Structure of L509V CAO1 - growth condition 1

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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Evidence for distinct rate-limiting steps in the cleavage of alkenes by carotenoid cleavage dioxygenases.

Khadka, N.Farquhar, E.R.Hill, H.E.Shi, W.von Lintig, J.Kiser, P.D.

(2019) J Biol Chem 294: 10596-10606

  • DOI: https://doi.org/10.1074/jbc.RA119.007535
  • Primary Citation of Related Structures:  
    6N1Y, 6N20, 6N21

  • PubMed Abstract: 

    Carotenoid cleavage dioxygenases (CCDs) use a nonheme Fe(II) cofactor to split alkene bonds of carotenoid and stilbenoid substrates. The iron centers of CCDs are typically five-coordinate in their resting states, with solvent occupying an exchangeable site. The involvement of this iron-bound solvent in CCD catalysis has not been experimentally addressed, but computational studies suggest two possible roles. 1) Solvent dissociation provides a coordination site for O 2 , or 2) solvent remains bound to iron but changes its equilibrium position to allow O 2 binding and potentially acts as a proton source. To test these predictions, we investigated isotope effects (H 2 O versus D 2 O) on two stilbenoid-cleaving CCDs, Novosphingobium aromaticivorans oxygenase 2 (NOV2) and Neurospora crassa carotenoid oxygenase 1 (CAO1), using piceatannol as a substrate. NOV2 exhibited an inverse isotope effect ( k H / k D ∼ 0.6) in an air-saturated buffer, suggesting that solvent dissociates from iron during the catalytic cycle. By contrast, CAO1 displayed a normal isotope effect ( k H / k D ∼ 1.7), suggesting proton transfer in the rate-limiting step. X-ray absorption spectroscopy on NOV2 and CAO1 indicated that the protonation states of the iron ligands are unchanged within pH 6.5-8.5 and that the Fe(II)-aquo bond is minimally altered by substrate binding. We pinpointed the origin of the differential kinetic behaviors of NOV2 and CAO1 to a single amino acid difference near the solvent-binding site of iron, and X-ray crystallography revealed that the substitution alters binding of diffusible ligands to the iron center. We conclude that solvent-iron dissociation and proton transfer are both associated with the CCD catalytic mechanism.

  • Organizational Affiliation

    Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carotenoid oxygenase
A, B, C, D
526Neurospora crassaMutation(s): 1 
Gene Names: GE21DRAFT_6499
Find proteins for A0A0B0DIC8 (Neurospora crassa)
Explore A0A0B0DIC8 
Go to UniProtKB:  A0A0B0DIC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B0DIC8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.21α = 90
b = 101.21β = 90
c = 450.18γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description