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PDBsum entry 2ix5

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2ix5
Jmol
Contents
Protein chains
416 a.a. *
Ligands
CAA ×4
FAD ×4
Waters ×164
* Residue conservation analysis
PDB id:
2ix5
Name: Oxidoreductase
Title: Short chain specific acyl-coa oxidase from arabidopsis thaliana, acx4 in complex with acetoacetyl-coa
Structure: Acyl-coenzyme a oxidase 4, peroxisomal. Chain: a, b, c, d. Synonym: acyl-coa oxidase, aox 4, short- chain acyl-coa oxi saox, atcx4, g6p, atg6. Engineered: yes
Source: Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: arabidopsis biological resource center
Biol. unit: Tetramer (from PDB file)
Resolution:
2.70Å     R-factor:   0.189     R-free:   0.232
Authors: J.Mackenzie,L.Pedersen,S.Arent,A.Henriksen
Key ref:
J.Mackenzie et al. (2006). Controlling electron transfer in Acyl-CoA oxidases and dehydrogenases: a structural view. J Biol Chem, 281, 31012-31020. PubMed id: 16887802 DOI: 10.1074/jbc.M603405200
Date:
07-Jul-06     Release date:   08-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q96329  (ACOX4_ARATH) -  Acyl-coenzyme A oxidase 4, peroxisomal
Seq:
Struc:
436 a.a.
416 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.3.3.6  - Acyl-CoA oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acyl-CoA + O2 = trans-2,3-dehydroacyl-CoA + H2O2
Acyl-CoA
Bound ligand (Het Group name = CAA)
matches with 94.12% similarity
+ O(2)
= trans-2,3-dehydroacyl-CoA
+ H(2)O(2)
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   3 terms 
  Biological process     metabolic process   13 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M603405200 J Biol Chem 281:31012-31020 (2006)
PubMed id: 16887802  
 
 
Controlling electron transfer in Acyl-CoA oxidases and dehydrogenases: a structural view.
J.Mackenzie, L.Pedersen, S.Arent, A.Henriksen.
 
  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.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. The role of the N-and C-terminal tails of ACX4 in burying the FAD cofactor. The N terminus of subunit B (green) and the C terminus of subunit C (tan) are made transparent to show how they enclose the FAD cofactor.
Figure 3.
FIGURE 3. Superposition of A. thaliana ACX1 (green and gray) and ACX4 (beige and black) dimer. The N-terminal extension of ACX4 (red) covering the electron transfer flavoproteins docking area of ACDs is superposable on the C terminus of ACX1 (orange).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 31012-31020) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18444898 I.A.Graham (2008).
Seed storage oil mobilization.
  Annu Rev Plant Biol, 59, 115-142.  
17277896 B.K.Zolman, M.Nyberg, and B.Bartel (2007).
IBR3, a novel peroxisomal acyl-CoA dehydrogenase-like protein required for indole-3-butyric acid response.
  Plant Mol Biol, 64, 59-72.  
17994768 P.F.Fitzpatrick, D.M.Bozinovski, A.Héroux, P.G.Shaw, M.P.Valley, and A.M.Orville (2007).
Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase.
  Biochemistry, 46, 13800-13808.
PDB codes: 2reh 2zaf
17434787 S.Goepfert, and Y.Poirier (2007).
Beta-oxidation in fatty acid degradation and beyond.
  Curr Opin Plant Biol, 10, 245-251.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.