4IET

Cys-persulfenate bound Cysteine Dioxygenase at pH 6.8 in the presence of Cys


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cysteine dioxygenase structures from pH4 to 9: consistent cys-persulfenate formation at intermediate pH and a Cys-bound enzyme at higher pH.

Driggers, C.M.Cooley, R.B.Sankaran, B.Hirschberger, L.L.Stipanuk, M.H.Karplus, P.A.

(2013) J.Mol.Biol. 425: 3121-3136

  • DOI: 10.1016/j.jmb.2013.05.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mammalian cysteine dioxygenase (CDO) is a mononuclear non-heme iron protein that catalyzes the conversion of cysteine (Cys) to cysteine sulfinic acid by an unclarified mechanism. One structural study revealed that a Cys-persulfenate (or Cys-persulfen ...

    Mammalian cysteine dioxygenase (CDO) is a mononuclear non-heme iron protein that catalyzes the conversion of cysteine (Cys) to cysteine sulfinic acid by an unclarified mechanism. One structural study revealed that a Cys-persulfenate (or Cys-persulfenic acid) formed in the active site, but quantum mechanical calculations have been used to support arguments that it is not an energetically feasible reaction intermediate. Here, we report a series of high-resolution structures of CDO soaked with Cys at pH values from 4 to 9. Cys binding is minimal at pH≤5 and persulfenate formation is consistently seen at pH values between 5.5 and 7. Also, a structure determined using laboratory-based X-ray diffraction shows that the persulfenate, with an apparent average O-O separation distance of ~1.8Å, is not an artifact of synchrotron radiation. At pH≥8, the active-site iron shifts from 4- to 5-coordinate, and Cys soaks reveal a complex with Cys, but no dioxygen, bound. This 'Cys-only' complex differs in detail from a previously published 'Cys-only' complex, which we reevaluate and conclude is not reliable. The high-resolution structures presented here do not resolve the CDO mechanism but do imply that an iron-bound persulfenate (or persulfenic acid) is energetically accessible in the CDO active site, and that CDO active-site chemistry in the crystals is influenced by protonation/deprotonation events with effective pKa values near ~5.5 and ~7.5 that influence Cys binding and oxygen binding/reactivity, respectively. Furthermore, this work provides reliable ligand-bound models for guiding future mechanistic considerations.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, 2011 Ag and Life Sciences Building, Oregon State University, Corvallis, OR 97331, 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.153 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.600α = 90.00
b = 57.600β = 90.00
c = 122.400γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
PHENIXphasing
ADSCdata collection
PHENIXmodel building
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2013-09-11
    Type: Database references
  • Version 1.3: 2015-06-24
    Type: Data collection