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

The structure of xylose isomerase (XyI) from Streptomyces diastaticus No. 7 strain M1033 (SDXyI) has been refined at 1.85 Angstrom resolution to conve ntional and free R factors of 0.166 and 0.219, respectively. SDXyI was crys tallized in space group P2(1)2(1)2, with unit-cell parameters a = 87.976, b = 98.836, c = 93.927 Angstrom. One dimer of the tetrametric molecule is fo und in each asymmetric unit. Each monomer consists of two domains: a large N-terminal domain (residues 1-320), containing a parallel eight-stranded al pha/beta barrel, and a small C-terminal loop (residues 321-387), containing five helices linked by random coil. The four monomers are essentially iden tical in the tetramer, possessing non-crystallographic 222 symmetry with on e twofold axis essentially coincident with the crystallographic twofold axi s in the space group P2(1)2(1)2, which may explain why the diffraction patt ern has strong pseudo-I222 symmetry even at medium resolution. The crystal structures of XyIs from different bacterial strains, especially from Strept omyces, are similar. The alpha 2 helix of the alpha/beta barrel has a diffe rent position in the structures of different XyIs. The conformation of C-te rminal fragment 357-364 in the SDXyI structure has a small number of differ ences to that of other XyIs. Two Co2+ ions rather than Mg2+ ions exist in t he active site of the SDXyI structure; SDXyI seems to prefer to bind Co2+ i ons rather than Mg2+ ions.