PDBsum entry 1sda

Go to PDB code: 
protein metals Protein-protein interface(s) links
Oxidoreductase(copper) PDB id
Protein chains
152 a.a. *
_ZN ×4
_CU ×4
Waters ×4
* Residue conservation analysis
PDB id:
Name: Oxidoreductase(copper)
Title: Crystal structure of peroxynitrite-modified bovine cu,zn superoxide dismutase
Structure: Copper,zinc superoxide dismutase. Chain: o, y, b, g. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
2.50Å     R-factor:   0.187    
Authors: C.D.Smith,M.Carson,M.Van Der Woerd,J.Chen,H.Ischiropoulos, J.S.Beckman
Key ref: C.D.Smith et al. (1992). Crystal structure of peroxynitrite-modified bovine Cu,Zn superoxide dismutase. Arch Biochem Biophys, 299, 350-355. PubMed id: 1444476
13-Jan-93     Release date:   31-Oct-93    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00442  (SODC_BOVIN) -  Superoxide dismutase [Cu-Zn]
152 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: 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     protein complex   11 terms 
  Biological process     reactive oxygen species metabolic process   45 terms 
  Biochemical function     antioxidant activity     10 terms  


    Added reference    
Arch Biochem Biophys 299:350-355 (1992)
PubMed id: 1444476  
Crystal structure of peroxynitrite-modified bovine Cu,Zn superoxide dismutase.
C.D.Smith, M.Carson, M.van der Woerd, J.Chen, H.Ischiropoulos, J.S.Beckman.
The crystal structure of bovine Cu,Zn superoxide dismutase modified with peroxynitrite (ONOO-) was determined by X-ray diffraction, utilizing the existing three-dimensional model of the native structure deposited in the Brookhaven Protein Data Bank (J. A. Tainer et al., J. Mol. Biol. 160, 181-217, 1982). The native structure and the modified derivative were refined to R factors of 19.0 and 18.7% respectively using diffraction data from 6.0 to 2.5 A. The major result after reaction with peroxynitrite was the appearance of electron density 1.45 A from a single epsilon carbon of Tyr-108, the only tyrosine residue in the sequence. Tyr-108 is a solvent-exposed residue 18 A from the copper atom in the active site. The electron density was consistent with nitration of Tyr-108 at one of the epsilon carbons to form 3-nitrotyrosine. We propose that the nitration occurs in solution by transfer of a nitronium-like species from the active site on one superoxide dismutase dimer to the Tyr-108 of a second dimer.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20167432 Z.Chen, C.Muscoli, T.Doyle, L.Bryant, S.Cuzzocrea, V.Mollace, R.Mastroianni, E.Masini, and D.Salvemini (2010).
NMDA-receptor activation and nitroxidative regulation of the glutamatergic pathway during nociceptive processing.
  Pain, 149, 100-106.  
19393377 J.S.Beckman (2009).
Understanding peroxynitrite biochemistry and its potential for treating human diseases.
  Arch Biochem Biophys, 484, 114-116.  
19309264 K.A.Trumbull, and J.S.Beckman (2009).
A role for copper in the toxicity of zinc-deficient superoxide dismutase to motor neurons in amyotrophic lateral sclerosis.
  Antioxid Redox Signal, 11, 1627-1639.  
19607887 T.Doyle, L.Bryant, I.Batinic-Haberle, J.Little, S.Cuzzocrea, E.Masini, I.Spasojevic, and D.Salvemini (2009).
Supraspinal inactivation of mitochondrial superoxide dismutase is a source of peroxynitrite in the development of morphine antinociceptive tolerance.
  Neuroscience, 164, 702-710.  
17975673 C.Muscoli, S.Cuzzocrea, M.M.Ndengele, V.Mollace, F.Porreca, F.Fabrizi, E.Esposito, E.Masini, G.M.Matuschak, and D.Salvemini (2007).
Therapeutic manipulation of peroxynitrite attenuates the development of opiate-induced antinociceptive tolerance in mice.
  J Clin Invest, 117, 3530-3539.  
  17237348 P.Pacher, J.S.Beckman, and L.Liaudet (2007).
Nitric oxide and peroxynitrite in health and disease.
  Physiol Rev, 87, 315-424.  
15197101 M.Thiyagarajan, C.L.Kaul, and S.S.Sharma (2004).
Neuroprotective efficacy and therapeutic time window of peroxynitrite decomposition catalysts in focal cerebral ischemia in rats.
  Br J Pharmacol, 142, 899-911.  
11451436 F.Yamakura, T.Matsumoto, T.Fujimura, H.Taka, K.Murayama, T.Imai, and K.Uchida (2001).
Modification of a single tryptophan residue in human Cu,Zn-superoxide dismutase by peroxynitrite in the presence of bicarbonate.
  Biochim Biophys Acta, 1548, 38-46.  
11368922 T.Grune, L.O.Klotz, J.Gieche, M.Rudeck, and H.Sies (2001).
Protein oxidation and proteolysis by the nonradical oxidants singlet oxygen or peroxynitrite.
  Free Radic Biol Med, 30, 1243-1253.  
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.  
10769119 O.Guittet, P.Decottignies, L.Serani, Y.Henry, P.Le Maréchal, O.Laprévote, and M.Lepoivre (2000).
Peroxynitrite-mediated nitration of the stable free radical tyrosine residue of the ribonucleotide reductase small subunit.
  Biochemistry, 39, 4640-4648.  
  9792452 A.Richter, M.Baack, H.P.Holthoff, M.Ritzi, and R.Knippers (1998).
Mobilization of chromatin-bound Mcm proteins by micrococcal nuclease.
  Biol Chem, 379, 1181-1187.  
9603906 F.Yamakura, H.Taka, T.Fujimura, and K.Murayama (1998).
Inactivation of human manganese-superoxide dismutase by peroxynitrite is caused by exclusive nitration of tyrosine 34 to 3-nitrotyrosine.
  J Biol Chem, 273, 14085-14089.  
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.