2IX5

Short chain specific acyl-CoA oxidase from Arabidopsis thaliana, ACX4 in complex with acetoacetyl-CoA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Controlling Electron Transfer in Acyl-Coa Oxidases and Dehydrogenases: A Structural View.

Mackenzie, J., Pedersen, L., Arent, S., Henriksen, A.

(2006) J Biol Chem 281: 31012

  • DOI: 10.1074/jbc.M603405200
  • Primary Citation of Related Structures:  
    2IX6, 2IX5

  • PubMed Abstract: 

    • Plants produce a unique peroxisomal short chain-specific acyl-CoA oxidase (ACX4) for beta-oxidation of lipids. The short chain-specific oxidase has little resemblance to other peroxisomal acyl-CoA oxidases but has an approximately 30% sequence identity to mitochondrial acyl-CoA dehydrogenases ...

    Plants produce a unique peroxisomal short chain-specific acyl-CoA oxidase (ACX4) for beta-oxidation of lipids. The short chain-specific oxidase has little resemblance to other peroxisomal acyl-CoA oxidases but has an approximately 30% sequence identity to mitochondrial acyl-CoA dehydrogenases. Two biochemical features have been linked to structural properties by comparing the structures of short chain-specific Arabidopsis thaliana ACX4 with and without a substrate analogue bound in the active site to known acyl-CoA oxidases and dehydrogenase structures: (i) a solvent-accessible acyl binding pocket is not required for oxygen reactivity, and (ii) the oligomeric state plays a role in substrate pocket architecture but is not linked to oxygen reactivity. The structures indicate that the acyl-CoA oxidases may encapsulate the electrons for transfer to molecular oxygen by blocking the dehydrogenase substrate interaction site with structural extensions. A small binding pocket observed adjoining the flavin adenine dinucleotide N5 and C4a atoms could increase the number of productive encounters between flavin adenine dinucleotide and O2.

    Related Citations: 
    • Expression, Purification and Crystallization of Two Peroxisomal Acyl-Coa Oxidases from Arabidopsis Thaliana
      Pedersen, L., Henriksen, A.
      (2004) Acta Crystallogr D Biol Crystallogr 60: 1125
    • Arabidopsis Mutants in Short- and Medium-Chain Acyl-Coa Oxidase Activities Accumulate Acyl-Coas and Reveal that Fatty Acid Beta-Oxidation is Essential for Embryo Development
      Rylott, E.L., Rogers, C.A., Gilday, A.D., Edgell, T., Larson, T.R., Graham, I.A.
      (2003) J Biol Chem 278: 21370
    Organizational Affiliation: 

    Biostructure Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACYL-COENZYME A OXIDASE 4, PEROXISOMALA, B, C, D436Arabidopsis thalianaMutation(s): 0 
Gene Names: ACX4, G6, At3g51840, ATEM1.9
EC: 1.3.3.6
UniProt
Find proteins for Q96329 (Arabidopsis thaliana)
Explore Q96329 
Go to UniProtKB:  Q96329
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.747α = 90
b = 144.747β = 90
c = 149.208γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-17
    Changes: Data collection