PDBsum entry 1bzo

Go to PDB code: 
protein metals links
Oxidoreductase PDB id
Protein chain
151 a.a. *
IUM ×2
Waters ×102
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Three-dimensional structure of prokaryotic cu,zn superoxide dismutase from p.Leiognathi, solved by x-ray crystallography.
Structure: Protein (superoxide dismutase). Chain: a. Engineered: yes
Source: Photobacterium leiognathi. Organism_taxid: 658. Cellular_location: periplasmic space. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
2.10Å     R-factor:   0.190     R-free:   0.260
Authors: D.Bordo,D.Matak,K.Djinovic-Carugo,C.Rosano,A.Pesce, M.Bolognesi,M.E.Stroppolo,M.Falconi,A.Battistoni,A.Desideri
Key ref:
D.Bordo et al. (1999). Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase. J Mol Biol, 285, 283-296. PubMed id: 9878406 DOI: 10.1006/jmbi.1998.2267
02-Nov-98     Release date:   09-Apr-99    
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 1 residue position (black cross)

 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: Iron or manganese or (zinc and copper)
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.1998.2267 J Mol Biol 285:283-296 (1999)
PubMed id: 9878406  
Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.
D.Bordo, D.Matak, K.Djinovic-Carugo, C.Rosano, A.Pesce, M.Bolognesi, M.E.Stroppolo, M.Falconi, A.Battistoni, A.Desideri.
Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct quaternary structure, as compared to that of the homologous eukaryotic enzymes. Here we report a newly determined crystal structure of the dimeric Cu,Zn superoxide dismutase from Photobacterium leiognathi (crystallized in space group R32, refined at 2.5 A resolution, R-factor 0.19) and analyse it in comparison with that of the monomeric enzyme from Escherichia coli. The dimeric assembly, observed also in a previously studied monoclinic crystal form of P. leiognathi Cu,Zn superoxide dismutase, is based on a ring-shaped subunit contact region, defining a solvated interface cavity. Three clusters of neighbouring residues play a direct role in the stabilization of the quaternary assembly. The present analysis, extended to the amino acid sequences of the other 11 known prokaryotic Cu,Zn superoxide dismutases, shows that at least in five other prokaryotic enzymes the interface residue clusters are under strong evolutionary constraint, suggesting the attainment of a quaternary structure coincident with that of P. leiognathi Cu,Zn superoxide dismutase. Calculation of electrostatic fields for both the enzymes from E. coli and P. leiognathi shows that the monomeric/dimeric association behaviour displayed by prokaryotic Cu, Zn superoxide dismutases is related to the distribution of surface charged residues. Moreover, Brownian dynamics simulations reproduce closely the observed enzyme:substrate association rates, highlighting the role of the active site neighbouring residues in determining the dismutase catalytic properties.
  Selected figure(s)  
Figure 1.
Figure 1. (a) Stereo view of the C^a traces of the optimally superimposed three-dimensional structures of PSOD subunit, ESOD and XSOD (subunit A) represented in blue, orange and green, respectively. The active site Cu,Zn ions, almost exactly superimposed, are shown as blue and magenta spheres, respectively. The molecular regions showing the main structural differences among the three structures have been labelled. (b) C^a trace of the dimeric assembly of the prokaryotic PSOD and (c) of the eukaryotic XSOD. In both cases, the 2-fold axis relating the two subunits is perpendicular to the plane of the Figure. The Figure was prepared with the program MOLSCRIPT [Kraulis 1991].
Figure 4.
Figure 4. Evolutionary trees for the prokaryotic Cu,Zn SOD enzymes, deduced (a) from whole amino acid sequence multiple alignment, and (b) from multiple alignment of only the amino acids that in PSOD are involved in dimer formation.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 283-296) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19707802 H.I.Lee, J.W.Lee, T.C.Yang, S.O.Kang, and B.M.Hoffman (2010).
ENDOR and ESEEM investigation of the Ni-containing superoxide dismutase.
  J Biol Inorg Chem, 15, 175-182.  
20333421 K.C.Ryan, O.E.Johnson, D.E.Cabelli, T.C.Brunold, and M.J.Maroney (2010).
Nickel superoxide dismutase: structural and functional roles of Cys2 and Cys6.
  J Biol Inorg Chem, 15, 795-807.  
18470930 M.Calvaresi, M.Garavelli, and A.Bottoni (2008).
Computational evidence for the catalytic mechanism of glutaminyl cyclase. A DFT investigation.
  Proteins, 73, 527-538.  
17416645 R.Krishnakumar, B.Kim, E.A.Mollo, J.A.Imlay, and J.M.Slauch (2007).
Structural properties of periplasmic SodCI that correlate with virulence in Salmonella enterica serovar Typhimurium.
  J Bacteriol, 189, 4343-4352.  
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.  
15135531 D.H.Kho, S.B.Yoo, J.S.Kim, E.J.Kim, and J.K.Lee (2004).
Characterization of Cu- and Zn-containing superoxide dismutase of Rhodobacter sphaeroides.
  FEMS Microbiol Lett, 234, 261-267.  
15155722 L.Spagnolo, I.Törö, M.D'Orazio, P.O'Neill, J.Z.Pedersen, O.Carugo, G.Rotilio, A.Battistoni, and K.Djinovic-Carugo (2004).
Unique features of the sodC-encoded superoxide dismutase from Mycobacterium tuberculosis, a fully functional copper-containing enzyme lacking zinc in the active site.
  J Biol Chem, 279, 33447-33455.
PDB code: 1pzs
15485869 P.A.Doucette, L.J.Whitson, X.Cao, V.Schirf, B.Demeler, J.S.Valentine, J.C.Hansen, and P.J.Hart (2004).
Dissociation of human copper-zinc superoxide dismutase dimers using chaotrope and reductant. Insights into the molecular basis for dimer stability.
  J Biol Chem, 279, 54558-54566.  
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.  
12548728 J.Koca, C.G.Zhan, R.C.Rittenhouse, and R.L.Ornstein (2003).
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.
  J Comput Chem, 24, 368-378.  
12784219 M.Falconi, M.Brunelli, A.Pesce, M.Ferrario, M.Bolognesi, and A.Desideri (2003).
Static and dynamic water molecules in Cu,Zn superoxide dismutase.
  Proteins, 51, 607-615.  
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
12001230 M.Falconi, L.Parrilli, A.Battistoni, and A.Desideri (2002).
Flexibility in monomeric Cu,Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation.
  Proteins, 47, 513-520.  
11371434 M.Falconi, M.E.Stroppolo, P.Cioni, G.Strambini, A.Sergi, M.Ferrario, and A.Desideri (2001).
Dynamics-function correlation in Cu, Zn superoxide dismutase: a spectroscopic and molecular dynamics simulation study.
  Biophys J, 80, 2556-2567.  
11093265 W.S.Valdar, and J.M.Thornton (2001).
Protein-protein interfaces: analysis of amino acid conservation in homodimers.
  Proteins, 42, 108-124.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.