PDBsum entry 1sdy

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Oxidoreductase(superoxide acceptor) PDB id
Protein chains
153 a.a. *
_ZN ×4
_CU ×4
Waters ×513
* Residue conservation analysis
PDB id:
Name: Oxidoreductase(superoxide acceptor)
Title: Structure solution and molecular dynamics refinement of the yeast cu,zn enzyme superoxide dismutase
Structure: Copper,zinc superoxide dismutase. Chain: a, b, c, d. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Tetramer (from PQS)
2.50Å     R-factor:   0.158    
Authors: K.Djinovic,G.Gatti,A.Coda,L.Antolini,G.Pelosi,A.Desideri, M.Falconi,F.Marmocchi,G.Rotilio,M.Bolognesi
Key ref: K.Djinović et al. (1991). Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase. Acta Crystallogr B, 47, 918-927. PubMed id: 1772629
14-Jun-91     Release date:   31-Jan-94    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00445  (SODC_YEAST) -  Superoxide dismutase [Cu-Zn]
154 a.a.
153 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   5 terms 
  Biological process     positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress   11 terms 
  Biochemical function     antioxidant activity     5 terms  


    Added reference    
Acta Crystallogr B 47:918-927 (1991)
PubMed id: 1772629  
Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase.
K.Djinović, G.Gatti, A.Coda, L.Antolini, G.Pelosi, A.Desideri, M.Falconi, F.Marmocchi, G.Rolilio, M.Bolognesi.
Cu,Zn yeast superoxide dismutase was crystallized from polyethylene glycol solutions. The crystals belong to the P2(1)2(1)2 space group, with cell dimensions a = 105.3, b = 143.0, c = 62.1 A; two dimers of Mr = 32,000 each are contained in the asymmetric unit. Diffraction data at 2.5 A resolution were collected with the image-plate system at the EMBL synchrotron radiation facility in Hamburg. The structure was determined by molecular replacement using as a search model the 'blue-green' dimer of the bovine Cu,Zn superoxide dismutase. The crystallographic refinement of the molecular replacement solution was performed by means of molecular dynamics techniques and resulted in an R factor of 0.268 for the data between 6.0 and 2.5 A. The model was subsequently subjected to conventional restrained crystallographic refinement of the coordinates and temperature factors. The current R value for the data between 6.0 and 2.5 A is 0.220. Owing to the large radius of convergence of the molecular dynamics-crystallographic refinement, the convergence of the refinement process was reached after 18.1 ps of simulation time. The geometry of the active site of the enzyme appears essentially preserved compared with the bovine superoxide dismutase. The beta-barrel structure in the yeast enzyme is closed at the upper part by an efficient hydrogen-bonding scheme.

Literature references that cite this PDB file's key reference

  PubMed id Reference
11952792 L.Banci, I.Bertini, F.Cramaro, R.Del Conte, and M.S.Viezzoli (2002).
The solution structure of reduced dimeric copper zinc superoxide dismutase. The structural effects of dimerization.
  Eur J Biochem, 269, 1905-1915.
PDB code: 1l3n
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