PDBsum entry 1ibd

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protein metals links
Oxidoreductase PDB id
Protein chain
151 a.a. *
Waters ×95
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: X-ray 3d structure of p.Leiognathi cu,zn sod mutant v29a
Structure: Cu,zn 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)
2.00Å     R-factor:   0.214     R-free:   0.269
Authors: M.E.Stroppolo,A.Pesce,M.D'Orazio,P.O'Neill,D.Bordo,C.Rosano, M.Milani,A.Battistoni,M.Bolognesi,A.Desideri
Key ref:
M.E.Stroppolo et al. (2001). Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase. J Mol Biol, 308, 555-563. PubMed id: 11327787 DOI: 10.1006/jmbi.2001.4606
28-Mar-01     Release date:   09-May-01    
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   3 terms 
  Biochemical function     antioxidant activity     4 terms  


    Added reference    
DOI no: 10.1006/jmbi.2001.4606 J Mol Biol 308:555-563 (2001)
PubMed id: 11327787  
Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.
M.E.Stroppolo, A.Pesce, M.D'Orazio, P.O'Neill, D.Bordo, C.Rosano, M.Milani, A.Battistoni, M.Bolognesi, A.Desideri.
The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.
  Selected figure(s)  
Figure 1.
Figure 1. A schematic view of the PSOD dimer displaying one enzyme subunit as a van der Waals surface (green), the interface trapped water molecules (red spheres) and the second subunit shown as a skeletal C^a trace including the active site Cu,Zn pair (cyan and purple atoms, respectively). Drawn with Dino.[39]
Figure 2.
Figure 2. (a) A stereo view of the subunit interface residues in wild-type PSOD. The blue molecular surface indicating the enzyme association interface hosts the side-chains of residues (skeletal side-chains) building up the subunit contact area. The residues individually mutated in the present study are drawn in purple and specifically labeled. (b) The PSOD subunit interface is portrayed as shown in (a), including five out of the ten interface water molecules (red spheres) buried once the active dimeric enzyme is assembled through crystallographic two-fold symmetry. Drawn with Dino.[39]
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 308, 555-563) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18828904 M.D'Orazio, R.Scotti, L.Nicolini, L.Cervoni, G.Rotilio, A.Battistoni, and R.Gabbianelli (2008).
Regulatory and structural properties differentiating the chromosomal and the bacteriophage-associated Escherichia coli O157:H7 Cu, Zn superoxide dismutases.
  BMC Microbiol, 8, 166.  
18362154 S.Ammendola, P.Pasquali, F.Pacello, G.Rotilio, M.Castor, S.J.Libby, N.Figueroa-Bossi, L.Bossi, F.C.Fang, and A.Battistoni (2008).
Regulatory and structural differences in the Cu,Zn-superoxide dismutases of Salmonella enterica and their significance for virulence.
  J Biol Chem, 283, 13688-13699.  
15449711 R.Gabbianelli, M.D'Orazio, F.Pacello, P.O'Neill, L.Nicolini, G.Rotilio, and A.Battistoni (2004).
Distinctive functional features in prokaryotic and eukaryotic Cu,Zn superoxide dismutases.
  Biol Chem, 385, 749-754.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.