Structure of xylose isomerase from Streptomyces diastaticus no. 7 strain M1033 at 1.85 A resolution.
The structure of xylose isomerase (XyI) from Streptomyces diastaticus No. 7 strain M1033 (SDXyI) has been refined at 1.85 A resolution to conventional and free R factors of 0.166 and 0.219, respectively. SDXyI was crystallized in space group P2(1)2(1)2, with unit-cell parameters a = 87.976, b = 98.836, c = 93.927 A. 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 alpha/beta 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 P2(1)2(1)2, 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 alpha2 helix of the alpha/beta 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 Co(2+) ions rather than Mg(2+) ions exist in the active site of the SDXyI structure; SDXyI seems to prefer to bind Co(2+) ions rather than Mg(2+) ions.
Zhu
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Department of Molecular Biology, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China.
Teng
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M
Niu
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L
Xu
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C
Wang
Y
Y
D019747:Aldose-Ketose Isomerases / Q000737:chemistry* / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D003035:Cobalt / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D019281:Dimerization; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D008345:Manganese / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D017386:Sequence Homology, Amino Acid; D012996:Solutions; D013302:Streptomyces / Q000145:classification / Q000201:enzymology*; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
D001426:Bacterial Proteins; D012996:Solutions; D014867:Water; D003035:Cobalt; D008345:Manganese; D019747:Aldose-Ketose Isomerases; C023298:xylose isomerase; D008274:Magnesium