Hydrogen Location in Stages of an Enzyme-Catalyzed Reaction: Time-of-Flight Neutron Structure of d-Xylose Isomerase with Bound d-Xylulose
- 26 June 2008
- journal article
- other
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 47 (29), 7595-7597
- https://doi.org/10.1021/bi8005434
Abstract
The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme d-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, d-xylulose, shows, unexpectedly, that O5 of d-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism.Keywords
This publication has 12 references indexed in Scilit:
- Neutron protein crystallography: beyond the folding structure of biological macromoleculesActa Crystallographica Section A Foundations of Crystallography, 2007
- Locating active-site hydrogen atoms in d -xylose isomerase: Time-of-flight neutron diffractionProceedings of the National Academy of Sciences of the United States of America, 2006
- Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift,Biochemistry, 2004
- A preliminary time-of-flight neutron diffraction study ofStreptomyces rubiginosusD-xylose isomeraseActa Crystallographica Section D-Biological Crystallography, 2004
- A metal‐mediated hydride shift mechanism for xylose isomerase based on the 1.6 Å Streptomycs rubiginosus structure with xylitol and D‐xyloseProteins-Structure Function and Bioinformatics, 1991
- Mechanism for aldose-ketose interconversion by d-xylose isomerase involving ring opening followed by a 1,2-hydride shiftJournal of Molecular Biology, 1990
- Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by D-xylose isomerase.Proceedings of the National Academy of Sciences of the United States of America, 1990
- The 3.0 Å crystal structure of xylose isomerase from Streptomyces olivochromogenesProtein Engineering, Design and Selection, 1987
- An intramolecular C-2 → C-1 hydrogen transfer during the acid-catalyzed conversion of d-xylose to d-threo-pentulose (d-xylulose)Archives of Biochemistry and Biophysics, 1976
- Stereochemical evidence for a cis-enediol intermediate in Mn-dependent aldose isomerasesBiochimica et Biophysica Acta (BBA) - Enzymology, 1969