, whereas the close homologue DWARF14-LIKE (D14L) participates in the signaling pathway of karrikins (KARs), which are derived from burnt vegetation as smoke stimulants of seed germination. We provide the first evidence for direct binding of the bioactive SL analogue GR24 to D14. Isothermal titration calorimetry measurements show a D14-GR24 binding affinity in the sub-micromolar range. Similarly, bioactive KAR1 directly binds D14L in the micromolar range. The crystal structure of rice D14 shows a compact α-/β-fold hydrolase domain forming a deep ligand-binding pocket capable of accommodating GR24. Insertion of four α-helices between β6 strand and αD helix forms the helical cap of the pocket, although the pocket is open to the solvent. The pocket contains the conserved catalytic triad Ser-His-Asp aligned with the oxyanion hole, suggesting hydrolase activity. Although these structural characteristics are conserved in D14L, the D14L pocket is smaller than that of D14. The KAR-insensitive mutation kai2-1 is located at the prominent long β6-αD1 loop, which is characteristic in D14 and D14L, but not in related α-/β-fold hydrolases.

  • Organizational Affiliation

    Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrolase, alpha/beta fold family protein272Arabidopsis thalianaMutation(s): 0 
Gene Names: AT4g37470F6G17.120
Find proteins for Q9SZU7 (Arabidopsis thaliana)
Explore Q9SZU7 
Go to UniProtKB:  Q9SZU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SZU7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.15 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.953α = 90
b = 55.603β = 115.81
c = 53.128γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-02-06
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description