8WDG

Subatomic crystal structure of glucose isomerase from Streptomyces rubiginosus

Summary for 8WDG

• Entry DOI: 10.2210/pdb8wdg/pdb
• Descriptor: Xylose isomerase, MAGNESIUM ION, Xylitol, ... (4 entities in total)
• Functional Keywords: glucose isomerase, subatomic resolution, isomerase
• Biological source: Streptomyces rubiginosus
• Total number of polymer chains: 1
• Total formula weight: 43206.01

Authors

Nam, K.H. (deposition date: 2023-09-15, release date: 2023-10-04, Last modification date: 2024-04-17)

Primary citation

Xu, Y.,Nam, K.H.
Xylitol binding to the M1 site of glucose isomerase induces a conformational change in the substrate binding channel.
Biochem.Biophys.Res.Commun., 682:21-26, 2023

PubMed Abstract: Glucose isomerase (GI) is extensively used in the food industry for production of high-fructose corn syrup and for the production of biofuels and other renewable chemicals. Structure-based studies on GI inhibitors are important for improving its efficiency in industrial applications. Here, we report the subatomic crystal structure of Streptomyces rubiginosus GI (SruGI) complexed with its inhibitor, xylitol, at 0.99 Å resolution. Electron density map and temperature factor analysis showed partial binding of xylitol to the M1 metal binding site of SruGI, providing two different conformations of the metal binding site and the substrate binding channel. The xylitol molecule induced a conformational change in the M2 metal ion-interacting Asp255 residue, which subsequently led to a conformational change in the side chain of Asp181 residue. This led to the positional shift of Pro25 by 1.71 Å and side chain rotation of Phe26 by 21°, where located on the neighboring protomer in tetrameric SruGI. The conformation change of these two residues affect the size of the substrate-binding channel of GI. Therefore, xylitol binding to M1 site of SruGI induces not only a conformational changes of the metal-binding site, but also conformational change of substrate-binding channel of the tetrameric SruGI. These results expand our knowledge about the mechanism underlying the inhibitory effect of xylitol on GI.

PubMed: 37793321
DOI: 10.1016/j.bbrc.2023.09.087

Experimental method

X-RAY DIFFRACTION (0.99 Å)