University of Oulu

Kelpšas, V., Caldararu, O., Blakeley, M. P., Coquelle, N., Wierenga, R. K., Ryde, U., von Wachenfeldt, C., & Oksanen, E. (2021). Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps. IUCrJ, 8(4), 633–643. https://doi.org/10.1107/s2052252521004619

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

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Author: Kelpšas, Vinardas1; Caldararu, Octav2; Blakeley, Matthew P.3;
Organizations: 1Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
2Department of Chemistry, Lund University, 221 00 Lund, Sweden
3Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
4Faculty of Biochemistry and Molecular Medicine, University of Oulu, Pentti Kaiteran katu 1, 90570 Oulu, Finland
5European Spallation Source Consortium ESS ERIC, Odarslo¨ vsva¨gen 113, 224 84 Lund, Sweden
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.4 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe2021091646390
Language: English
Published: International Union of Crystallography, 2021
Publish Date: 2021-09-16
Description:

Abstract

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.

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Series: IUCrJ
ISSN: 2052-2525
ISSN-E: 2052-2525
ISSN-L: 2052-2525
Volume: 8
Issue: 4
Pages: 633 - 643
DOI: 10.1107/S2052252521004619
OADOI: https://oadoi.org/10.1107/S2052252521004619
Type of Publication: A1 Journal article – refereed
Field of Science: 1182 Biochemistry, cell and molecular biology
Subjects:
Funding: Funding for this research was provided by: Crafoordska Stiftelsen (grant No. 20140973 to Esko Oksanen); Veten­skapsrådet (grant No. 2018-05003 to Ulf Ryde; grant No. 2019-05578_3 to Claes von Wachenfeldt); eSSENCE: The e-Science Collaboration (award to Ulf Ryde).
Copyright information: © 2021 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
  https://creativecommons.org/licenses/by/4.0/