3BFR

The crystal structure of Sod2 from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 67: 1173-1178

  • DOI: 10.1107/S1744309111029186
  • Primary Citation of Related Structures:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Superoxide dismutase [Mn]
A
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SOD2
EC: 1.15.1.1
Find proteins for P00447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SOD2
Go to UniProtKB:  P00447
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN3
Query on MN3

Download SDF File 
Download CCD File 
A
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • Space Group: P 2 3
Unit Cell:
Length (Å)Angle (°)
a = 92.740α = 90.00
b = 92.740β = 90.00
c = 92.740γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MAR345dtbdata collection
REFMACrefinement
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-23
    Type: Database references
  • Version 1.3: 2012-04-25
    Type: Database references