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PDBsum entry 1bs3

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1bs3
Jmol
Contents
Protein chains
201 a.a. *
Metals
__F ×2
_FE ×2
Waters ×478
* Residue conservation analysis
PDB id:
1bs3
Name: Oxidoreductase
Title: P.Shermanii sod(fe+3) fluoride
Structure: Superoxide dismutase. Chain: a, b. Synonym: sod. Other_details: competitively inhibited by flouride. Fluorid substrate binding site.
Source: Propionibacterium freudenreichii subsp shermanii. Organism_taxid: 1752. Strain: pz3. Atcc: german collection of microorganisms (dsm) 4902. Collection: german collection of microorganisms (dsm) 4902. Cellular_location: cytoplasm
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
1.55Å     R-factor:   0.174     R-free:   0.206
Authors: M.Schmidt
Key ref:
M.Schmidt (1999). Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH-value A crystallographic analysis. Eur J Biochem, 262, 117-127. PubMed id: 10231372 DOI: 10.1046/j.1432-1327.1999.00359.x
Date:
31-Aug-98     Release date:   15-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P80293  (SODM_PROFR) -  Superoxide dismutase [Mn/Fe]
Seq:
Struc:
201 a.a.
201 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   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1046/j.1432-1327.1999.00359.x Eur J Biochem 262:117-127 (1999)
PubMed id: 10231372  
 
 
Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH-value A crystallographic analysis.
M.Schmidt.
 
  ABSTRACT  
 
The structure of the Propionibacterium freudenreichii subspecies shermanii superoxide dismutase (SOD) was determined at various pH values. As a comparison, the structure of the fluoride coordinated SOD was solved. The SOD crystallizes at pH 6.1 in the space group C2221 with two subunits, A and B, in the asymmetric unit. An increase of the pH value changes the cell parameters slightly but not the symmetry of the crystals. The overall structure of the SOD remains a compact tetrameter and is comparable to that at pH 6.1 no matter whether the pH increases or fluoride is added. At values above pH 7.4, an additional hydroxide ion can bind to the active center. Its position is similar to the binding site of the fluoride. The coordination number changes from five to six if the pH increases or fluoride is added. The binding behavior of the hydroxide ion is different for subunit A and B. Structures at different pH-values are comparable with models derived by spectroscopic methods. The influence of temperature on the binding properties of the hydroxide ion was investigated using analysis of an X-ray structure solved at pH 8.1 and 140 K. Compared to the structure at room temperature, the structural changes are observable but remain small. The consequences of hydroxide binding to the iron are discussed.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. The active center of the fluoride coordinated SOD in subunit A. Electron density at Tyr35: 2F^obsF^calc contoured at 1.3 ; thick sticks show main conformation, thin sticks show conformation observed at pH 6.1 (as indicated); arrow, electron density not explained by the main conformation. Electron density at the fluoride ion: F^obsF^calc map contoured at 3.5 . Azi, position of the azide ion if added.
Figure 8.
Fig. 8. The active center in subunit A at pH 8.1, 140 K. Electron density at Tyr35: 2F^obsF^calc, contoured at 1.3 . Thick sticks, average conformation; thin sticks, pH 6.1 and pH 10 Tyr35 conformers. Electron density at the sixth coordinated molecule, 2F^obsF^calc and F^obsF^calc map contoured at 1.3 and 3.5 , respectively.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (1999, 262, 117-127) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20972560 H.Xiang, G.Pan, C.R.Vossbrinck, R.Zhang, J.Xu, T.Li, Z.Zhou, C.Lu, and Z.Xiang (2010).
A Tandem Duplication of Manganese Superoxide Dismutase in Nosema bombycis and Its Evolutionary Origins.
  J Mol Evol, 71, 401-414.  
17887751 A.Dey, F.E.Jenney, M.W.Adams, M.K.Johnson, K.O.Hodgson, B.Hedman, and E.I.Solomon (2007).
Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity.
  J Am Chem Soc, 129, 12418-12431.  
12839748 P.Leverrier, D.Dimova, V.Pichereau, Y.Auffray, P.Boyaval, and G.Jan (2003).
Susceptibility and adaptive response to bile salts in Propionibacterium freudenreichii: physiological and proteomic analysis.
  Appl Environ Microbiol, 69, 3809-3818.  
12586392 R.E.Marquis, S.A.Clock, and M.Mota-Meira (2003).
Fluoride and organic weak acids as modulators of microbial physiology.
  FEMS Microbiol Rev, 26, 493-510.  
10848964 S.Sugio, B.Y.Hiraoka, and F.Yamakura (2000).
Crystal structure of cambialistic superoxide dismutase from porphyromonas gingivalis.
  Eur J Biochem, 267, 3487-3495.
PDB code: 1qnn
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