PDBsum entry 1z9n

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Jmol PyMol
Protein chains
155 a.a. *
HEM ×2
_ZN ×4
_CU ×4
Waters ×1082
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: X-ray structure of a cu-zn superoxide dismutase from haemoph ducreyi with haem bound at the dimer interface
Structure: Superoxide dismutase [cu-zn]. Chain: a, b, c, d. Fragment: mature protein with haem bound. Engineered: yes
Source: Haemophilus ducreyi. Organism_taxid: 730. Gene: sodc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.50Å     R-factor:   0.158     R-free:   0.193
Authors: K.Djinovic Carugo,I.Toeroe
Key ref: I.Töro et al. (2009). Structural basis of heme binding in the Cu,Zn superoxide dismutase from Haemophilus ducreyi. J Mol Biol, 386, 406-418. PubMed id: 19103206
03-Apr-05     Release date:   19-Sep-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q59452  (SODC_HAEDU) -  Superoxide dismutase [Cu-Zn]
199 a.a.
155 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     periplasmic space   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     antioxidant activity     4 terms  


    Added reference    
J Mol Biol 386:406-418 (2009)
PubMed id: 19103206  
Structural basis of heme binding in the Cu,Zn superoxide dismutase from Haemophilus ducreyi.
I.Töro, C.Petrutz, F.Pacello, M.D'Orazio, A.Battistoni, K.Djinović-Carugo.
The Cu,Zn superoxide dismutase from Haemophilus ducreyi is characterized by the unique ability to bind heme at its dimer interface. Here we report the high-resolution crystal structures of this protein in the heme-loaded (holo) and heme-free (apo) forms. Heme is asymmetrically bound between the two enzyme subunits, where heme iron is coordinated by two histidine residues, His64 and His 124, provided by the two subunits. Moreover, the binding of heme to the protein is ensured by stabilizing contacts between the prosthetic group and a limited number of other residues, most of which are not present in other bacterial enzyme variants. We show that the introduction of only three mutations at the dimer interface of the enzyme from Haemophilus parainfluenzae, a closely related bacterial species, is sufficient to induce heme-binding ability by this enzyme variant. Heme binding does not alter protein activity. Moreover, the binding of the prosthetic group does not induce any significant structural perturbation at the subunit level and requires only limited local structural rearrangements that widen the cleft at the dimer interface and cause a limited shift in the relative orientation between the subunits. The presence of a preformed heme-binding pocket and the significant solvent exposure of the cofactor to the solvent are compatible with the suggested protective role of the enzyme against heme toxicity or with its involvement in heme trafficking in the periplasmic space.