Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 196971.58 
• Atom Count: 13070 
• Residue Count: 1744 
• Unique protein chains: 1

2IX5

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

• DOI: 10.2210/pdb2IX5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2006-07-07 Released: 2006-08-08 
• Deposition Author(s): Mackenzie, J., Pedersen, L., Arent, S., Henriksen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.232 
• R-Value Work: 0.186 

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

• PubMed: 16887802 
• DOI: 10.1074/jbc.M603405200
• Primary Citation of Related Structures:  
  2IX6


• 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. 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.

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Related Citations: 

• 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
• Expression, Purification and Crystallization of Two Peroxisomal Acyl-Coa Oxidases from Arabidopsis Thaliana
  Pedersen, L.,Henriksen, A.
  (2004) Acta Crystallogr., Sect.D 60: 1125




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ACYL-COENZYME A OXIDASE 4, PEROXISOMAL	A, B, C, D	436	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ACX4 (G6) EC: 1.3.3.6
Find proteins for Q96329 (Arabidopsis thaliana) Go to UniProtKB:  Q96329

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CAA	A, B, C, D	ACETOACETYL-COENZYME A C25 H40 N7 O18 P3 S OJFDKHTZOUZBOS-CITAKDKDSA-N
FAD	A, B, C, D	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.232 
• R-Value Work: 0.186 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 144.747	α = 90.00
b = 144.747	β = 90.00
c = 149.208	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-07 
• Released Date: 2006-08-08 
• Deposition Author(s): Mackenzie, J., Pedersen, L., Arent, S., Henriksen, A.

Revision History 

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