5HZG

The crystal structure of the strigolactone-induced AtD14-D3-ASK1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DWARF14 is a non-canonical hormone receptor for strigolactone

Yao, R.Ming, Z.Yan, L.Li, S.Wang, F.Ma, S.Yu, C.Yang, M.Chen, L.Chen, L.Li, Y.Yan, C.Miao, D.Sun, Z.Yan, J.Sun, Y.Wang, L.Chu, J.Fan, S.He, W.Deng, H.Nan, F.Li, J.Rao, Z.Lou, Z.Xie, D.

(2016) Nature 536: 469-473

  • DOI: 10.1038/nature19073
  • Primary Citation of Related Structures:  
    5HYW, 5HZG

  • PubMed Abstract: 
  • Classical hormone receptors reversibly and non-covalently bind active hormone molecules, which are generated by biosynthetic enzymes, to trigger signal transduction. The α/β hydrolase DWARF14 (D14), which hydrolyses the plant branching hormone strigolactone and interacts with the F-box protein D3/MAX2, is probably involved in strigolactone detection ...

    Classical hormone receptors reversibly and non-covalently bind active hormone molecules, which are generated by biosynthetic enzymes, to trigger signal transduction. The α/β hydrolase DWARF14 (D14), which hydrolyses the plant branching hormone strigolactone and interacts with the F-box protein D3/MAX2, is probably involved in strigolactone detection. However, the active form of strigolactone has yet to be identified and it is unclear which protein directly binds the active form of strigolactone, and in which manner, to act as the genuine strigolactone receptor. Here we report the crystal structure of the strigolactone-induced AtD14-D3-ASK1 complex, reveal that Arabidopsis thaliana (At)D14 undergoes an open-to-closed state transition to trigger strigolactone signalling, and demonstrate that strigolactone is hydrolysed into a covalently linked intermediate molecule (CLIM) to initiate a conformational change of AtD14 to facilitate interaction with D3. Notably, analyses of a highly branched Arabidopsis mutant d14-5 show that the AtD14(G158E) mutant maintains enzyme activity to hydrolyse strigolactone, but fails to efficiently interact with D3/MAX2 and loses the ability to act as a receptor that triggers strigolactone signalling in planta. These findings uncover a mechanism underlying the allosteric activation of AtD14 by strigolactone hydrolysis into CLIM, and define AtD14 as a non-canonical hormone receptor with dual functions to generate and sense the active form of strigolactone.


    Organizational Affiliation

    Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Strigolactone esterase D14A,
D [auth E]
267Arabidopsis thalianaMutation(s): 0 
Gene Names: D14At3g03990T11I18.10
EC: 3.1
UniProt
Find proteins for Q9SQR3 (Arabidopsis thaliana)
Explore Q9SQR3 
Go to UniProtKB:  Q9SQR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SQR3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
F-box/LRR-repeat MAX2 homologB,
E [auth F]
740Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: D3Os06g0154200LOC_Os06g06050OSJNBa0085L11.6-1
UniProt
Find proteins for Q5VMP0 (Oryza sativa subsp. japonica)
Explore Q5VMP0 
Go to UniProtKB:  Q5VMP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VMP0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SKP1-like protein 1AC,
F [auth G]
169Arabidopsis thalianaMutation(s): 0 
Gene Names: SKP1AASK1SKP1UIP1At1g75950T4O12.17
UniProt
Find proteins for Q39255 (Arabidopsis thaliana)
Explore Q39255 
Go to UniProtKB:  Q39255
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39255
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6OM
Query on 6OM

Download Ideal Coordinates CCD File 
G [auth A],
H [auth E]
(2Z)-2-methylbut-2-ene-1,4-diol
C5 H10 O2
FLXLJBCLEUWWCG-DJWKRKHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.397α = 90
b = 172.979β = 90
c = 186.845γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the National Natural Science Foundation of ChinaChina31230008
the National Natural Science Foundation of ChinaChina81322023
Ministry of Science and TechnologyChina2011CB915404
Ministry of Science and TechnologyChina2013CB911100

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references