3ELN

A Putative Fe2+-bound Persulfenate Intermediate in Cysteine Dioxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/bi801546n

  • 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 e ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine dioxygenase type 1
A
200Rattus norvegicusMutation(s): 0 
Gene Names: Cdo1
EC: 1.13.11.20
Find proteins for P21816 (Rattus norvegicus)
Go to UniProtKB:  P21816
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2CO
Query on 2CO

Download SDF File 
Download CCD File 
A
S-HYDROPEROXYCYSTEINE
C3 H7 N O4 S
BXTMIEGCNKHUKA-REOHCLBHSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 57.523α = 90.00
b = 57.523β = 90.00
c = 122.190γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
CNSrefinement
CNSphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2019-07-24
    Type: Data collection, Refinement description