2B5H

1.5 A Resolution Crystal Structure of Recombinant R. Norvegicus Cysteine Dioxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Mammalian Cysteine Dioxygenase: A NOVEL MONONUCLEAR IRON CENTER FOR CYSTEINE THIOL OXIDATION.

Simmons, C.R.Liu, Q.Huang, Q.Hao, Q.Begley, T.P.Karplus, P.A.Stipanuk, M.H.

(2006) J.Biol.Chem. 281: 18723-18733

  • DOI: 10.1074/jbc.M601555200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cysteine dioxygenase is a mononuclear iron-dependent enzyme responsible for the oxidation of cysteine with molecular oxygen to form cysteine sulfinate. This reaction commits cysteine to either catabolism to sulfate and pyruvate or the taurine biosynt ...

    Cysteine dioxygenase is a mononuclear iron-dependent enzyme responsible for the oxidation of cysteine with molecular oxygen to form cysteine sulfinate. This reaction commits cysteine to either catabolism to sulfate and pyruvate or the taurine biosynthetic pathway. Cysteine dioxygenase is a member of the cupin superfamily of proteins. The crystal structure of recombinant rat cysteine dioxygenase has been determined to 1.5-A resolution, and these results confirm the canonical cupin beta-sandwich fold and the rare cysteinyltyrosine intramolecular cross-link (between Cys(93) and Tyr(157)) seen in the recently reported murine cysteine dioxygenase structure. In contrast to the catalytically inactive mononuclear Ni(II) metallocenter present in the murine structure, crystallization of a catalytically competent preparation of rat cysteine dioxygenase revealed a novel tetrahedrally coordinated mononuclear iron center involving three histidines (His(86), His(88), and His(140)) and a water molecule. Attempts to acquire a structure with bound ligand using either cocrystallization or soaking crystals with cysteine revealed the formation of a mixed disulfide involving Cys(164) near the active site, which may explain previously observed substrate inhibition. This work provides a framework for understanding the molecular mechanisms involved in thiol dioxygenation and sets the stage for exploration of the chemistry of both the novel mononuclear iron center and the catalytic role of the cysteinyl-tyrosine linkage.


    Organizational Affiliation

    Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine dioxygenase type I
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.553α = 90.00
b = 57.553β = 90.00
c = 123.070γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-07-24
    Type: Data collection, Refinement description