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PDBsum entry 1cob

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1cob
Jmol
Contents
Protein chains
151 a.a. *
Metals
_CO ×2
_CU ×2
Waters ×199
* Residue conservation analysis
PDB id:
1cob
Name: Oxidoreductase
Title: Crystal structure solution and refinement of the semisynthetic cobalt substituted bovine erythrocyte enzyme superoxide dismutase at 2.0 angstroms resolution
Structure: Superoxide dismutase. Chain: a, b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.176    
Authors: K.Djinovic,A.Coda,L.Antolini,G.Pelosi,A.Desideri,M.Falconi, G.Rotilio,M.Bolognesi
Key ref: K.Djinovic et al. (1992). Crystal structure solution and refinement of the semisynthetic cobalt-substituted bovine erythrocyte superoxide dismutase at 2.0 A resolution. J Mol Biol, 226, 227-238. PubMed id: 1619651
Date:
19-Feb-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00442  (SODC_BOVIN) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc:
152 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.15.1.1  - 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    
 
 
J Mol Biol 226:227-238 (1992)
PubMed id: 1619651  
 
 
Crystal structure solution and refinement of the semisynthetic cobalt-substituted bovine erythrocyte superoxide dismutase at 2.0 A resolution.
K.Djinovic, A.Coda, L.Antolini, G.Pelosi, A.Desideri, M.Falconi, G.Rotilio, M.Bolognesi.
 
  ABSTRACT  
 
The semisynthetic Co-substituted bovine erythrocyte superoxide dismutase (SOD) has been crystallized in a new crystalline form and the structure determined at 2.0 A (1 A = 0.1 nm) resolution. The crystals belong to space group P2(1)2(1)2(1) with cell constants: a = 51.0, b = 147.6, c = 47.5 A, and contain one dimeric molecule of 32,000 M(r) per asymmetric unit. The structure has been solved by molecular replacement techniques using the Cu,Zn bovine enzyme as a search model, and refined by molecular dynamics with the crystallographic pseudo-energy term, followed by conventional crystallographic refinement. The R-factor for the 18,964 unique reflections in the resolution range from 10.0 to 2.0 A is 0.176 for a model comprising 2188 protein atoms and 200 solvent molecules; the root-mean-square deviation from the ideal bond lengths is 0.010 A, and the average atomic temperature factor is 26.5 A2. The dimeric molecule of the enzyme is composed of two identical subunits related by a non-crystallographic 2-fold axis. The subunit has as its structural scaffolding the conventional SOD-flattened antiparallel eight-stranded beta-barrel, with three external loops. The co-ordination geometry of the metal center in the active site is fairly well preserved when compared with the native Cu,Zn bovine enzyme. Co2+ is in tetrahedral co-ordination, while the Cu2+ ligands show an uneven distortion from the square planar geometry. The least-squares superposition of the metals ligands and the catalytically important Arg141 of the native and Co-substituted enzyme yields a root-mean-square value of 0.401 A, the largest deviation occurring at the Co2+ ligand Asp81. An additional copper ligand, compatible with a water molecule, is observed at 2.38 A from Cu2+ in the active-site channel, at the supposed binding site of the O2- anion substrate. Several ordered water molecules have been observed on the protein surface and in the active-site channel; their structural locations coincide remarkably with those of related water molecules found in the crystal structure of the phylogenetically distant superoxide dismutase from yeast.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20516618 I.Ascone, C.Savino, R.Kahn, and R.Fourme (2010).
Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa.
  Acta Crystallogr D Biol Crystallogr, 66, 654-663.
PDB code: 3hw7
16952188 M.Isobe, H.Kai, T.Kurahashi, S.Suwan, S.Pitchayawasin-Thapphasaraphong, T.Franz, N.Tani, K.Higashi, and H.Nishida (2006).
The molecular mechanism of the termination of insect diapause, part 1: A timer protein, TIME-EA4, in the diapause eggs of the silkworm Bombyx mori is a metallo-glycoprotein.
  Chembiochem, 7, 1590-1598.  
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
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
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.  
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
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
9692968 M.A.Jairajpuri, N.Azam, K.Baburaj, E.Bulliraju, and S.Durani (1998).
Charge and solvation effects in anion recognition centers: an inquiry exploiting reactive arginines.
  Biochemistry, 37, 10780-10791.  
  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.  
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.  
  8845760 X.Chen, D.Whitmire, and J.P.Bowen (1996).
Xylanase homology modeling using the inverse protein folding approach.
  Protein Sci, 5, 705-708.  
7851420 M.Sette, M.Paci, A.Desideri, and G.Rotilio (1995).
A two-dimensional NMR study of bovine Cu, Co superoxide dismutase. Further assignments in the region surrounding the active site.
  Eur J Biochem, 227, 441-447.  
8477710 M.Sette, M.Paci, A.Desideri, and G.Rotilio (1993).
Two-dimensional NMR assignment of hyperfine-shifted resonances of very fast relaxing metal binding sites of proteins by NOE spectroscopy. The case of Cu, Co superoxide dismutase.
  Eur J Biochem, 213, 391-397.  
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.

 

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