4KWL

Rat cysteine dioxygenase with 3-mercaptopropionic acid persulfide bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanistic implications of persulfenate and persulfide binding in the active site of cysteine dioxygenase.

Souness, R.J.Kleffmann, T.Tchesnokov, E.P.Wilbanks, S.M.Jameson, G.B.Jameson, G.N.

(2013) Biochemistry 52: 7606-7617

  • DOI: https://doi.org/10.1021/bi400661a
  • Primary Citation of Related Structures:  
    4KWJ, 4KWK, 4KWL

  • PubMed Abstract: 

    Describing the organization of substrates and substrate analogues in the active site of cysteine dioxygenase identifies potential intermediates in this critical yet poorly understood reaction, the oxidation of cysteine to cysteine sulfinic acid. The fortuitous formation of persulfides under crystallization conditions has allowed their binding in the active site of cysteine dioxygenase to be studied. The crystal structures of cysteine persulfide and 3-mercaptopropionic acid persulfide bound to iron(II) in the active site show that binding of the persulfide occurs via the distal sulfide and, in the case of the cysteine persulfide, the amine also binds. Persulfide was detected by mass spectrometry in both the crystal and the drop, suggesting its origin is chemical rather than enzymatic. A mechanism involving the formation of the relevant disulfide from sulfide produced by hydrolysis of dithionite is proposed. In comparison, persulfenate {observed bound to cysteine dioxygenase [Simmons, C. R., et al. (2008) Biochemistry 47, 11390]} is shown through mass spectrometry to occur only in the crystal and not in the surrounding drop, suggesting that in the crystalline state the persulfenate does not lie on the reaction pathway. Stabilization of both the persulfenate and the persulfides does, however, suggest the position in which dioxygen binds during catalysis.


  • Organizational Affiliation

    Department of Chemistry and MacDiarmid Institute for Advanced Materials and Nanotechnology and ‡Department of Biochemistry, University of Otago , P.O. Box 56, Dunedin 9054, New Zealand.


Macromolecules
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
EC: 1.13.11.20
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3SS
Query on 3SS

Download Ideal Coordinates CCD File 
C [auth A]3-disulfanylpropanoic acid
C3 H6 O2 S2
CXXDUKKBFUFJDF-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.56α = 90
b = 57.56β = 90
c = 122γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description