PDBsum entry 1clk

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Isomerase PDB id
Protein chain
387 a.a. *
Waters ×392
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of streptomyces diastaticus no.7 strain m1 isomerase at 1.9 a resolution with pseudo-i222 space group
Structure: Xylose isomerase. Chain: a. Synonym: d-xylose ketol isomerase, d-glucose isomearse. Ec:
Source: Streptomyces diastaticus. Organism_taxid: 1956. Strain: streptomyces diastaticus no.7 strain m1033
Biol. unit: Tetramer (from PDB file)
1.90Å     R-factor:   0.186    
Authors: L.Niu,M.Teng,X.Zhu,W.Gong
Key ref:
X.Zhu et al. (2000). Structure of xylose isomerase from Streptomyces diastaticus no. 7 strain M1033 at 1.85 A resolution. Acta Crystallogr D Biol Crystallogr, 56, 129-136. PubMed id: 10666592 DOI: 10.1107/S0907444999015097
29-Apr-99     Release date:   03-May-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P50910  (XYLA_STRDI) -  Xylose isomerase
388 a.a.
387 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Xylose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-xylopyranose = D-xylulose
= D-xylulose
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     carbohydrate metabolic process   3 terms 
  Biochemical function     isomerase activity     4 terms  


    Key reference    
DOI no: 10.1107/S0907444999015097 Acta Crystallogr D Biol Crystallogr 56:129-136 (2000)
PubMed id: 10666592  
Structure of xylose isomerase from Streptomyces diastaticus no. 7 strain M1033 at 1.85 A resolution.
X.Zhu, M.Teng, L.Niu, C.Xu, Y.Wang.
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.
  Selected figure(s)  
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.  
  Figures were selected by an automated process.