PDBsum entry 2goj

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
Jmol PyMol
Protein chains
196 a.a. *
FE2 ×2
Waters ×305
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: The crystal structure of the enzyme fe-superoxide dismutase plasmodium falciparum
Structure: Fe-superoxide dismutase. Chain: a, b. Engineered: yes
Source: Plasmodium falciparum. Organism_taxid: 137071. Strain: hb3. Gene: sod. Expressed in: escherichia coli k12. Expression_system_taxid: 83333.
2.00Å     R-factor:   0.158     R-free:   0.194
Authors: M.V.A.S.Navarro,R.C.Garratt
Key ref:
J.F.Bachega et al. (2009). Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity. Proteins, 77, 26-37. PubMed id: 19384994 DOI: 10.1002/prot.22412
13-Apr-06     Release date:   28-Aug-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q27740  (SODF_PLAFX) -  Superoxide dismutase [Fe]
198 a.a.
196 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  


    Added reference    
DOI no: 10.1002/prot.22412 Proteins 77:26-37 (2009)
PubMed id: 19384994  
Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity.
J.F.Bachega, M.V.Navarro, L.Bleicher, R.K.Bortoleto-Bugs, D.Dive, P.Hoffmann, E.Viscogliosi, R.C.Garratt.
Superoxide dismutases (SODs) are a crucial class of enzymes in the combat against intracellular free radical damage. They eliminate superoxide radicals by converting them into hydrogen peroxide and oxygen. In spite of their very different life cycles and infection strategies, the human parasites Plasmodium falciparum, Trypanosoma cruzi and Trypanosoma brucei are known to be sensitive to oxidative stress. Thus the parasite Fe-SODs have become attractive targets for novel drug development. Here we report the crystal structures of FeSODs from the trypanosomes T. brucei at 2.0 A and T. cruzi at 1.9 A resolution, and that from P. falciparum at a higher resolution (2.0 A) to that previously reported. The homodimeric enzymes are compared to the related human MnSOD with particular attention to structural aspects which are relevant for drug design. Although the structures possess a very similar overall fold, differences between the enzymes at the entrance to the channel which leads to the active site could be identified. These lead to a slightly broader and more positively charged cavity in the parasite enzymes. Furthermore, a statistical coupling analysis (SCA) for the whole Fe/MnSOD family reveals different patterns of residue coupling for Mn and Fe SODs, as well as for the dimeric and tetrameric states. In both cases, the statistically coupled residues lie adjacent to the conserved core surrounding the metal center and may be expected to be responsible for its fine tuning, leading to metal ion specificity.
  Selected figure(s)  
Figure 6.
Figure 6. SCA clusters mapped onto the three-dimensional structure of TbSODB2. The highly conserved core ( G 0.8 G[max]) is shown as a mesh. (a) Cluster 1 shows that most of the residues are located close to the dimer interface. Others, such as E56 which are statistically coupled to dimers, probably disfavour the formation of tetramers. (b) cluster 2 shows that the majority of the FeSOD associated residues lie adjacent to the conserved core where they are likely to play a role in fine-tuning the active site redox potential. (c) cluster 3 shows a similar phenomenon for the MnSOD associated residues. In (b) and (c) the active site metal and ligands are explicitly shown.
Figure 7.
Figure 7. Positions affected by polymorphism mapped onto the structure of PfSOD1, in all cases the affected positions lie distant to both the dimerization interface and the active site and its associated substrate channel.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 77, 26-37) copyright 2009.  
  Figures were selected by the author.