PDBsum entry 2nnx

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chain
153 a.a. *
_ZN ×8
Waters ×308
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of the h46r, h48q double mutant of human [ superoxide dismutase
Structure: Superoxide dismutase [cu-zn]. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sod1. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Biol. unit: Tetramer (from PQS)
2.30Å     R-factor:   0.189     R-free:   0.241
Authors: J.P.Schuermann,P.J.Hart
Key ref:
J.Wang et al. (2007). Disease-associated mutations at copper ligand histidine residues of superoxide dismutase 1 diminish the binding of copper and compromise dimer stability. J Biol Chem, 282, 345-352. PubMed id: 17092942 DOI: 10.1074/jbc.M604503200
24-Oct-06     Release date:   07-Nov-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00441  (SODC_HUMAN) -  Superoxide dismutase [Cu-Zn]
154 a.a.
153 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - 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: 10.1074/jbc.M604503200 J Biol Chem 282:345-352 (2007)
PubMed id: 17092942  
Disease-associated mutations at copper ligand histidine residues of superoxide dismutase 1 diminish the binding of copper and compromise dimer stability.
J.Wang, A.Caruano-Yzermans, A.Rodriguez, J.P.Scheurmann, H.H.Slunt, X.Cao, J.Gitlin, P.J.Hart, D.R.Borchelt.
A subset of superoxide dismutase 1 (Cu/Zn-SOD1) mutants that cause familial amyotrophic lateral sclerosis (FALS) have heightened reactivity with (-)ONOO and H(2)O(2) in vitro. This reactivity requires a copper ion bound in the active site and is a suggested mechanism of motor neuron injury. However, we have found that transgenic mice that express SOD1-H46R/H48Q, which combines natural FALS mutations at ligands for copper and which is inactive, develop motor neuron disease. Using a direct radioactive copper incorporation assay in transfected cells and the established tools of single crystal x-ray diffraction, we now demonstrate that this variant does not stably bind copper. We find that single mutations at copper ligands, including H46R, H48Q, and a quadruple mutant H46R/H48Q/H63G/H120G, also diminish the binding of radioactive copper. Further, using native polyacrylamide gel electrophoresis and a yeast two-hybrid assay, the binding of copper was found to be related to the formation of the stable dimeric enzyme. Collectively, our data demonstrate a relationship between copper and assembly of SOD1 into stable dimers and also define disease-causing SOD1 mutants that are unlikely to robustly produce toxic radicals via copper-mediated chemistry.
  Selected figure(s)  
Figure 1.
FIGURE 1. The metal-binding sites of the human FALS SOD1 double mutant H46R/H48Q (left) and the wild-type enzyme (right). The structure surrounding the copper-binding site of one subunit of SOD1-H46R/H48Q is compared with SOD1-wt (right). All subunits in the crystal of SOD1-H46R/H48Q showed perturbed copper-binding sites. The structure shown is that of the crystal subunits that most closely resemble SOD1-wt. Arg-143 and residues corresponding to metal ions ligands in the wild-type enzyme (metal ligand 46, 48, 63, 71, 80, 83, and 120) are labeled. The metal ions are represented by spheres. Metal ligand and hydrogen bonds are shown as dotted lines. In the left image, the side chain of the Arg residue substituted at position 46 donates a hydrogen bond to the carbonyl oxygen of Thr-137 on the opposite side of the active site channel, preventing the binding of copper ion (see text).
Figure 2.
FIGURE 2. FALS mutations at copper-binding histidine residues of SOD1 dramatically reduce affinity for copper. A, CHO cells were transfected to express human SOD variants before being metabolically labeled with 50 µCi/ml of ^64Cu for 3 h. 100 µg of each cell lysate was separated on a non-reducing 10% polyacrylamide gel containing 0.1% SDS. The ^64Cu autoradiogram shows Cu-labeled endogenous hamster SOD1 dimer (solid arrow) in all samples, and Cu-labeled human SOD1 dimer (solid arrowhead) only in the WT sample. B, a duplicate of the gel used for ^64Cu autoradiogram was analyzed by SOD1 immunoblot, which reveals endogenous hamster SOD1 monomer and human SOD1 monomers that are not labeled by ^64Cu. Note: apo refers to the absence or presence of copper.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 345-352) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20382740 A.M.El-Kadi, V.Bros-Facer, W.Deng, A.Philpott, E.Stoddart, G.Banks, G.S.Jackson, E.M.Fisher, M.R.Duchen, L.Greensmith, A.L.Moore, and M.Hafezparast (2010).
The legs at odd angles (Loa) mutation in cytoplasmic dynein ameliorates mitochondrial function in SOD1G93A mouse model for motor neuron disease.
  J Biol Chem, 285, 18627-18639.  
20399791 C.Münch, and A.Bertolotti (2010).
Exposure of hydrophobic surfaces initiates aggregation of diverse ALS-causing superoxide dismutase-1 mutants.
  J Mol Biol, 399, 512-525.  
21098299 J.R.Auclair, K.J.Boggio, G.A.Petsko, D.Ringe, and J.N.Agar (2010).
Strategies for stabilizing superoxide dismutase (SOD1), the protein destabilized in the most common form of familial amyotrophic lateral sclerosis.
  Proc Natl Acad Sci U S A, 107, 21394-21399.  
20871097 M.Prudencio, A.Durazo, J.P.Whitelegge, and D.R.Borchelt (2010).
An examination of wild-type SOD1 in modulating the toxicity and aggregation of ALS-associated mutant SOD1.
  Hum Mol Genet, 19, 4774-4789.  
20052996 Z.You, X.Cao, A.B.Taylor, P.J.Hart, and R.L.Levine (2010).
Characterization of a covalent polysulfane bridge in copper-zinc superoxide dismutase .
  Biochemistry, 49, 1191-1198.
PDB code: 3k91
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.  
19416874 C.M.Karch, M.Prudencio, D.D.Winkler, P.J.Hart, and D.R.Borchelt (2009).
Role of mutant SOD1 disulfide oxidation and aggregation in the pathogenesis of familial ALS.
  Proc Natl Acad Sci U S A, 106, 7774-7779.  
19309264 K.A.Trumbull, and J.S.Beckman (2009).
A role for copper in the toxicity of zinc-deficient superoxide dismutase to motor neurons in amyotrophic lateral sclerosis.
  Antioxid Redox Signal, 11, 1627-1639.  
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.  
19320055 M.Son, Q.Fu, K.Puttaparthi, C.M.Matthews, and J.L.Elliott (2009).
Redox susceptibility of SOD1 mutants is associated with the differential response to CCS over-expression in vivo.
  Neurobiol Dis, 34, 155-162.  
19596823 S.V.Seetharaman, M.Prudencio, C.Karch, S.P.Holloway, D.R.Borchelt, and P.J.Hart (2009).
Immature copper-zinc superoxide dismutase and familial amyotrophic lateral sclerosis.
  Exp Biol Med (Maywood), 234, 1140-1154.  
18337307 J.B.Proescher, M.Son, J.L.Elliott, and V.C.Culotta (2008).
Biological effects of CCS in the absence of SOD1 enzyme activation: implications for disease in a mouse model for ALS.
  Hum Mol Genet, 17, 1728-1737.  
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
17448900 S.Watanabe, S.Nagano, J.Duce, M.Kiaei, Q.X.Li, S.M.Tucker, A.Tiwari, R.H.Brown, M.F.Beal, L.J.Hayward, V.C.Culotta, S.Yoshihara, S.Sakoda, and A.I.Bush (2007).
Increased affinity for copper mediated by cysteine 111 in forms of mutant superoxide dismutase 1 linked to amyotrophic lateral sclerosis.
  Free Radic Biol Med, 42, 1534-1542.  
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.