3WIO

Crystal structure of OSD14 in complex with hydroxy D-ring


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of strigolactone perception by DWARF14

Nakamura, H.Xue, Y.-L.Miyakawa, T.Hou, F.Qin, H.-M.Fukui, K.Shi, X.Ito, E.Ito, S.Park, S.-H.Miyauchi, Y.Asano, A.Totsuka, N.Ueda, T.Tanokura, M.Asami, T.

(2013) Nat Commun 4: 2613-2613

  • DOI: https://doi.org/10.1038/ncomms3613
  • Primary Citation of Related Structures:  
    3VXK, 3WIO

  • PubMed Abstract: 

    Strigolactones (SLs) are phytohormones that inhibit shoot branching and function in the rhizospheric communication with symbiotic fungi and parasitic weeds. An α/β-hydrolase protein, DWARF14 (D14), has been recognized to be an essential component of plant SL signalling, although its precise function remains unknown. Here we present the SL-dependent interaction of D14 with a gibberellin signalling repressor SLR1 and a possible mechanism of phytohormone perception in D14-mediated SL signalling. D14 functions as a cleavage enzyme of SLs, and the cleavage reaction induces the interaction with SLR1. The crystal structure of D14 shows that 5-hydroxy-3-methylbutenolide (D-OH), which is a reaction product of SLs, is trapped in the catalytic cavity of D14 to form an altered surface. The D14 residues recognizing D-OH are critical for the SL-dependent D14-SLR1 interaction. These results provide new insight into crosstalk between gibberellin and SL signalling pathways.


  • Organizational Affiliation

    1] Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable strigolactone esterase D14
A, B
274Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: D14D88HTD2LOC_Os03g10620Os03g0203200
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
H3M
Query on H3M

Download Ideal Coordinates CCD File 
C [auth A](5R)-5-hydroxy-3-methylfuran-2(5H)-one
C5 H6 O3
HQIZYPQNJWENRT-SCSAIBSYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.38α = 90
b = 88.13β = 90
c = 119.02γ = 90
Software Package:
Software NamePurpose
Crystaldata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description