6C80 | pdb_00006c80

Crystal structure of a flax cytokinin oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.184 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.152 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

Structural and functional insights into the modulation of the activity of a flax cytokinin oxidase by flax rust effector AvrL567-A.

Wan, L.Koeck, M.Williams, S.J.Ashton, A.R.Lawrence, G.J.Sakakibara, H.Kojima, M.Bottcher, C.Ericsson, D.J.Hardham, A.R.Jones, D.A.Ellis, J.G.Kobe, B.Dodds, P.N.

(2019) Mol Plant Pathol 20: 211-222

  • DOI: https://doi.org/10.1111/mpp.12749
  • Primary Citation Related Structures: 
    6C80

  • PubMed Abstract: 

    During infection, plant pathogens secrete effector proteins to facilitate colonization. In comparison with our knowledge of bacterial effectors, the current understanding of how fungal effectors function is limited. In this study, we show that the effector AvrL567-A from the flax rust fungus Melampsora lini interacts with a flax cytosolic cytokinin oxidase, LuCKX1.1, using both yeast two-hybrid and in planta bimolecular fluorescence assays. Purified LuCKX1.1 protein shows catalytic activity against both N6-(Δ2-isopentenyl)-adenine (2iP) and trans-zeatin (tZ) substrates. Incubation of LuCKX1.1 with AvrL567-A results in increased catalytic activity against both substrates. The crystal structure of LuCKX1.1 and docking studies with AvrL567-A indicate that the AvrL567 binding site involves a flexible surface-exposed region that surrounds the cytokinin substrate access site, which may explain its effect in modulating LuCKX1.1 activity. Expression of AvrL567-A in transgenic flax plants gave rise to an epinastic leaf phenotype consistent with hormonal effects, although no difference in overall cytokinin levels was observed. We propose that, during infection, plant pathogens may differentially modify the levels of extracellular and intracellular cytokinins.


  • Organizational Affiliation
    • School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia.

Macromolecule Content 

  • Total Structure Weight: 111.96 kDa 
  • Atom Count: 8,405 
  • Modeled Residue Count: 964 
  • Deposited Residue Count: 978 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cytokinin oxidase LuCKX1.1
A, B
489Linum usitatissimumMutation(s): 0 
EC: 1.5.99.12
UniProt
Find proteins for A0A0U1ZL01 (Linum usitatissimum)
Explore A0A0U1ZL01 
Go to UniProtKB:  A0A0U1ZL01
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1ZL01
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PG6

Query on PG6



Download:Ideal Coordinates CCD File
I [auth A]1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth A],
L [auth B],
M [auth B],
N [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
O [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NH4

Query on NH4



Download:Ideal Coordinates CCD File
J [auth A],
V [auth B]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.184 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.226α = 90
b = 58.929β = 95.62
c = 188.867γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP120100685

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-01-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.5: 2024-06-05
    Changes: Data collection, Database references
  • Version 1.6: 2024-11-06
    Changes: Structure summary