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PDBsum entry 1kmg

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protein metals links
Oxidoreductase PDB id
1kmg
Jmol
Contents
Protein chain
153 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
1kmg
Name: Oxidoreductase
Title: The solution structure of monomeric copper-free superoxide dismutase
Structure: Superoxide dismutase. 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: 35 models
Authors: L.Banci,I.Bertini,F.Cantini,M.D'Onofrio,M.S.Viezzoli
Key ref:
L.Banci et al. (2002). Structure and dynamics of copper-free SOD: The protein before binding copper. Protein Sci, 11, 2479-2492. PubMed id: 12237469 DOI: 10.1110/ps.0210802
Date:
15-Dec-01     Release date:   02-Oct-02    
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: 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     extracellular region   20 terms 
  Biological process     cellular response to potassium ion   66 terms 
  Biochemical function     antioxidant activity     13 terms  

 

 
    Added reference    
 
 
DOI no: 10.1110/ps.0210802 Protein Sci 11:2479-2492 (2002)
PubMed id: 12237469  
 
 
Structure and dynamics of copper-free SOD: The protein before binding copper.
L.Banci, I.Bertini, F.Cantini, M.D'Onofrio, M.S.Viezzoli.
 
  ABSTRACT  
 
The solution structure of the copper-free state of a monomeric form of superoxide dismutase (153 amino acids) was determined through (13)C and (15)N labeling. The protein contained two mutations at the native subunit-subunit interface (F50E and G51E) to obtain a soluble monomeric species and a mutation in the active site channel (E133Q). About 93% of carbon atoms, 95% of nitrogen atoms, and 96% of the protons were assigned. A total of 2467 meaningful NOEs and 170 dihedral angles provided a family of 35 conformers with RMSD values of 0.76 +/- 0.09 A for the backbone and 1.22 +/- 0.13 A for all heavy atoms. The secondary structure elements, connected by loops, produce the typical superoxide dismutase Greek key fold, formed by an eight-stranded beta-barrel. The comparison with the copper-bound monomeric and dimeric structures shows that the metal ligands have a conformation very close to that of the copper-bound forms. This feature indicates that the copper-binding site is preorganized and well ordered also in the absence of the copper ion. The active-site channel shows a sizable increase in width, achieving a suitable conformation to receive the copper ion. The histidines ring NH resonances that bind the copper ion and the region around the active-site channel experience, as found from (15)N relaxation studies, conformational exchange processes. The increased width of the channel and the higher mobility of the histidine rings of the copper site in the copper-free form with respect to the holoprotein is discussed in terms of the process of copper insertion.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. S2 values of (A) EZnM2E133QSOD and (B) CuZnM2E133QSOD.
Figure 6.
Fig. 6. Comparison between EZnM2E133QSOD and CuZnM2E133QSOD structures. Backbone of EZnM2E133QSOD (dark gray) and CuZnM2E133QSOD (light gray). The zinc ions are white and the copper ion is dark gray. (Inset) Metal-binding sites, including metal-coordinating amino acid residues.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2002, 11, 2479-2492) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20404910 A.K.Svensson, O.Bilsel, C.Kayatekin, J.A.Adefusika, J.A.Zitzewitz, and C.R.Matthews (2010).
Metal-free ALS variants of dimeric human Cu,Zn-superoxide dismutase have enhanced populations of monomeric species.
  PLoS One, 5, e10064.  
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.  
20205585 N.J.Robinson, and D.R.Winge (2010).
Copper metallochaperones.
  Annu Rev Biochem, 79, 537-562.  
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.  
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.  
18645238 M.Yogavel, P.C.Mishra, J.Gill, P.K.Bhardwaj, S.Dutt, S.Kumar, P.S.Ahuja, and A.Sharma (2008).
Structure of a superoxide dismutase and implications for copper-ion chelation.
  Acta Crystallogr D Biol Crystallogr, 64, 892-901.  
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
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
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.  
16145699 F.Arnesano, L.Banci, I.Bertini, A.Fantoni, L.Tenori, and M.S.Viezzoli (2005).
Structural interplay between calcium(II) and copper(II) binding to S100A13 protein.
  Angew Chem Int Ed Engl, 44, 6341-6344.
PDB codes: 1yur 1yus 1yut 1yuu
15897454 L.Banci, I.Bertini, V.Calderone, F.Cramaro, R.Del Conte, A.Fantoni, S.Mangani, A.Quattrone, and M.S.Viezzoli (2005).
A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.
  Proc Natl Acad Sci U S A, 102, 7541-7546.
PDB codes: 1s4i 1u3n
15215895 Y.Furukawa, A.S.Torres, and T.V.O'Halloran (2004).
Oxygen-induced maturation of SOD1: a key role for disulfide formation by the copper chaperone CCS.
  EMBO J, 23, 2872-2881.  
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.