2FON

X-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycopersicon esculentum (tomato)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.212 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure determination and analysis of acyl-CoA oxidase (ACX1) from tomato.

Powers, R.A.Rife, C.L.Schilmiller, A.L.Howe, G.A.Garavito, R.M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 683-686

  • DOI: https://doi.org/10.1107/S0907444906014107
  • Primary Citation of Related Structures:  
    2FON

  • PubMed Abstract: 

    The flavoenzyme acyl-CoA oxidase (ACX) catalyzes the first committed step in beta-oxidation and is required for the biosynthesis of jasmonic acid, a signaling molecule involved in plant defense. Recently, a mutant in tomato was identified that is deficient in jasmonic acid production and compromised in its wound response. This results from a single point mutation in acx1, which causes the conserved residue Thr138 to be substituted by isoleucine. To understand the structural basis for this mutation, the crystal structure of LeACX1 was determined to 2.74 Angstrom resolution by molecular replacement. Unexpectedly, an unusual packing arrangement was observed in which three monomers of LeACX1 are present in the asymmetric unit. Although the tertiary structure of LeACX1 is essentially similar to the previously determined structures of ACX enzymes, the packing within the unit cells is distinctly different.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
peroxisomal acyl-CoA oxidase 1A
A, B, C
683Solanum lycopersicumMutation(s): 0 
Gene Names: ACX1A
EC: 1.3.3.6
UniProt
Find proteins for Q5D8D3 (Solanum lycopersicum)
Explore Q5D8D3 
Go to UniProtKB:  Q5D8D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5D8D3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.2α = 90
b = 240.33β = 90
c = 89.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations