3RN4

Crystal structure of iron-substituted Sod2 from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of native and Fe-substituted SOD2 from Saccharomyces cerevisiae

Kang, Y.He, Y.-X.Zhao, M.-X.Li, W.-F.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1173-1178

  • DOI: 10.1107/S1744309111029186
  • Primary Citation of Related Structures:  
    3BFR, 3RN4

  • PubMed Abstract: 
  • The manganese-specific superoxide dismutase SOD2 from the yeast Saccharomyces cerevisiae is a protein that resides in the mitochondrion and protects it against attack by superoxide radicals. However, a high iron concentration in the mitochondria resu ...

    The manganese-specific superoxide dismutase SOD2 from the yeast Saccharomyces cerevisiae is a protein that resides in the mitochondrion and protects it against attack by superoxide radicals. However, a high iron concentration in the mitochondria results in iron misincorporation at the active site, with subsequent inactivation of SOD2. Here, the crystal structures of SOD2 bound with the native metal manganese and with the `wrong' metal iron are presented at 2.05 and 1.79 Å resolution, respectively. Structural comparison of the two structures shows no significant conformational alteration in the overall structure or in the active site upon binding the non-native metal iron. Moreover, residues Asp163 and Lys80 are proposed to potentially be responsible for the metal specificity of the Mn-specific SOD. Additionally, the surface-potential distribution of SOD2 revealed a conserved positively charged electrostatic zone in the proximity of the active site that probably functions in the same way as in Cu/Zn-SODs by facilitating the diffusion of the superoxide anion to the metal ion.


    Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Superoxide dismutase [Mn], mitochondrialA215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SOD2YHR008C
EC: 1.15.1.1
Find proteins for P00447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00447 
Go to UniProtKB:  P00447
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.69α = 90
b = 92.69β = 90
c = 92.69γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references