Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.34 kDa 
• Atom Count: 2634 
• Modelled Residue Count: 267 
• Deposited Residue Count: 272 
• Unique protein chains: 1

3W06

Crystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L)

• PDB DOI: 10.2210/pdb3W06/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-19 Released: 2013-01-23 
• Deposition Author(s): Kagiyama, M., Hirano, Y., Mori, T., Kim, S.Y., Kyozuka, J., Seto, Y., Yamaguchi, S., Hakoshima, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.162 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 

Literature

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

• PubMed: 23301669 
• DOI: 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, alpha/beta fold family protein	A	272	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At4g37470, F6G17.120, KAI2, D14L, HTL
UniProt
Find proteins for Q9SZU7 (Arabidopsis thaliana) Explore Q9SZU7  Go to UniProtKB:  Q9SZU7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 50.953	α = 90
b = 55.603	β = 115.81
c = 53.128	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-19 
• Released Date: 2013-01-23 
Deposition Author(s): Kagiyama, M., Hirano, Y., Mori, T., Kim, S.Y., Kyozuka, J., Seto, Y., Yamaguchi, S., Hakoshima, T.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-02-06
  Changes: Database references