Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 196.97 kDa 
• Atom Count: 13234 
• Modelled Residue Count: 1664 
• Deposited Residue Count: 1744 
• Unique protein chains: 1

2IX5

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

• PDB DOI: 10.2210/pdb2IX5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 2.70 Å
• R-Value Free: 0.232 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

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:  
  2IX5, 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: 

• 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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACYL-COENZYME A OXIDASE 4, PEROXISOMAL	A, B, C, D	436	Arabidopsis thaliana	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAA	E [auth A], G [auth B], I [auth C], K [auth D]	ACETOACETYL-COENZYME A C25 H40 N7 O18 P3 S OJFDKHTZOUZBOS-CITAKDKDSA-N
FAD	F [auth A], H [auth B], J [auth C], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

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 = 144.747	α = 90
b = 144.747	β = 90
c = 149.208	γ = 120

Software Package:

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

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
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-17
  Changes: Data collection