Crystal Structure of Acyl-CoA oxidase complexed with 3-OH-dodecanoate

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 

Starting Model: experimental
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Three-Dimensional Structure of Rat-Liver Acyl-CoA Oxidase in Complex with a Fatty Acid: Insights into Substrate-Recognition and Reactivity toward Molecular Oxygen.

Tokuoka, K.Nakajima, Y.Hirotsu, K.Miyahara, I.Nishina, Y.Shiga, K.Tamaoki, H.Setoyama, C.Tojo, H.Miura, R.

(2006) J Biochem 139: 789-795

  • DOI: https://doi.org/10.1093/jb/mvj088
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The three-dimensional structure of rat-liver acyl-CoA oxidase-II (ACO-II) in a complex with a C12-fatty acid was solved by the molecular replacement method based on the uncomplexed ACO-II structure. The crystalline form of the complex was obtained by cocrystallization of ACO-II with dodecanoyl-CoA. The crystalline complex possessed, in the active-site crevice, only the fatty acid moiety that had been formed through hydrolysis of the thioester bond. The overall dimeric structure and the folding pattern of each subunit are essentially superimposable on those of uncomplexed ACO-II. The active site including the flavin ring of FAD, the crevice embracing the fatty acyl moiety, and adjacent amino acid side chains are superimposably conserved with the exception of Glu421, whose carboxylate group is tilted away to accommodate the fatty acid. One of the carboxyl oxygens of the bound fatty acid is hydrogen-bonded to the amide hydrogen of Glu421, the presumed catalytic base, and to the ribityl 2'-hydroxyl group of FAD. This hydrogen-bonding network correlates well with the substrate recognition/activation in acyl-CoA dehydrogenase. The binding mode of C12-fatty acid suggests that the active site does not close upon substrate binding, but remains spacious during the entire catalytic process, the oxygen accessibility in the oxidative half-reaction thereby being maintained.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi-ku, Osaka 558-8585.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-CoA oxidase661Rattus norvegicusMutation(s): 0 
Find proteins for P07872 (Rattus norvegicus)
Explore P07872 
Go to UniProtKB:  P07872
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07872
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C27 H33 N9 O15 P2
Query on HXD

Download Ideal Coordinates CCD File 
C12 H24 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.5α = 90
b = 103.2β = 90
c = 161.9γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description