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PDBsum entry 1bxb

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Isomerase PDB id
1bxb
Jmol
Contents
Protein chains
387 a.a. *
Waters ×1084
* Residue conservation analysis

References listed in PDB file
Key reference
Title Crystal structures of thermostable xylose isomerases from thermus caldophilus and thermus thermophilus: possible structural determinants of thermostability.
Authors C.Chang, B.C.Park, D.S.Lee, S.W.Suh.
Ref. J Mol Biol, 1999, 288, 623-634. [DOI no: 10.1006/jmbi.1999.2696]
PubMed id 10329168
Abstract
The crystal structures of highly thermostable xylose isomerases from Thermus thermophilus (TthXI) and Thermus caldophilus (TcaXI), both with the optimum reaction temperature of 90 degrees C, have been determined by X-ray crystallography. The model of TcaXI has been refined to an R-factor of 17.8 % for data extending to 2.3 A and that of TthXI to 17.1 % for data extending to 2.2 A. The tetrameric arrangement of subunits characterized by the 222-symmetry and the tertiary fold of each subunit in both TcaXI and TthXI are basically the same as in other xylose isomerases. Each monomer is composed of two domains. Domain I (residues 1 to 321) folds into the (beta/alpha)8-barrel. Domain II (residues 322 to 387), lacking beta-strands, makes extensive contacts with domain I of an adjacent subunit. Each monomer of TcaXI contains ten beta-strands, 15 alpha-helices, and six 310-helices, while that of TthXI contains ten beta-strands, 16 alpha-helices, and five 310-helices. Although the electron density does not indicate the presence of bound metal ions in the present models of both TcaXI and TthXI, the active site residues show the conserved structural features. In order to understand the structural basis for thermostability of these enzymes, their structures have been compared with less thermostable XIs from Arthrobacter B3728 and Actinoplanes missouriensis (AXI and AmiXI), with the optimum reaction temperatures of 80 degrees C and 75 degrees C, respectively. Analyses of various factors that may affect protein thermostability indicate that the possible structural determinants of the enhanced thermostability of TcaXI/TthXI over AXI/AmiXI are (i) an increase in ion pairs and ion-pair networks, (ii) a decrease in the large inter-subunit cavities, (iii) a removal of potential deamidation/isoaspartate formation sites, and (iv) a shortened loop.
Figure 1.
Figure 1. (a) A ribbon diagram of TcaXI (left) and TthXI subunits. Each subunit has two domains. a-Helices are in cyan, 310-helices in green, and b-strands in orange. Secondary structures have been assigned with the program PROMOTIF (Hutchinson & Thorton, 1995). (b) Backbone superposition of TcaXI (white), TthXI (yellow), AXI (purple), and AmiXI (cyan) subunits. Figures drawn with MOLSCRIPT (Kraulis, 1991) and rendered by Raster3D (Merritt & Murphy, 1994).
Figure 2.
Figure 2. Structure-based alignment of TcaXI, TthXI, AXI, and AmiXI sequences. Secondary structures as assigned by PROMOTIF (Hutchinson & Thornton, 1995) are shaded in different gray scales. Residues involved in binding the substrate and metal ions are indicated by + and -, respectively.
The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 288, 623-634) copyright 1999.
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