9J3F | pdb_00009j3f

The structure of phospholipase TleB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A phospholipase effector of the type VI secretion system modulates plant reproduction.

Tan, Z.-.M.Yang, J.-.T.Xiao, Q.-.J.Su, J.-.T.Wang, Z.-.H.Jiang, Y.-.T.Liu, J.-.S.Pei, T.-.T.Liang, X.An, Y.Xue, H.-.W.Qin, W.-.M.Lin, W.-.H.Dong, T.

(2025) mBio 16: e0154625-e0154625

  • DOI: https://doi.org/10.1128/mbio.01546-25
  • Primary Citation of Related Structures:  
    9J3F

  • PubMed Abstract: 

    Phytobacteria play diverse roles in plant biology, ranging from promoting health to causing diseases that threaten global food security and the economy. In contrast to the extensive studies of phytopathogens targeting leaves and roots, their impact on plant reproductive processes has been largely overlooked. Here, we demonstrate that a bacterial effector TleB of the type VI secretion system in Xanthomonas oryzae can modulate seed production of Arabidopsis thaliana . Using biochemical, structural, and physiological analyses, we determined TleB as a phospholipase that mediates interspecies microbial competition in X. oryzae . Additionally, TleB plays a key role in the infection of inflorescences by X. oryzae , which leads to significantly reduced seed production. Lipidomic and biochemical assays show that TleB binds to a number of anionic phospholipids that are key signaling molecules. A fluorescence reporter for auxin distribution showed TleB-mediated diminished signals in planta . Additionally, transgenic plants expressing TleB exhibited significantly altered seed counts. These findings introduce a novel paradigm in which phytopathogens can affect plant reproduction in a traditionally non-susceptible host, prompting a reevaluation of diverse phytobacteria-host interactions in reproductive processes and offering new insights into plant health and crop protection.IMPORTANCEPhytobacteria are typically identified as pathogens based on visible effects on leaves and roots; those lacking such phenotypes are often considered nonpathogenic. Similarly, plant hosts that show no phenotypic changes are considered nonhosts and, thus, less studied. Our research challenges this classification by highlighting that bacteria-plant interactions on inflorescences, though less apparent and more delayed, can cause profound impacts on seed production. This discovery not only shifts the focus from the more commonly studied vegetative and root infections to the reproductive aspects of plant-pathogen interactions but also necessitates a reevaluation of host-pathogen dynamics with an emphasis on long-term effects such as seed production.


  • Organizational Affiliation
    • School of Life Sciences and Biotechnology, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tle1 phospholipase domain-containing protein779Xanthomonas oryzae pv. oryzae PXO99AMutation(s): 0 
Gene Names: PXO_02034
UniProt
Find proteins for A0A0K0GNK3 (Xanthomonas oryzae pv. oryzae (strain PXO99A))
Explore A0A0K0GNK3 
Go to UniProtKB:  A0A0K0GNK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K0GNK3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.64α = 90
b = 70.366β = 99.26
c = 78.775γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-08-06 
  • Deposition Author(s): Tan, Z.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32030001

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Database references