5ZYD
Crystal Structure of Glucose Isomerase Soaked with Glucose
Summary for 5ZYD
| Entry DOI | 10.2210/pdb5zyd/pdb |
| Related | 5Y4I 5Y4J |
| Descriptor | Xylose isomerase, MAGNESIUM ION, ACETATE ION, ... (4 entities in total) |
| Functional Keywords | glucose isomerase, xylose isomerase, isomerase |
| Biological source | Streptomyces rubiginosus |
| Total number of polymer chains | 1 |
| Total formula weight | 43366.65 |
| Authors | Nam, K.H. (deposition date: 2018-05-24, release date: 2018-11-28, Last modification date: 2023-11-22) |
| Primary citation | Bae, J.E.,Hwang, K.Y.,Nam, K.H. Structural analysis of substrate recognition by glucose isomerase in Mn2+binding mode at M2 site in S. rubiginosus Biochem. Biophys. Res. Commun., 503:770-775, 2018 Cited by PubMed Abstract: Glucose isomerase (GI) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S. rubiginosus (SruGI) complexed with a xylitol inhibitor in one metal binding mode. Although we assessed inhibitor binding at the M1 site, the metal binding at the M2 site and the substrate recognition mechanism for SruGI remains the unclear. Here, we report the crystal structure of the two metal binding modes of SruGI and its complex with glucose. This study provides a snapshot of metal binding at the SruGI M2 site in the presence of Mn, but not in the presence of Mg. Metal binding at the M2 site elicits a configuration change at the M1 site. Glucose molecule can only bind to the M1 site in presence of Mn at the M2 site. Glucose and Mn at the M2 site were bridged by water molecules using a hydrogen bonding network. The metal binding geometry of the M2 site indicates a distorted octahedral coordination with an angle of 55-110°, whereas the M1 site has a relatively stable octahedral coordination with an angle of 85-95°. We suggest a two-step sequential process for SruGI substrate recognition, in Mn binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition. PubMed: 29909012DOI: 10.1016/j.bbrc.2018.06.074 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.4 Å) |
Structure validation
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