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

• 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
• ISSN: 2052-2525; 2052-2525
• DOI: 10.1107/S2052252521004619

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.