Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps

Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem fr...

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Bibliographic Details
Published in:IUCrJ 2021-07, Vol.8 (4), p.633-643
Main Authors: Kelpšas, Vinardas, Caldararu, Octav, Blakeley, Matthew P., Coquelle, Nicolas, Wierenga, Rikkert K., Ryde, Ulf, von Wachenfeldt, Claes, Oksanen, Esko
Format: Article
Language:English
Subjects:
Biochemistry and Molecular Biology
Biokemi och molekylärbiologi
Biologi
Biological Sciences
Carbonyl groups
Carbonyls
Density functional theory
Deuterons
enzyme mechanisms
Enzymes
Glycolysis
Hydrogen
Hydrogen bonds
isomerization
Monosaccharides
Natural Sciences
Naturvetenskap
neutron crystallography
neutron diffraction
Phosphates
Protonation
Protons
qm/mm
quantum refinement
Reaction intermediates
Reaction mechanisms
refinement
Research Papers
structural biology
Sugars
triosephosphate isomerase
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Summary:Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from its ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the subsequent enediol intermediate by phosphoglycolohydroxamate (PGH). Here, neutron structures of Leishmania mexicana TIM have been determined with both inhibitors, and joint neutron/X-ray refinement followed by quantum refinement has been performed. The structures show that in the PGA complex the postulated general base Glu167 is protonated, while in the PGH complex it remains deprotonated. The deuteron is clearly localized on Glu167 in the PGA–TIM structure, suggesting an asymmetric hydrogen bond instead of a low-barrier hydrogen bond. The full picture of the active-site protonation states allowed an investigation of the reaction mechanism using density-functional theory calculations.
ISSN:2052-2525
2052-2525
DOI:10.1107/S2052252521004619