PDBsum entry 1oal

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protein metals links
Oxidoreductase PDB id
Jmol PyMol
Protein chain
151 a.a. *
Waters ×100
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Active site copper and zinc ions modulate the quaternary structure of prokaryotic cu,zn superoxide dismutase
Structure: Superoxide dismutase. Chain: a. Engineered: yes. Mutation: yes
Source: Photobacterium leiognathi. Organism_taxid: 658. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
1.5Å     R-factor:   0.159     R-free:   0.194
Authors: P.Cioni,A.Pesce,B.M.D.Rocca,L.Castellifalconiparrilli, M.Bolognesi,G.Strambini,A.Desideri
Key ref:
P.Cioni et al. (2003). Active-site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase. J Mol Biol, 326, 1351-1360. PubMed id: 12595249 DOI: 10.1016/S0022-2836(03)00047-0
15-Jan-03     Release date:   27-Feb-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00446  (SODC_PHOLE) -  Superoxide dismutase [Cu-Zn]
173 a.a.
151 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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     periplasmic space   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     antioxidant activity     4 terms  


    Added reference    
DOI no: 10.1016/S0022-2836(03)00047-0 J Mol Biol 326:1351-1360 (2003)
PubMed id: 12595249  
Active-site copper and zinc ions modulate the quaternary structure of prokaryotic Cu,Zn superoxide dismutase.
P.Cioni, A.Pesce, B.Morozzo della Rocca, S.Castelli, M.Falconi, L.Parrilli, M.Bolognesi, G.Strambini, A.Desideri.
The influence of the constitutive metal ions on the equilibrium properties of dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase has been studied for the wild-type and for two mutant protein forms bearing a negative charge in the amino acid clusters at the dimer association interface. Depletion of copper and zinc dissociates the two mutant proteins into monomers, which reassemble toward the dimeric state upon addition of stoichiometric amounts of zinc. Pressure-dependent dissociation is observed for the copper-depleted wild-type and mutated enzymes, as monitored by the fluorescence shift of a unique tryptophan residue located at the subunit association interface. The spectral shift occurs slowly, reaching a plateau after 15-20 minutes, and is fully reversible. The recovery of the original fluorescence properties, after decompression, is fast (less than four minutes), suggesting that the isolated subunit has a relatively stable structure, and excluding the presence of stable intermediates during the dimer-monomer transition. The dimer dissociation process is still incomplete at 6.5 kbar for the copper-depleted wild-type and mutated enzymes, at variance with what is generally observed for oligomeric proteins that dissociate below 3 kbar. Measurement of the degree of dissociation, at two different protein concentrations, allows us to calculate the standard volume variation upon association, Delta V, and the dissociation constant K(d0), at atmospheric pressure, (25 ml/mol and 3 x 10(-7)M, respectively). The holoprotein is fully dimeric even at 6.5 kbar, which allows us to evaluate a lower Delta G degrees limit of 11.5 kcal/mol, corresponding to a dissociation constant K(d0)<10(-9)M.
  Selected figure(s)  
Figure 1.
Figure 1. Stereo view of the C^a trace of the PSOD subunit, displaying the active-site Cu, Zn ions (as cyan and magenta spheres, respectively) together with liganding residues. The mutated residues 24 and 40 are highlighted in yellow (Lys and Met in the wild-type PSOD, respectively) and red (either Asp or Glu in the mutant PSODs, respectively). Key residues, belonging to the first and second residue clusters at the subunit association interface are shown in light grey. The side-chains conformation of residues Lys24, Leu85 and Pro96, which vary in the Met40->Glu mutant, are indicated in dark grey. The Zn-subloop region is highlighted in blue. The Figure was drawn with MOLSCRIPT.[37.]
Figure 5.
Figure 5. Effect of protein concentration on pressure dissociation Cu-depleted WT SOD: (0M) 5 µM SOD; (sB) 50 µM SOD. The degree of dissociation was calculated from the center of spectral mass (see Materials and Methods). Other conditions were the same as for Figure 4. Inset: plot of ln(a[p]2/(1 -a[p])) versus pressure for the 5 µM protein sample.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 1351-1360) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20516618 I.Ascone, C.Savino, R.Kahn, and R.Fourme (2010).
Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa.
  Acta Crystallogr D Biol Crystallogr, 66, 654-663.
PDB code: 3hw7
15681652 L.Maragliano, M.Falconi, A.Sergi, P.Cioni, S.Castelli, A.Lania, M.E.Stroppolo, G.Strambini, M.Ferrario, and A.Desideri (2005).
Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface.
  Biophys J, 88, 2875-2882.  
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