8VCA

Crystal Structure of plant Carboxylesterase 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into strigolactone catabolism by carboxylesterases reveal a conserved conformational regulation.

Palayam, M.Yan, L.Nagalakshmi, U.Gilio, A.K.Cornu, D.Boyer, F.D.Dinesh-Kumar, S.P.Shabek, N.

(2024) Nat Commun 15: 6500-6500

  • DOI: https://doi.org/10.1038/s41467-024-50928-3
  • Primary Citation of Related Structures:  
    8VCA, 8VCD, 8VCE

  • PubMed Abstract: 

    Phytohormone levels are regulated through specialized enzymes, participating not only in their biosynthesis but also in post-signaling processes for signal inactivation and cue depletion. Arabidopsis thaliana (At) carboxylesterase 15 (CXE15) and carboxylesterase 20 (CXE20) have been shown to deplete strigolactones (SLs) that coordinate various growth and developmental processes and function as signaling molecules in the rhizosphere. Here, we elucidate the X-ray crystal structures of AtCXE15 (both apo and SL intermediate bound) and AtCXE20, revealing insights into the mechanisms of SL binding and catabolism. The N-terminal regions of CXE15 and CXE20 exhibit distinct secondary structures, with CXE15 characterized by an alpha helix and CXE20 by an alpha/beta fold. These structural differences play pivotal roles in regulating variable SL hydrolysis rates. Our findings, both in vitro and in planta, indicate that a transition of the N-terminal helix domain of CXE15 between open and closed forms facilitates robust SL hydrolysis. The results not only illuminate the distinctive process of phytohormone breakdown but also uncover a molecular architecture and mode of plasticity within a specific class of carboxylesterases.


  • Organizational Affiliation

    Department of Plant Biology, College of Biological Sciences, University of California-Davis, Davis, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxylesterase 15329Arabidopsis 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: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.915α = 90
b = 83.915β = 90
c = 117.177γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2047396
National Science Foundation (NSF, United States)United States2139805
Department of Energy (DOE, United States)United StatesDE-SC0023158

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Database references