Metal Ion Roles and the Movement of Hydrogen during Reaction Catalyzed by D-Xylose Isomerase
The complementarity of X-ray and neutron diffraction techniques is again demonstrated by the study of the enzyme D-xylose isomerase (XI) (EC 5.3.1.5), a crucial enzyme in sugar metabolism, with important commercial applications, notably in the production of biofuels and soft-drink sweeteners.
Enzyme catalysis is often a multistep process that can be understood at a molecular level only through a detailed characterization of each step. Structural information from X-ray crystallographic studies of enzymes in complex with their substrates, cofactors, inhibitors, transition state analogs, and products can be thought of as providing static snapshots of different steps along a reaction pathway and can lead to hypotheses about reaction mechanisms.
Unfortunately, one limitation of X-ray studies is the inability to determine the location of H atoms which is at the core of the reaction mechanisms since labile H atom positions proved dif?cult to locate even at the ultra-high resolution of 0.9 A.
Neutron diffraction studies, on the other hand, can provide H locations, especially if hydrogen is replaced by its isotope deuterium. Transferable hydrogen (attached to N or O) can be replaced by deuterium by soaking the enzyme in D2O. Alternatively, a perdeuterated molecule may be synthesized.
New neutron data from two states in the reaction catalyzed by this enzyme were collected at the PCS at LANSCE and D19 at the ILL. A generalized X-ray and neutron (XN) crystallographic analysis approach that exploits the complementarities of X-ray and neutron data was performed.
The results obtained concerning the sugar binding, ring opening, isomerization, metal coordination and inhibition (see figure 1), do not support some aspects of previous proposals for the reaction mechanism, but rather lead to new suggestions as to how changes might take place over the course of the reaction. These as summarized in the figure 2.
This project is part of an ongoing collaboration between ILL, Los Alamos and ISIS. D19 was rebuilt as part of the Millennium programme - in collaboration with Durham, Keele, and Bath Universities, with funding from the EPSRC.
Ref.: Andrey Y. Kovalevsky, Leif Hanson, S. Zoe Fisher, Marat Mustyakimov, Sax A. Mason, V. Trevor Forsyth, Matthew P. Blakeley, David. A. Keen, Trixie Wagner, H.L. Carrell, Amy K. Katz, Jenny P. Glusker and Paul Langan, Structure 18, 688-699, 2010.
Full article in the journal Structure
