A Putative Fe2+-bound Persulfenate Intermediate in Cysteine Dioxygenase

Experimental Data Snapshot

  • Resolution: 1.42 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.135 

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A putative Fe2+-bound persulfenate intermediate in cysteine dioxygenase.

Simmons, C.R.Krishnamoorthy, K.Granett, S.L.Schuller, D.J.Dominy, J.E.Begley, T.P.Stipanuk, M.H.Karplus, P.A.

(2008) Biochemistry 47: 11390-11392

  • DOI: https://doi.org/10.1021/bi801546n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The common reactions of dioxygen, superoxide, and hydroperoxides with thiolates are thought to proceed via persulfenate intermediates, yet these have never been visualized. Here we report a 1.4 A resolution crystal structure of the Fe(2+)-dependent enzyme cysteine dioxygenase (CDO) containing this putative intermediate trapped in its active site pocket. The complex raises the possibility that, distinct from known dioxygenases and proposed CDO mechanisms, the Fe-proximal oxygen atom may be involved in the primary oxidation event yielding a unique three-membered Fe-S-O cyclic intermediate. A nonpolar environment of the distal oxygen would facilitate isomerization of the persulfenate to the sulfinate product.

  • Organizational Affiliation

    Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine dioxygenase type 1200Rattus norvegicusMutation(s): 0 
Gene Names: Cdo1
Find proteins for P21816 (Rattus norvegicus)
Explore P21816 
Go to UniProtKB:  P21816
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21816
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.523α = 90
b = 57.523β = 90
c = 122.19γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations