2GYI

DESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT XYLOSE ISOMERASE INHIBITOR, D-THREONOHYDROXAMIC ACID, AND HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE ENZYME-INHIBITOR COMPLEX

Replaces:  1GYI

Summary for 2GYI

• Entry DOI: 10.2210/pdb2gyi/pdb
• Descriptor: XYLOSE ISOMERASE, MAGNESIUM ION, 2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC ACID, ... (4 entities in total)
• Functional Keywords: isomerase(intramolecular oxidoreductase)
• Biological source: Streptomyces olivochromogenes
• Cellular location: Cytoplasm: P15587
• Total number of polymer chains: 2
• Total formula weight: 86089.15

Authors

Allen, K.N.,Lavie, A.,Petsko, G.A.,Ringe, D. (deposition date: 1994-09-01, release date: 1995-07-10, Last modification date: 2024-02-14)

Primary citation

Allen, K.N.,Lavie, A.,Petsko, G.A.,Ringe, D.
Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex
Biochemistry, 34:3742-3749, 1995

PubMed Abstract: The binding of a potent inhibitor to the enzyme D-xylose isomerase from Streptomyces olivochromogenes was examined by kinetics and X-ray crystallography. The inhibitor D-threonohydroxamic acid (THA) was designed to mimic the putative transition state of the isomerization step catalyzed by the enzyme on the substrate xylose. THA was synthesized and found to be a slow-binding competitive inhibitor with the substrate glucose. The Ki < or = 100 nM was at least one million-fold less than the KM for glucose. The X-ray crystallographic structure of xylose isomerase with THA soaked into the crystals (concentration = 1000Ki) was obtained to 1.6-A resolution and refined to an R factor of 21.6%. The free enzyme and the enzyme in the xylose isomerase-THA complex show no significant structural differences. THA binds in an analogous fashion to glucose, in a linear conformation, forming ligands with Mg-1 and Mg-2 and hydrogen bonds with His53 and Lys182. On the basis of these similarities to glucose binding and its potent inhibition, we propose that THA resembles the transition state for the enzyme-catalyzed hydride transfer reaction. The THA C2 hydroxyl forms a bridging ligand between Mg-1 and Mg-2; it must be deprotonated to do so. By analogy, we propose that, during the catalytic reaction, C2 of the substrate glucose is deprotonated, and that this proton can be moved to the C1 hydroxyl concomitant with hydride transfer. We find evidence for metal movement during catalysis upon deprotonation of the C2 hydroxyl, to allow formation of a bridging ligand.(ABSTRACT TRUNCATED AT 250 WORDS)

PubMed: 7893671
DOI: 10.1021/bi00011a032

Experimental method

X-RAY DIFFRACTION (1.6 Å)