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

Kelpšas, Vinardas LU ; Caldararu, Octav LU ; Blakeley, Matthew P. ; Coquelle, Nicolas ; Wierenga, Rikkert K. ; Ryde, Ulf LU orcid ; von Wachenfeldt, Claes LU and Oksanen, Esko LU (2021) In IUCrJ 8(Pt 4). p.633-643
Abstract

Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy-acetone 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... (More)

Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy-acetone 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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author
; ; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
IUCrJ
volume
8
issue
Pt 4
pages
11 pages
publisher
International Union of Crystallography
external identifiers
  • pmid:34258011
ISSN
2052-2525
DOI
10.1107/S2052252521004619
language
English
LU publication?
yes
additional info
© Vinardas Kelpšas et al. 2021.
id
919ad478-3766-416d-a4bd-db7afa71e590
date added to LUP
2022-01-22 09:11:57
date last changed
2022-01-26 02:22:29
@article{919ad478-3766-416d-a4bd-db7afa71e590,
  abstract     = {{<p>Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy-acetone 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 <i>Leishmania mexicana</i> 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.</p>}},
  author       = {{Kelpšas, Vinardas and Caldararu, Octav and Blakeley, Matthew P. and Coquelle, Nicolas and Wierenga, Rikkert K. and Ryde, Ulf and von Wachenfeldt, Claes and Oksanen, Esko}},
  issn         = {{2052-2525}},
  language     = {{eng}},
  month        = {{07}},
  number       = {{Pt 4}},
  pages        = {{633--643}},
  publisher    = {{International Union of Crystallography}},
  series       = {{IUCrJ}},
  title        = {{Neutron structures of <i>Leishmania mexicana</i> triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps}},
  url          = {{http://dx.doi.org/10.1107/S2052252521004619}},
  doi          = {{10.1107/S2052252521004619}},
  volume       = {{8}},
  year         = {{2021}},
}