PDBsum entry 1msd

Oxidoreductase (superoxide acceptor)

PDB id: 1msd

Contents

Protein chains

198 a.a. *

Metals

_MN ×2

* Residue conservation analysis

PDB id:

1msd

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)

Resolution:

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

Date:

10-Nov-92 Release date: 15-Jul-93

Protein chains

P04179  (SODM_HUMAN) -  Superoxide dismutase [Mn], mitochondrial from Homo sapiens

Seq: 222 a.a.

Struc: 198 a.a.

Enzyme reactions

• Enzyme class: E.C.1.15.1.1 - superoxide dismutase.
• Reaction: 2 superoxide + 2 H⁺ = H2O2 + O2
• Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

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.

ABSTRACT

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.