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PDBsum entry 1e9p

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1e9p
Jmol
Contents
Protein chains
151 a.a. *
151 a.a. *
Metals
_CU ×3
_ZN
Waters ×173
* Residue conservation analysis
PDB id:
1e9p
Name: Oxidoreductase
Title: Crystal structure of bovine cu, zn sod to 1.7 angstrom (3 of 3)
Structure: Superoxide dismutase. Chain: a. Superoxide dismutase. Chain: b. Ec: 1.13.1.1
Source: Bos taurus. Organism_taxid: 9913. Organism_taxid: 9913
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
1.70Å     R-factor:   0.185     R-free:   0.202
Authors: M.A.Hough,S.S.Hasnain
Key ref:
M.A.Hough et al. (2000). Conformational variability of the Cu site in one subunit of bovine CuZn superoxide dismutase: the importance of mobility in the Glu119-Leu142 loop region for catalytic function. J Mol Biol, 304, 231-241. PubMed id: 11080458 DOI: 10.1006/jmbi.2000.4186
Date:
25-Oct-00     Release date:   03-Dec-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00442  (SODC_BOVIN) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc:
152 a.a.
151 a.a.*
Protein chain
Pfam   ArchSchema ?
P00442  (SODC_BOVIN) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc:
152 a.a.
151 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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    
 
 
DOI no: 10.1006/jmbi.2000.4186 J Mol Biol 304:231-241 (2000)
PubMed id: 11080458  
 
 
Conformational variability of the Cu site in one subunit of bovine CuZn superoxide dismutase: the importance of mobility in the Glu119-Leu142 loop region for catalytic function.
M.A.Hough, R.W.Strange, S.S.Hasnain.
 
  ABSTRACT  
 
The structure of the catalytic site in one subunit of bovine CuZn superoxide dismutase is shown to be highly variable. A series of crystal structures at approximately 1.7 A have been determined using data collected from different crystals. Several conformations are observed for the copper site from one of the subunits. These conformations lie between those expected for the Cu(II) and Cu(I) forms of the enzyme and may represent a slow positional rearrangement of the Cu site during the crystallisation process due to the presence of a trace reductant in the mother liquor. These states perhaps indicate some functionally relevant structural steps that ultimately result in the breakage of the imidazolate bridge between the two metal sites.This behaviour is not observed for the second subunit of the dimeric enzyme, which remains in the five-coordinate, distorted square planar geometry in all cases. We suggest that this asymmetric behaviour may be caused by the lack of mobility for the Glu119-Leu142 loop region in the second subunit caused by crystal contacts. This region forms one wall of the active-site cavity, and its mobility has been suggested, via molecular dynamics studies, to be important for the catalytic mechanism.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Superposition of the subunit A active sites of SODa (green), SODb (orange), SODc (blue) with that of 1CBJ (red). Structural comparison was performed by least squares superposition of all protein backbone atoms using INSIGHTII.
Figure 3.
Figure 3. (a) XAFS spectrum of a crystalline slurry sample is compared with the fully oxidised solution sample of BSOD. (b) XANES spectrum of the above crystalline sample is compared with three other crystalline samples. Clear variation is seen in both peaks A and B. (c) Left panel shows an expanded view of peak B for the five crystalline samples. Right panel shows calculated spectra with varying distance of one of the ligands.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 304, 231-241) copyright 2000.  
  Figures were selected by the author.  

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
18521547 J.Liu, L.Ma, S.Yin, and F.Hong (2008).
Effects of Ce3+ on conformation and activity of superoxide dismutase.
  Biol Trace Elem Res, 125, 170-178.  
17976014 G.Koellensperger, S.Daubert, R.Erdmann, S.Hann, and H.Rottensteiner (2007).
Characterisation of zinc-binding domains of peroxisomal RING finger proteins using size exclusion chromatography/inductively coupled plasma-mass spectrometry.
  Biol Chem, 388, 1209-1214.  
16233812 H.Nagami, N.Yoshimoto, H.Umakoshi, T.Shimanouchi, and R.Kuboi (2005).
Liposome-assisted activity of superoxide dismutase under oxidative stress.
  J Biosci Bioeng, 99, 423-428.  
16212541 V.M.Moiseev, E.V.Rodina, S.A.Kurilova, N.N.Vorobyeva, T.I.Nazarova, and S.M.Avaeva (2005).
Substitutions of glycine residues Gly100 and Gly147 in conservative loops decrease rates of conformational rearrangements of Escherichia coli inorganic pyrophosphatase.
  Biochemistry (Mosc), 70, 858-866.  
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
11863429 L.Banci, I.C.Felli, and R.Kümmerle (2002).
Direct detection of hydrogen bonds in monomeric superoxide dismutase: biological implications.
  Biochemistry, 41, 2913-2920.  
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.  
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.