2DDH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.(Tokyo) 139: 789-795

  • DOI: 10.1093/jb/mvj088

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acyl-CoA oxidase
A
661Rattus norvegicusMutation(s): 0 
Gene Names: Acox1 (Acox)
EC: 1.3.3.6
Find proteins for P07872 (Rattus norvegicus)
Go to UniProtKB:  P07872
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HXD
Query on HXD

Download SDF File 
Download CCD File 
A
(3R)-3-HYDROXYDODECANOIC ACID
3-OH-DODECANOATE
C12 H24 O3
MUCMKTPAZLSKTL-LLVKDONJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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 = 85.500α = 90.00
b = 103.200β = 90.00
c = 161.900γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance