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PDBsum entry 3dc5

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3dc5
Jmol
Contents
Protein chains
194 a.a. *
Ligands
MLI
Metals
_MN ×2
Waters ×420
* Residue conservation analysis
PDB id:
3dc5
Name: Oxidoreductase
Title: Crystal structure of a manganese superoxide dismutases from caenorhabditis elegans
Structure: Superoxide dismutase [mn] 2. Chain: a, c. Engineered: yes
Source: Caenorhabditis elegans. Nematode. Organism_taxid: 6239. Gene: sod-3, c08a9.1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.70Å     R-factor:   0.191     R-free:   0.226
Authors: C.H.Trinh,T.Hunter,E.E.Stewart,S.E.V.Phillips,G.J.Hunter
Key ref: C.H.Trinh et al. (2008). Purification, crystallization and X-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans. Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1110-1114. PubMed id: 19052361
Date:
03-Jun-08     Release date:   09-Jun-09    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P41977  (SODM2_CAEEL) -  Superoxide dismutase [Mn] 2, mitochondrial
Seq:
Struc:
218 a.a.
194 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.15.1.1  - Superoxide dismutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 superoxide + 2 H+ = O2 + H2O2
2 × superoxide
+ 2 × H(+)
= O(2)
+ H(2)O(2)
      Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     superoxide dismutase activity     2 terms  

 

 
    Added reference    
 
 
Acta Crystallogr Sect F Struct Biol Cryst Commun 64:1110-1114 (2008)
PubMed id: 19052361  
 
 
Purification, crystallization and X-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans.
C.H.Trinh, T.Hunter, E.E.Stewart, S.E.Phillips, G.J.Hunter.
 
  ABSTRACT  
 
Caenorhabditis elegans expresses two manganese superoxide dismutase enzymes (MnSOD-2 and MnSOD-3) that are targeted to the mitochondrion. MnSOD-2 is constitutively expressed, while synthesis of MnSOD-3 is inducible. The structures of these two mononuclear metalloenzymes have been determined to 1.8 and 1.7 A resolution, respectively. Pink crystals formed in space group P4(1)2(1)2 for each, with unit-cell parameters a = b = 81.0, c = 137.4 A for MnSOD-2 and a = b = 81.8, c = 136.0 A for MnSOD-3. The final structure of MnSOD-3 was refined to R = 21.6% and R(free) = 26.2% at 293 K, and R = 18.9% and R(free) = 22.6% at 100 K, while that of MnSOD-2 was refined to R = 16.9% and R(free) = 20.1% at 100 K. The asymmetric unit cell is comprised of two subunits. The resulting structures are very similar to that of human MnSOD and form a tetramer corresponding to a dimer of dimers. The subunit interface between dimers is comprised of two four-helix bundles that stabilize the biologically significant homotetramer.