PDBsum entry 1srd

Go to PDB code: 
protein metals Protein-protein interface(s) links
Oxidoreductase(superoxide acceptor) PDB id
Protein chains
154 a.a. *
_ZN ×4
_CU ×4
Waters ×104
* Residue conservation analysis
PDB id:
Name: Oxidoreductase(superoxide acceptor)
Title: Three-dimensional structure of cu,zn-superoxide dismutase from spinach at 2.0 angstroms resolution
Structure: Copper,zinc superoxide dismutase. Chain: a, b, c, d. Engineered: yes
Source: Spinacia oleracea. Spinach. Organism_taxid: 3562
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.249    
Authors: Y.Kitagawa,Y.Katsube
Key ref: Y.Kitagawa et al. (1991). Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution. J Biochem, 109, 477-485. PubMed id: 1880134
15-Apr-93     Release date:   31-Jan-94    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P07505  (SODCP_SPIOL) -  Superoxide dismutase [Cu-Zn], chloroplastic
222 a.a.
154 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!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     superoxide dismutase activity     2 terms  


    Added reference    
J Biochem 109:477-485 (1991)
PubMed id: 1880134  
Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution.
Y.Kitagawa, N.Tanaka, Y.Hata, M.Kusunoki, G.P.Lee, Y.Katsube, K.Asada, S.Aibara, Y.Morita.
The three-dimensional structure of Cu,Zn-superoxide dismutase from spinach leaves has been determined by X-ray crystal structure analysis. The atomic coordinates were refined at 2.0 A resolution using the Hendrickson and Konnert program for stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry. The crystallographic residual error for the refined model was 24.9%, with a root mean square deviation of 0.03 A from the ideal bond length and an average atomic temperature factor of 9.6 A. A dimeric molecule of the enzyme is comprised of two identical subunits related by a non-crystallographic 2-fold axis. Each subunit of 154 amino acid residues is composed primarily of eight anti-parallel beta-strands that form a flattened cylinder, plus three external loops. The main-chain hydrogen bonds primarily link the beta-strands. The overall structure of this enzyme is quite similar to that of the bovine dismutase except for some parts. The single disulfide bridge (Cys57-Cys146) and the salt bridge (Arg79-Asp101) may stabilize the loop regions of the structure. The Cu2+ and Zn2+ ions in the active site lie 6.1 A apart at the bottom of the long channel. The Cu2+ ligands (ND1 of His-46, and NE2 of His-48, -63, and -120) show an uneven tetrahedral distortion from a square plane. The Zn2+ ligands (ND1 of His-63, -71, and -80 and OD1 of Asp-83) show an almost tetrahedral geometry. The imidazole ring of His-63 forms a bridge between the Cu2+ and Zn2+ ions.(ABSTRACT TRUNCATED AT 250 WORDS)

Literature references that cite this PDB file's key reference

  PubMed id Reference
19063897 D.S.Shin, M.Didonato, D.P.Barondeau, G.L.Hura, C.Hitomi, J.A.Berglund, E.D.Getzoff, S.C.Cary, and J.A.Tainer (2009).
Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.
  J Mol Biol, 385, 1534-1555.
PDB codes: 3f7k 3f7l
16508635 F.Okada, H.Shionoya, M.Kobayashi, T.Kobayashi, H.Tazawa, K.Onuma, Y.Iuchi, N.Matsubara, T.Ijichi, B.Dugas, and M.Hosokawa (2006).
Prevention of inflammation-mediated acquisition of metastatic properties of benign mouse fibrosarcoma cells by administration of an orally available superoxide dismutase.
  Br J Cancer, 94, 854-862.  
11679732 W.Liu, P.W.Li, G.P.Li, R.H.Zhu, and D.C.Wang (2001).
Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of Cu,Zn superoxide dismutase from Peking duck.
  Acta Crystallogr D Biol Crystallogr, 57, 1646-1649.  
15012221 K.Asada (1999).
THE WATER-WATER CYCLE IN CHLOROPLASTS: Scavenging of Active Oxygens and Dissipation of Excess Photons.
  Annu Rev Plant Physiol Plant Mol Biol, 50, 601-639.  
  9541385 P.J.Hart, H.Liu, M.Pellegrini, A.M.Nersissian, E.B.Gralla, J.S.Valentine, and D.Eisenberg (1998).
Subunit asymmetry in the three-dimensional structure of a human CuZnSOD mutant found in familial amyotrophic lateral sclerosis.
  Protein Sci, 7, 545-555.
PDB code: 1azv
9279123 W.Y.Sun, J.L.Fang, M.Cheng, P.Y.Xia, and W.X.Tang (1997).
Secondary structure dependent on metal ions of copper,zinc superoxide dismutase investigated by Fourier transform IR spectroscopy.
  Biopolymers, 42, 297-303.  
  8897614 A.Battistoni, S.Folcarelli, G.Rotilio, C.Capasso, A.Pesce, M.Bolognesi, and A.Desideri (1996).
Crystallization and preliminary X-ray analysis of the monomeric Cu,Zn superoxide dismutase from Escherichia coli.
  Protein Sci, 5, 2125-2127.  
8951656 M.Falconi, R.Gallimbeni, and E.Paci (1996).
Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation.
  J Comput Aided Mol Des, 10, 490-498.  
8836097 T.Fujii, Y.Hata, T.Wakagi, N.Tanaka, and T.Oshima (1996).
Novel zinc-binding centre in thermoacidophilic archaeal ferredoxins.
  Nat Struct Biol, 3, 834-837.
PDB code: 1xer
7647254 C.Andreani, A.Filabozzi, F.Menzinger, A.Desideri, A.Deriu, and D.Di Cola (1995).
Dynamics of hydrogen atoms in superoxide dismutase by quasielastic neutron scattering.
  Biophys J, 68, 2519-2523.  
8436140 M.E.Schininà, F.Bossa, A.Lania, C.R.Capo, P.Carlini, and L.Calabrese (1993).
The primary structure of turtle Cu,Zn superoxide dismutase. Structural and functional irrelevance of an insert conferring proteolytic susceptibility.
  Eur J Biochem, 211, 843-849.  
1784712 M.C.Lawrence (1991).
The application of the molecular replacement method to the de novo determination of protein structure.
  Q Rev Biophys, 24, 399-424.  
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 codes are shown on the right.