PDBsum entry 1jcv

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Oxidoreductase (superoxide acceptor) PDB id
Protein chain
153 a.a. *
Waters ×183
* Residue conservation analysis
PDB id:
Name: Oxidoreductase (superoxide acceptor)
Title: Reduced bridge-broken yeast cu/zn superoxide dismutase low t (-180c) structure
Structure: Cu/zn superoxide dismutase. Chain: a. Synonym: yeast cu/zn sod. Other_details: low (93k) temperature structure with the cop imidazolate bridge broken
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Dimer (from PQS)
1.55Å     R-factor:   0.190    
Authors: N.L.Ogihara,H.E.Parge,P.J.Hart,M.S.Weiss,J.S.Valentine,D.S.E J.A.Tainer
Key ref:
N.L.Ogihara et al. (1996). Unusual trigonal-planar copper configuration revealed in the atomic structure of yeast copper-zinc superoxide dismutase. Biochemistry, 35, 2316-2321. PubMed id: 8652572 DOI: 10.1021/bi951930b
07-Dec-95     Release date:   08-Mar-96    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00445  (SODC_YEAST) -  Superoxide dismutase [Cu-Zn]
154 a.a.
153 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     cytoplasm   5 terms 
  Biological process     positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress   11 terms 
  Biochemical function     antioxidant activity     5 terms  


    Added reference    
DOI no: 10.1021/bi951930b Biochemistry 35:2316-2321 (1996)
PubMed id: 8652572  
Unusual trigonal-planar copper configuration revealed in the atomic structure of yeast copper-zinc superoxide dismutase.
N.L.Ogihara, H.E.Parge, P.J.Hart, M.S.Weiss, J.J.Goto, B.R.Crane, J.Tsang, K.Slater, J.A.Roe, J.S.Valentine, D.Eisenberg, J.A.Tainer.
The three-dimensional structure of yeast copper-zinc superoxide dismutase (CuZnSOD) has been determined in a new crystal form in space group R32 and refined against X-ray diffraction data using difference Fourier and restrained crystallographic refinement techniques. The unexpected result is that the copper ion has moved approximately 1 angstrom from its position in previously reported CuZnSOD models, the copper-imidazolate bridge is broken, and a roughly trigonal planar ligand geometry characteristic of Cu(I) rather than Cu(II) is revealed. Final R values for the two nearly identical room temperature structures are 18.6% for all 19 149 reflections in the 10.0-1.7 angstrom resolution range and 18. 2% for 17 682 reflections (F > 2 sigma) in the 10.0-1.73 angstrom resolution range. A third structure has been determined using X-ray data collected at -180 degrees C. The final R value for this structure is 19.0% (R(free) = 22.9%) for all 24 356 reflections in the 10.0-1.55 angstrom resolution range. Virtually no change in the positions of the ligands to the zinc center is observed in these models. The origin of the broken bridge and altered Cu-ligand geometry is discussed.

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
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.  
17150313 B.Dash, R.Metz, H.J.Huebner, W.Porter, and T.D.Phillips (2007).
Molecular characterization of two superoxide dismutases from Hydra vulgaris.
  Gene, 387, 93.  
17888947 B.R.Roberts, J.A.Tainer, E.D.Getzoff, D.A.Malencik, S.R.Anderson, V.C.Bomben, K.R.Meyers, P.A.Karplus, and J.S.Beckman (2007).
Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS.
  J Mol Biol, 373, 877-890.
PDB code: 2r27
15328354 F.Dupeyrat, C.Vidaud, A.Lorphelin, and C.Berthomieu (2004).
Long distance charge redistribution upon Cu,Zn-superoxide dismutase reduction: significance for dismutase function.
  J Biol Chem, 279, 48091-48101.  
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.  
15333927 R.M.Cardoso, C.H.Silva, A.P.Ulian de Araújo, T.Tanaka, M.Tanaka, and R.C.Garratt (2004).
Structure of the cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni.
  Acta Crystallogr D Biol Crystallogr, 60, 1569-1578.
PDB codes: 1to4 1to5
12906825 M.A.Hough, and S.S.Hasnain (2003).
Structure of fully reduced bovine copper zinc superoxide dismutase at 1.15 A.
  Structure, 11, 937-946.
PDB code: 1q0e
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
11468394 M.J.Ellis, F.E.Dodd, R.W.Strange, M.Prudêncio, G.Sawers, R.R.Eady, and S.S.Hasnain (2001).
X-ray structure of a blue copper nitrite reductase at high pH and in copper-free form at 1.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 1110-1118.
PDB codes: 1hau 1haw
10858280 J.F.Eisses, J.P.Stasser, M.Ralle, J.H.Kaplan, and N.J.Blackburn (2000).
Domains I and III of the human copper chaperone for superoxide dismutase interact via a cysteine-bridged Dicopper(I) cluster.
  Biochemistry, 39, 7337-7342.  
10736160 L.T.Hall, R.J.Sanchez, S.P.Holloway, H.Zhu, J.E.Stine, T.J.Lyons, B.Demeler, V.Schirf, J.C.Hansen, A.M.Nersissian, J.S.Valentine, and P.J.Hart (2000).
X-ray crystallographic and analytical ultracentrifugation analyses of truncated and full-length yeast copper chaperones for SOD (LYS7): a dimer-dimer model of LYS7-SOD association and copper delivery.
  Biochemistry, 39, 3611-3623.
PDB code: 1ej8
10026301 P.J.Hart, M.M.Balbirnie, N.L.Ogihara, A.M.Nersissian, M.S.Weiss, J.S.Valentine, and D.Eisenberg (1999).
A structure-based mechanism for copper-zinc superoxide dismutase.
  Biochemistry, 38, 2167-2178.
PDB codes: 1b4l 1b4t 1f18 1f1a 1f1d 1f1g 1yaz 2jcw
10446130 P.J.Schmidt, T.D.Rae, R.A.Pufahl, T.Hamma, J.Strain, T.V.O'Halloran, and V.C.Culotta (1999).
Multiple protein domains contribute to the action of the copper chaperone for superoxide dismutase.
  J Biol Chem, 274, 23719-23725.  
9718300 L.Banci, M.Benedetto, I.Bertini, R.Del Conte, M.Piccioli, and M.S.Viezzoli (1998).
Solution structure of reduced monomeric Q133M2 copper, zinc superoxide dismutase (SOD). Why is SOD a dimeric enzyme?.
  Biochemistry, 37, 11780-11791.
PDB code: 1ba9
9521765 M.Leone, A.Cupane, V.Militello, M.E.Stroppolo, and A.Desideri (1998).
Fourier transform infrared analysis of the interaction of azide with the active site of oxidized and reduced bovine Cu,Zn superoxide dismutase.
  Biochemistry, 37, 4459-4464.  
  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
9083106 L.M.Murphy, R.W.Strange, and S.S.Hasnain (1997).
A critical assessment of the evidence from XAFS and crystallography for the breakage of the imidazolate bridge during catalysis in CuZn superoxide dismutase.
  Structure, 5, 371-379.  
8901564 T.J.Lyons, H.Liu, J.J.Goto, A.Nersissian, J.A.Roe, J.A.Graden, C.Café, L.M.Ellerby, D.E.Bredesen, E.B.Gralla, and J.S.Valentine (1996).
Mutations in copper-zinc superoxide dismutase that cause amyotrophic lateral sclerosis alter the zinc binding site and the redox behavior of the protein.
  Proc Natl Acad Sci U S A, 93, 12240-12244.  
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.