Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose.

Andrey Y Kovalevsky, Amy K Katz, H L Carrell, Leif Hanson, Marat Mustyakimov, S Zoe Fisher, Leighton Coates, Benno P Schoenborn, Gerard J Bunick, Jenny P Glusker, Paul Langan

Index: Biochemistry 47(29) , 7595-7, (2008)

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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.