Structure of xylose isomerase from Streptomyces diastaticus No. 7 strain M1033 at 1.85 Å resolution

The structure of xylose isomerase (XyI) from Streptomyces diastaticus No. 7 strain M1033 (SDXyI) has been refined at 1.85 Å resolution to conventional and free R factors of 0.166 and 0.219, respectively. SDXyI was crystallized in space group P2₁2₁2, with unit-cell parameters a = 87.976, b = 98.836, c = 93.927 Å. One dimer of the tetrametric molecule is found in each asymmetric unit. Each monomer consists of two domains: a large N-terminal domain (residues 1–320), containing a parallel eight-stranded α/β barrel, and a small C-terminal loop (residues 321–387), containing five helices linked by random coil. The four monomers are essentially identical in the tetramer, possessing non-crystallographic 222 symmetry with one twofold axis essentially coincident with the crystallographic twofold axis in the space group P2₁2₁2, which may explain why the diffraction pattern has strong pseudo-I222 symmetry even at medium resolution. The crystal structures of XyIs from different bacterial strains, especially from Streptomyces, are similar. The α2 helix of the α/β barrel has a different position in the structures of different XyIs. The conformation of C-terminal fragment 357–364 in the SDXyI structure has a small number of differences to that of other XyIs. Two Co²⁺ ions rather than Mg²⁺ ions exist in the active site of the SDXyI structure; SDXyI seems to prefer to bind Co²⁺ ions rather than Mg²⁺ ions.