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Oxidoreductase PDB id
1rk7
Jmol
Contents
Protein chain
153 a.a. *
* Residue conservation analysis
PDB id:
1rk7
Name: Oxidoreductase
Title: Solution structure of apo cu,zn superoxide dismutase: role of metal ions in protein folding
Structure: Superoxide dismutase [cu-zn]. Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sod1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 30 models
Authors: L.Banci,I.Bertini,F.Cramaro,R.Del Conte,M.S.Viezzoli
Key ref:
L.Banci et al. (2003). Solution structure of Apo Cu,Zn superoxide dismutase: role of metal ions in protein folding. Biochemistry, 42, 9543-9553. PubMed id: 12911296 DOI: 10.1021/bi034324m
Date:
21-Nov-03     Release date:   02-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00441  (SODC_HUMAN) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc: 		154 a.a.
153 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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     extracellular region   15 terms 
  Biological process     aging   57 terms 
  Biochemical function     antioxidant activity     10 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi034324m Biochemistry 42:9543-9553 (2003)
PubMed id: 12911296  
 
 
Solution structure of Apo Cu,Zn superoxide dismutase: role of metal ions in protein folding.
L.Banci, I.Bertini, F.Cramaro, R.Del Conte, M.S.Viezzoli.
 
  ABSTRACT  
 
The solution structure of the demetalated copper, zinc superoxide dismutase is obtained for the monomeric Glu133Gln/Phe50Glu/Gly51Glu mutant through NMR spectroscopy. The demetalated protein still has a well-defined tertiary structure; however, two beta-strands containing two copper ligands (His46 and His48, beta4) and one zinc ligand (Asp83, beta5) are shortened, and the sheet formed by these strands and strands beta7 and beta8 moves away from the other strands of the beta-barrel to form an open clam with respect to a closed conformation in the holoprotein. Furthermore, loop IV which contains three zinc ligands (His63, His71, and His80) and loop VII which contributes to the definition of the active cavity channel are severely disordered, and experience extensive mobility as it results from thorough (15)N relaxation measurements. These structural and mobility data, if compared with those of the copper-depleted protein and holoprotein, point out the role of each metal ion in the protein folding, leading to the final tertiary structure of the holoprotein, and provide hints for the mechanisms of metal delivery by metal chaperones.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153892 K.W.Cheong, T.C.Leow, R.N.Rahman, M.Basri, M.B.Rahman, and A.B.Salleh (2011).
Reductive Alkylation Causes the Formation of a Molten Globule-Like Intermediate Structure in Geobacillus zalihae Strain T1 Thermostable Lipase.
  Appl Biochem Biotechnol, 164, 362-375.  
20184893 C.Kayatekin, J.A.Zitzewitz, and C.R.Matthews (2010).
Disulfide-reduced ALS variants of Cu, Zn superoxide dismutase exhibit increased populations of unfolded species.
  J Mol Biol, 398, 320-331.  
20213043 H.T.Li, M.Jiao, J.Chen, and Y.Liang (2010).
Roles of zinc and copper in modulating the oxidative refolding of bovine copper, zinc superoxide dismutase.
  Acta Biochim Biophys Sin (Shanghai), 42, 183-194.  
19805550 A.Durazo, B.F.Shaw, M.Chattopadhyay, K.F.Faull, A.M.Nersissian, J.S.Valentine, and J.P.Whitelegge (2009).
Metal-free superoxide dismutase-1 and three different amyotrophic lateral sclerosis variants share a similar partially unfolded beta-barrel at physiological temperature.
  J Biol Chem, 284, 34382-34389.  
19497878 A.Nordlund, L.Leinartaite, K.Saraboji, C.Aisenbrey, G.Gröbner, P.Zetterström, J.Danielsson, D.T.Logan, and M.Oliveberg (2009).
Functional features cause misfolding of the ALS-provoking enzyme SOD1.
  Proc Natl Acad Sci U S A, 106, 9667-9672.
PDB code: 3hff
19651777 A.Tiwari, A.Liba, S.H.Sohn, S.V.Seetharaman, O.Bilsel, C.R.Matthews, P.J.Hart, J.S.Valentine, and L.J.Hayward (2009).
Metal deficiency increases aberrant hydrophobicity of mutant superoxide dismutases that cause amyotrophic lateral sclerosis.
  J Biol Chem, 284, 27746-27758.  
19635794 K.S.Molnar, N.M.Karabacak, J.L.Johnson, Q.Wang, A.Tiwari, L.J.Hayward, S.J.Coales, Y.Hamuro, and J.N.Agar (2009).
A common property of amyotrophic lateral sclerosis-associated variants: destabilization of the copper/zinc superoxide dismutase electrostatic loop.
  J Biol Chem, 284, 30965-30973.  
19828437 K.Teilum, M.H.Smith, E.Schulz, L.C.Christensen, G.Solomentsev, M.Oliveberg, and M.Akke (2009).
Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization.
  Proc Natl Acad Sci U S A, 106, 18273-18278.  
19369197 L.Banci, I.Bertini, M.Boca, V.Calderone, F.Cantini, S.Girotto, and M.Vieru (2009).
Structural and dynamic aspects related to oligomerization of apo SOD1 and its mutants.
  Proc Natl Acad Sci U S A, 106, 6980-6985.
PDB codes: 3ecu 3ecv 3ecw
19436494 A.Nordlund, and M.Oliveberg (2008).
SOD1-associated ALS: a promising system for elucidating the origin of protein-misfolding disease.
  HFSP J, 2, 354-364.  
18840448 C.Kayatekin, J.A.Zitzewitz, and C.R.Matthews (2008).
Zinc binding modulates the entire folding free energy surface of human Cu,Zn superoxide dismutase.
  J Mol Biol, 384, 540-555.  
19052230 F.Ding, and N.V.Dokholyan (2008).
Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation.
  Proc Natl Acad Sci U S A, 105, 19696-19701.  
18378676 X.Cao, S.V.Antonyuk, S.V.Seetharaman, L.J.Whitson, A.B.Taylor, S.P.Holloway, R.W.Strange, P.A.Doucette, J.S.Valentine, A.Tiwari, L.J.Hayward, S.Padua, J.A.Cohlberg, S.S.Hasnain, and P.J.Hart (2008).
Structures of the G85R variant of SOD1 in familial amyotrophic lateral sclerosis.
  J Biol Chem, 283, 16169-16177.
PDB codes: 2vr6 2vr7 2vr8 3cqp 3cqq
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
17255946 C.K.Bruns, and R.R.Kopito (2007).
Impaired post-translational folding of familial ALS-linked Cu, Zn superoxide dismutase mutants.
  EMBO J, 26, 855-866.  
17548825 R.W.Strange, C.W.Yong, W.Smith, and S.S.Hasnain (2007).
Molecular dynamics using atomic-resolution structure reveal structural fluctuations that may lead to polymerization of human Cu-Zn superoxide dismutase.
  Proc Natl Acad Sci U S A, 104, 10040-10044.
PDB code: 2v0a
16644738 B.F.Shaw, A.Durazo, A.M.Nersissian, J.P.Whitelegge, K.F.Faull, and J.S.Valentine (2006).
Local unfolding in a destabilized, pathogenic variant of superoxide dismutase 1 observed with H/D exchange and mass spectrometry.
  J Biol Chem, 281, 18167-18176.  
16291742 L.Banci, I.Bertini, F.Cantini, N.D'Amelio, and E.Gaggelli (2006).
Human SOD1 before harboring the catalytic metal: solution structure of copper-depleted, disulfide-reduced form.
  J Biol Chem, 281, 2333-2337.
PDB code: 2af2
16771675 Y.Furukawa, and T.V.O'Halloran (2006).
Posttranslational modifications in Cu,Zn-superoxide dismutase and mutations associated with amyotrophic lateral sclerosis.
  Antioxid Redox Signal, 8, 847-867.  
16105836 L.Banci, I.Bertini, N.D'Amelio, E.Gaggelli, E.Libralesso, I.Matecko, P.Turano, and J.S.Valentine (2005).
Fully metallated S134N Cu,Zn-superoxide dismutase displays abnormal mobility and intermolecular contacts in solution.
  J Biol Chem, 280, 35815-35821.  
15930159 R.B.Guo, P.Rigolet, L.Zargarian, S.Fermandjian, and X.G.Xi (2005).
Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom's syndrome helicase.
  Nucleic Acids Res, 33, 3109-3124.  
15062777 A.F.Miller (2004).
Superoxide dismutases: active sites that save, but a protein that kills.
  Curr Opin Chem Biol, 8, 162-168.  
15326189 F.Arnesano, L.Banci, I.Bertini, M.Martinelli, Y.Furukawa, and T.V.O'Halloran (2004).
The unusually stable quaternary structure of human Cu,Zn-superoxide dismutase 1 is controlled by both metal occupancy and disulfide status.
  J Biol Chem, 279, 47998-48003.  
15292213 J.L.Liu, P.Rigolet, S.X.Dou, P.Y.Wang, and X.G.Xi (2004).
The zinc finger motif of Escherichia coli RecQ is implicated in both DNA binding and protein folding.
  J Biol Chem, 279, 42794-42802.  
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.