4OU8

Crystal structure of apocarotenoid oxygenase in the presence of C8E6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Analysis of Carotenoid Isomerase Activity in a Prototypical Carotenoid Cleavage Enzyme, Apocarotenoid Oxygenase (ACO).

Sui, X.Kiser, P.D.Che, T.Carey, P.R.Golczak, M.Shi, W.von Lintig, J.Palczewski, K.

(2014) J Biol Chem 289: 12286-12299

  • DOI: https://doi.org/10.1074/jbc.M114.552836
  • Primary Citation of Related Structures:  
    4OU8, 4OU9

  • PubMed Abstract: 

    Carotenoid cleavage enzymes (CCEs) constitute a group of evolutionarily related proteins that metabolize a variety of carotenoid and non-carotenoid substrates. Typically, these enzymes utilize a non-heme iron center to oxidatively cleave a carbon-carbon double bond of a carotenoid substrate. Some members also isomerize specific double bonds in their substrates to yield cis-apocarotenoid products. The apocarotenoid oxygenase from Synechocystis has been hypothesized to represent one such member of this latter category of CCEs. Here, we developed a novel expression and purification protocol that enabled production of soluble, native ACO in quantities sufficient for high resolution structural and spectroscopic investigation of its catalytic mechanism. High performance liquid chromatography and Raman spectroscopy revealed that ACO exclusively formed all-trans products. We also found that linear polyoxyethylene detergents previously used for ACO crystallization strongly inhibited the apocarotenoid oxygenase activity of the enzyme. We crystallized the native enzyme in the absence of apocarotenoid substrate and found electron density in the active site that was similar in appearance to the density previously attributed to a di-cis-apocarotenoid intermediate. Our results clearly demonstrated that ACO is in fact a non-isomerizing member of the CCE family. These results indicate that careful selection of detergent is critical for the success of structural studies aimed at elucidating structures of CCE-carotenoid/retinoid complexes.


  • Organizational Affiliation

    From the Departments of Pharmacology and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apocarotenoid-15,15'-oxygenase
A, B, C, D
490Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: diox1sll1541
EC: 1.13.11.75
UniProt
Find proteins for P74334 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P74334 
Go to UniProtKB:  P74334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74334
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.561α = 90
b = 125.122β = 90
c = 203.012γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-02
    Changes: Database references
  • Version 1.2: 2014-05-21
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description