6JQA

Crystal structure of phyllogen, a phyllody inducing effector protein of phytoplasma.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.272 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of phyllogen, a phyllody-inducing effector protein of phytoplasma.

Iwabuchi, N.Maejima, K.Kitazawa, Y.Miyatake, H.Nishikawa, M.Tokuda, R.Koinuma, H.Miyazaki, A.Nijo, T.Oshima, K.Yamaji, Y.Namba, S.

(2019) Biochem Biophys Res Commun 513: 952-957

  • DOI: https://doi.org/10.1016/j.bbrc.2019.04.060
  • Primary Citation of Related Structures:  
    6JQA

  • PubMed Abstract: 

    Phytoplasmas are plant pathogenic bacteria that often induce unique phyllody symptoms in which the floral organs are transformed into leaf-like structures. Recently, a novel family of bacterial effector genes, called phyllody-inducing genes (phyllogens), was identified as being involved in the induction of phyllody by degrading floral MADS-domain transcription factors (MTFs). However, the structural characteristics of phyllogens are unknown. In this study, we elucidated the crystal structure of PHYL1 OY , a phyllogen of 'Candidatus Phytoplasma asteris' onion yellows strain, at a resolution of 2.4 Å. The structure of PHYL1 consisted of two α-helices connected by a random loop in a coiled-coil manner. In both α-helices, the distributions of hydrophobic residues were conserved among phyllogens. Amino acid insertion mutations into either α-helix resulted in the loss of phyllody-inducing activity and the ability of the phyllogen to degrade floral MTF. In contrast, the same insertion in the loop region did not affect either activity, indicating that both conserved α-helices are important for the function of phyllogens. This is the first report on the crystal structure of an effector protein of phytoplasmas.


  • Organizational Affiliation

    Department of Agricultural and Environmental Biology, 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
Phytoplasmal effector causing phyllody 191Onion yellows phytoplasma OY-WMutation(s): 0 
Gene Names: PHYL1
UniProt
Find proteins for X5IFG3 (Onion yellows phytoplasma OY-W)
Explore X5IFG3 
Go to UniProtKB:  X5IFG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX5IFG3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phytoplasmal effector causing phyllody 1
B, C
91Onion yellows phytoplasma OY-WMutation(s): 0 
Gene Names: PHYL1
UniProt
Find proteins for X5IFG3 (Onion yellows phytoplasma OY-W)
Explore X5IFG3 
Go to UniProtKB:  X5IFG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX5IFG3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phytoplasmal effector causing phyllody 191Onion yellows phytoplasma OY-WMutation(s): 0 
Gene Names: PHYL1
UniProt
Find proteins for X5IFG3 (Onion yellows phytoplasma OY-W)
Explore X5IFG3 
Go to UniProtKB:  X5IFG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX5IFG3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
IYR
Query on IYR
A
L-PEPTIDE LINKINGC9 H10 I N O3TYR
TYI
Query on TYI
A
L-PEPTIDE LINKINGC9 H9 I2 N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.272 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.843α = 90
b = 60.664β = 90
c = 124.874γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan25221201
Japan Society for the Promotion of ScienceJapanGS005
Japan Society for the Promotion of ScienceJapan16K14643
Japan Society for the Promotion of ScienceJapan17J09944
Japan Society for the Promotion of ScienceJapan17H06618

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references