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PDBsum entry 3esf

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
3esf
Jmol
Contents
Protein chains
197 a.a. *
Metals
_FE ×4
Waters ×706
* Residue conservation analysis
PDB id:
3esf
Name: Oxidoreductase
Title: Crystal structure of the enzyme fe-superoxide dismutase tbso trypanosoma brucei
Structure: Iron-containing superoxide dismutase b2. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Trypanosoma brucei. Organism_taxid: 5691. Gene: sodb2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.01Å     R-factor:   0.177     R-free:   0.219
Authors: J.F.R.Bachega,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
Date:
05-Oct-08     Release date:   12-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q2KN30  (Q2KN30_9TRYP) -  Superoxide dismutase
Seq:
Struc:
208 a.a.
197 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: Iron or manganese or (zinc and copper)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  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.
 
  ABSTRACT  
 
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.