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PDBsum entry 1sxc

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1sxc
Jmol
Contents
Protein chains
151 a.a. *
Metals
_ZN ×2
_CU ×2
Waters ×367
* Residue conservation analysis
PDB id:
1sxc
Name: Oxidoreductase
Title: Crystal structure of reduced bovine erythrocyte superoxide dismutase at 1.9 angstroms resolution
Structure: Superoxide dismutase. Chain: a, b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.156    
Authors: W.R.Rypniewski,S.Mangani,B.Bruni,P.Orioli,M.Casati, K.S.Wilson
Key ref:
W.R.Rypniewski et al. (1995). Crystal structure of reduced bovine erythrocyte superoxide dismutase at 1.9 A resolution. J Mol Biol, 251, 282-296. PubMed id: 7643403 DOI: 10.1006/jmbi.1995.0434
Date:
17-Mar-95     Release date:   03-Jun-95    
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: Iron or manganese or (zinc and copper)
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    
 
 
DOI no: 10.1006/jmbi.1995.0434 J Mol Biol 251:282-296 (1995)
PubMed id: 7643403  
 
 
Crystal structure of reduced bovine erythrocyte superoxide dismutase at 1.9 A resolution.
W.R.Rypniewski, S.Mangani, B.Bruni, P.L.Orioli, M.Casati, K.S.Wilson.
 
  ABSTRACT  
 
Cu,Zn superoxide dismutase was investigated crystallographically in the reduced form. Co-ordinate errors were estimated by comparing two independently refined models, based on two different data sets. This gave a detailed error estimation as opposed to the standard sigma A and Luzzati plots, which estimate only the overall error. The high quality of the final model, obtained after scaling together the two data sets, combined with the error estimates allowed a detailed analysis of the protein and solvent structures. An automatic procedure for building and refining solvent structure was tested and found to give reproducible results. Contrary to results obtained from spectroscopic studies, the co-ordination of the metal ions in the catalytic site is preserved in the crystal structure of the reduced enzyme, as compared with the crystal structure of the oxidised form. Analysis of the solvent reveals a well-defined chain of closely packed, hydrogen-bonded water molecules filling the active site groove. This structural feature could serve as a hydrogen bond relay for efficient delivery of protons to the active centre. Analysis of electron density suggests that Glu119 is covalently modified. The modification, if originated in vivo, could have a role in the catalytic mechanism and could affect the overall electrostatic field in the active site. There are significant differences between the active sites of the two crystallographically independent monomers. They are explained in terms of local differences in the crystal environment.
 
  Selected figure(s)  
 
Figure 13.
Figure 13. A van der Waals dot surface representation of the chain of solvent molecules filling the groove of the catalytic centre.
Figure 16.
Figure 16. Comparison of EPR spectra of (a) crystalline Cu(II),Zn SOD. (five crystals, approximate volume 4 × 10 -3 mm 3
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 251, 282-296) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20645325 E.Cremades, J.Echeverría, and S.Alvarez (2010).
The trigonal prism in coordination chemistry.
  Chemistry, 16, 10380-10396.  
19585034 J.Echeverría, E.Cremades, A.J.Amoroso, and S.Alvarez (2009).
Jahn-Teller distortions of six-coordinate CuII compounds: cis or trans?
  Chem Commun (Camb), (), 4242-4244.  
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.  
15937064 S.Wedgwood, R.H.Steinhorn, M.Bunderson, J.Wilham, S.Lakshminrusimha, L.A.Brennan, and S.M.Black (2005).
Increased hydrogen peroxide downregulates soluble guanylate cyclase in the lungs of lambs with persistent pulmonary hypertension of the newborn.
  Am J Physiol Lung Cell Mol Physiol, 289, L660-L666.  
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.  
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
12773543 M.L.Teoh, P.J.Walasek, and D.H.Evans (2003).
Leporipoxvirus Cu,Zn-superoxide dismutase (SOD) homologs are catalytically inert decoy proteins that bind copper chaperone for SOD.
  J Biol Chem, 278, 33175-33184.  
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
11134922 W.R.Rypniewski, P.R.Ostergaard, M.Nørregaard-Madsen, M.Dauter, and K.S.Wilson (2001).
Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
  Acta Crystallogr D Biol Crystallogr, 57, 8.
PDB codes: 1fn8 1fy4 1fy5 1gdn 1gdq 1gdu
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
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.  
  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.  
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.