PDBsum entry 1msd

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Oxidoreductase (superoxide acceptor) PDB id
Protein chains
198 a.a. *
_MN ×2
* Residue conservation analysis
PDB id:
Name: Oxidoreductase (superoxide acceptor)
Title: Comparison of the crystal structures of genetically engineered human manganese superoxide dismutase and manganese superoxide dismutase from thermus thermophilus. Differences in dimer-dimer interactions.
Structure: Manganese superoxide dismutase. Chain: a, b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Tetramer (from PQS)
3.20Å     R-factor:   0.207    
Authors: J.Sussman,U.G.Wagner,K.A.Pattridge,M.L.Ludwig
Key ref:
U.G.Wagner et al. (1993). Comparison of the crystal structures of genetically engineered human manganese superoxide dismutase and manganese superoxide dismutase from Thermus thermophilus: differences in dimer-dimer interaction. Protein Sci, 2, 814-825. PubMed id: 8495200 DOI: 10.1002/pro.5560020511
10-Nov-92     Release date:   15-Jul-93    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P04179  (SODM_HUMAN) -  Superoxide dismutase [Mn], mitochondrial
222 a.a.
198 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     superoxide dismutase activity     2 terms  


    Added reference    
DOI no: 10.1002/pro.5560020511 Protein Sci 2:814-825 (1993)
PubMed id: 8495200  
Comparison of the crystal structures of genetically engineered human manganese superoxide dismutase and manganese superoxide dismutase from Thermus thermophilus: differences in dimer-dimer interaction.
U.G.Wagner, K.A.Pattridge, M.L.Ludwig, W.C.Stallings, M.M.Werber, C.Oefner, F.Frolow, J.L.Sussman.
The three-dimensional X-ray structure of a recombinant human mitochondrial manganese superoxide dismutase (MnSOD) (chain length 198 residues) was determined by the method of molecular replacement using the related structure of MnSOD from Thermus thermophilus as a search model. This tetrameric human MnSOD crystallizes in space group P2(1)2(1)2 with a dimer in the asymmetric unit (Wagner, U.G., Werber, M.M., Beck, Y., Hartman, J.R., Frolow, F., & Sussman, J.L., 1989, J. Mol. Biol. 206, 787-788). Refinement of the protein structure (3,148 atoms with Mn and no solvents), with restraints maintaining noncrystallographic symmetry, converged at an R-factor of 0.207 using all data from 8.0 to 3.2 A resolution and group thermal parameters. The monomer-monomer interactions typical of bacterial Fe- and Mn-containing SODs are retained in the human enzyme, but the dimer-dimer interactions that form the tetramer are very different from those found in the structure of MnSOD from T. thermophilus. In human MnSOD one of the dimers is rotated by 84 degrees relative to its equivalent in the thermophile enzyme. As a result the monomers are arranged in an approximately tetrahedral array, the dimer-dimer packing is more intimate than observed in the bacterial MnSOD from T. thermophilus, and the dimers interdigitate. The metal-ligand interactions, determined by refinement and verified by computation of omit maps, are identical to those observed in T. thermophilus MnSOD.
  Selected figure(s)  
Figure 4.
Fig. 4. Distances between Ca positions of the human and bacterial crystals diffracted to -2.8 A resolution, but because they
Figure 6.
Fig. 6. Electron density in the vicinity of the Mn binding site of the B chain: difference (IFo] - IF,I) mapafter X- PLORrefinement ofamodel from which the metal ions were omitted (line 4 of Table 1). The positive contoursare at 40; the peak density at the metal site is about 60. \ .
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1993, 2, 814-825) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20972560 H.Xiang, G.Pan, C.R.Vossbrinck, R.Zhang, J.Xu, T.Li, Z.Zhou, C.Lu, and Z.Xiang (2010).
A tandem duplication of manganese superoxide dismutase in Nosema bombycis and its evolutionary origins.
  J Mol Evol, 71, 401-414.  
18798256 A.Mancini, A.Borrelli, A.Schiattarella, L.Aloj, M.Aurilio, F.Morelli, A.Pica, A.Occhiello, R.Lorizio, R.Mancini, A.Sica, L.Mazzarella, F.Sica, P.Grieco, E.Novellino, D.Pagnozzi, P.Pucci, and J.Rommelaere (2008).
Biophysical and biochemical characterization of a liposarcoma-derived recombinant MnSOD protein acting as an anticancer agent.
  Int J Cancer, 123, 2684-2695.  
11141052 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase.
  Biochemistry, 40, 15-27.
PDB codes: 1en4 1en5 1en6
11294629 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity.
  Biochemistry, 40, 4622-4632.
PDB codes: 1i08 1i0h
9698380 C.L.Borders, M.J.Bjerrum, M.A.Schirmer, and S.G.Oliver (1998).
Characterization of recombinant Saccharomyces cerevisiae manganese-containing superoxide dismutase and its H30A and K170R mutants expressed in Escherichia coli.
  Biochemistry, 37, 11323-11331.  
9537987 Y.Guan, M.J.Hickey, G.E.Borgstahl, R.A.Hallewell, J.R.Lepock, D.O'Connor, Y.Hsieh, H.S.Nick, D.N.Silverman, and J.A.Tainer (1998).
Crystal structure of Y34F mutant human mitochondrial manganese superoxide dismutase and the functional role of tyrosine 34.
  Biochemistry, 37, 4722-4730.
PDB codes: 1ap5 1ap6
9537988 Y.Hsieh, Y.Guan, C.Tu, P.J.Bratt, A.Angerhofer, J.R.Lepock, M.J.Hickey, J.A.Tainer, H.S.Nick, and D.N.Silverman (1998).
Probing the active site of human manganese superoxide dismutase: the role of glutamine 143.
  Biochemistry, 37, 4731-4739.
PDB code: 1qnm
9125514 T.Hunter, K.Ikebukuro, W.H.Bannister, J.V.Bannister, and G.J.Hunter (1997).
The conserved residue tyrosine 34 is essential for maximal activity of iron-superoxide dismutase from Escherichia coli.
  Biochemistry, 36, 4925-4933.  
8307013 B.Meier, A.P.Sehn, M.E.Schininà, and D.Barra (1994).
In vivo incorporation of copper into the iron-exchangeable and manganese-exchangeable superoxide dismutase from Propionibacterium shermanii. Amino acid sequence and identity of the protein moieties.
  Eur J Biochem, 219, 463-468.  
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 codes are shown on the right.