PDBsum entry 1dsw

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Oxidoreductase PDB id
Protein chain
153 a.a. *
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: The solution structure of a monomeric, reduced form of human copper, zinc superoxide dismutase bearing the same charge as the native protein
Structure: Superoxide dismutase (cu-zn). Chain: a. Fragment: m4sod is a monomeric variant of human sod. The mutant is studied in the reduced form, each molecule contains a cu(i) and a zn(ii) ions.. Engineered: yes. Mutation: yes. Other_details: copper, zinc superoxide dismutase (sod) is an enzyme which catalyzes the dismutation of superoxide
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: L.Banci,I.Bertini,R.Del Conte,R.Fadin,S.Mangani,M.S.Viezzoli
Key ref: L.Banci et al. (1999). The solution structure of a monomeric, reduced form of human copper,zinc superoxide dismutase bearing the same charge as the native protein. J Biol Inorg Chem, 4, 795-803. PubMed id: 10631612
10-Jan-00     Release date:   22-Mar-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00441  (SODC_HUMAN) -  Superoxide dismutase [Cu-Zn]
154 a.a.
153 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 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     extracellular region   20 terms 
  Biological process     cellular response to potassium ion   66 terms 
  Biochemical function     antioxidant activity     13 terms  


    Added reference    
J Biol Inorg Chem 4:795-803 (1999)
PubMed id: 10631612  
The solution structure of a monomeric, reduced form of human copper,zinc superoxide dismutase bearing the same charge as the native protein.
L.Banci, I.Bertini, R.Del Conte, R.Fadin, S.Mangani, M.S.Viezzoli.
The solution structure of a mutated (Phe50Glu, Gly51Glu, Val148Lys, Ile151Lys), reduced, monomeric form of human copper,zinc superoxide dismutase (SOD; 153 amino acids) has been determined through 2237 meaningful nuclear Overhauser enhancements, out of 2492, and 43 dihedral angle constraints. A characteristic of this mutant is that of having the same overall charge as the dimeric protein, but an activity of only 20% with respect to wild-type SOD. This protein, at variance with a previously characterized monomeric form (Phe50Glu, Gly51Glu, Glu133Gln), does not contain mutations in the active site. Therefore, its characterization allows us to understand the structural changes independently induced by the monomerization and by the active site mutation. The family of 36 conformers, which have a target function with respect to the experimental constraints lower than 1.5 A2, has RMSD values with respect to the average structure of 0.94 +/- 0.14 A2 and 1.50 +/- 0.14 A2 for the backbone and the heavy atoms, respectively. The overall folding, which includes the classical eight-stranded Greek-key beta-barrel and a short alpha-helix, is very close to that of the previously characterized monomeric mutant E133QM2SOD and to that of wild-type SOD. The region involved in the subunit-subunit interactions in the dimeric protein is confirmed to be disordered in the monomeric species. It is also observed that a sizable rearrangement of the charged groups of the electrostatic loop and of Arg143 takes place in the monomeric species. The width of the active site channel, both at its entrance and at the bottleneck of the active site, is discussed in the light of the influence on the enzymatic activity and the latter with respect to the overall charge. It is also confirmed that the NH proton of His63 shields the Cu(I) from the bulk solvent, thus supporting the suggestion that superoxide may interact with the reduced metal ion in an outer-sphere fashion.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18645238 M.Yogavel, P.C.Mishra, J.Gill, P.K.Bhardwaj, S.Dutt, S.Kumar, P.S.Ahuja, and A.Sharma (2008).
Structure of a superoxide dismutase and implications for copper-ion chelation.
  Acta Crystallogr D Biol Crystallogr, 64, 892-901.  
16291742 L.Banci, I.Bertini, F.Cantini, N.D'Amelio, and E.Gaggelli (2006).
Human SOD1 before harboring the catalytic metal: solution structure of copper-depleted, disulfide-reduced form.
  J Biol Chem, 281, 2333-2337.
PDB code: 2af2
15897454 L.Banci, I.Bertini, V.Calderone, F.Cramaro, R.Del Conte, A.Fantoni, S.Mangani, A.Quattrone, and M.S.Viezzoli (2005).
A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.
  Proc Natl Acad Sci U S A, 102, 7541-7546.
PDB codes: 1s4i 1u3n
12458194 A.Tiwari, and L.J.Hayward (2003).
Familial amyotrophic lateral sclerosis mutants of copper/zinc superoxide dismutase are susceptible to disulfide reduction.
  J Biol Chem, 278, 5984-5992.  
12237469 L.Banci, I.Bertini, F.Cantini, M.D'Onofrio, and M.S.Viezzoli (2002).
Structure and dynamics of copper-free SOD: The protein before binding copper.
  Protein Sci, 11, 2479-2492.
PDB code: 1kmg
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
11863429 L.Banci, I.C.Felli, and R.Kümmerle (2002).
Direct detection of hydrogen bonds in monomeric superoxide dismutase: biological implications.
  Biochemistry, 41, 2913-2920.  
10924104 L.Banci, I.Bertini, F.Cramaro, R.Del Conte, A.Rosato, and M.S.Viezzoli (2000).
Backbone dynamics of human Cu,Zn superoxide dismutase and of its monomeric F50E/G51E/E133Q mutant: the influence of dimerization on mobility and function.
  Biochemistry, 39, 9108-9118.  
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.