PDBsum entry 1clk

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Isomerase PDB id
Protein chain
387 a.a. *
Waters ×392
* Residue conservation analysis

References listed in PDB file
Key reference
Title Structure of xylose isomerase from streptomyces diastaticus no. 7 strain m1033 at 1.85 a resolution.
Authors X.Zhu, M.Teng, L.Niu, C.Xu, Y.Wang.
Ref. Acta Crystallogr D Biol Crystallogr, 2000, 56, 129-136. [DOI no: 10.1107/S0907444999015097]
PubMed id 10666592
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.
Figure 1.
Figure 1 The sequences of seven xylose isomerases for which crystal structures have been reported. SD, S. diastaticus No. 7 strain M1033 (Wang et al., 1994[Wang, Y., Huang, Z., Dai, X., Liu, J., Cui, T., Niu, L., Wang, C. & Xu, X. (1994). Chin. J. Biotechnol. 10, 97-103.]); SR, S. rubiginosus (Wong et al., 1991[Wong, H. C., Ting, Y., Lin, H. C., Reichert, F., Myambo, K., Watt, K. W., Toy, P. L. & Drummond, R. J. (1991). J. Bacteriol. 173, 6849-6858.]); SO, S. olivochromogenes (Lavie et al., 1994[Lavie, A., Allen, K. N., Petsko, G. A. & Ringe, D. (1994). Biochemistry, 33, 5459-5480.]); SA, S. albus (Dauter et al., 1990[Dauter, Z., Terry, H., Witzel, H. & Wilson, K. S. (1990). Acta Cryst. B46, 833-841.]); SM, S. murinus (Rasmussen et al., 1994[Rasmussen, H., La Cour, T., Nyborg, J. & Schülein, M. (1994). Acta Cryst. D50, 124-131.]); AB, Arthrobacter strain B3728 (Loviny-Anderton et al., 1991[Loviny-Anderton, T., Shaw, P. C., Shin, M. K. & Hartley, B. S. (1991). Biochem. J. 277, 263-271.]); AM, Actinoplanes missouriensis (Amore & Hollenberg, 1989[Amore, R. & Hollenberg, C. P. (1989). Nucleic Acids Res. 17, 7515-7515.]).
Figure 2.
Figure 2 The C^ tracings of the SDXyI structure: (a) monomer, the 2 helix Asp64-Thr81 of the / -barrel; the fragment Glu357-Ala364 and the metal sites are indicated, (b) `butterfly' dimer or asymmetric unit dimer, (c) `yin-yang' dimer and (d) `diagonal' dimer. The figures were rendered using MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).
The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 129-136) copyright 2000.
Secondary reference #1
Title Crystal structure of streptomyces diastaticus no.7 strain m1033 xylose isomerase
Authors X.Zhu, W.Gong, L.Niu, M.Teng, C.Xu, C.Wu, T.Cui, Y.Wang, C.Wang.
Ref. sci china, ser c: life sci, 1996, 39, 636.
Secondary reference #2
Title Growth of single crystals and preliminary analysis of glucose isomerase from streptomyces m1033
Authors G.Y.Zhang, L.W.Niu, W.Z.Huang, C.Wang, J.Liu, Y.Cui, X.A.Liu, Y.Z.Wang, X.Xu, D.C.Liang.
Ref. chin sci bull, 1991, 36, 1646.
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