8ZRO | pdb_00008zro

Arabidopsis Carboxylesterase CXE15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 
    0.284 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8ZRO

This is version 2.0 of the entry. See complete history

Literature

Molecular Basis for Catalysis and Regulation of the Strigolactone Catabolic Enzyme CXE15.

Shahul Hameed, U.F.Balakrishna, A.Wang, J.Y.Alvarez, D.Momin, A.A.Schwarzenberg, A.Al-Babili, S.Arold, S.T.

(2025) Nat Commun 16: 10290-10290

  • DOI: https://doi.org/10.1038/s41467-025-65204-1
  • Primary Citation Related Structures: 
    8ZR6, 8ZRF, 8ZRG, 8ZRO

  • PubMed Abstract: 

    Strigolactones (SLs) are pivotal plant hormones involved in developmental, physiological, and adaptive processes. SLs also facilitate symbiosis with arbuscular mycorrhizal fungi and trigger germination of root parasitic Striga plants. The carboxylesterase CXE15, recently identified as the SL catabolic enzyme in Arabidopsis thaliana, plays a crucial role in regulating SL levels. Our study elucidates the structural and regulatory mechanisms of CXE15. We present four crystal structures capturing the conformational dynamics of CXE15, revealing a unique N-terminal extension (Nt) that transitions from a β-sheet in monomers to an intertwined helical structure in dimers. Only the dimeric form is catalytically active, as it forms a hydrophobic cavity for SLs between its two active sites. The moderate dimerisation affinity allows for genetic regulation through protein expression levels. Additionally, we identify an environment-controlled regulation mechanism. Under oxidising conditions, a disulphide bond forms between Cys14 of the two monomers, blocking the active site and inhibiting SL cleavage. This redox-sensitive inhibition of SL catabolism, triggered by reactive oxygen species (ROS) in response to abiotic stress, suggests a mechanism for maintaining high SL levels under beneficial conditions. Our findings provide molecular insights into the regulation of SL homeostasis and catabolism under stress conditions.


  • Organizational Affiliation
    • KAUST Center of Excellence for Smart Health, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Macromolecule Content 

  • Total Structure Weight: 71.67 kDa 
  • Atom Count: 4,870 
  • Modeled Residue Count: 619 
  • Deposited Residue Count: 642 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Strigolactones hydrolase CXE15
A, B
321Arabidopsis thalianaMutation(s): 0 
Gene Names: CXE15At5g06570F15M7.10
EC: 3.1.1
UniProt
Find proteins for Q9FG13 (Arabidopsis thaliana)
Explore Q9FG13 
Go to UniProtKB:  Q9FG13
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FG13
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free:  0.284 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.399α = 90
b = 99.399β = 90
c = 114.161γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSaudi ArabiaKing Abdullah University of Science and Technology

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 2.0: 2025-12-03
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary