Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases
Shen, Ruidan ; Crean, Rory M ; Johnson, Sean J ; Kamerlin, Shina C L LU
and Hengge, Alvan C
(2021)
In JACS Au
1(5).
p.646-659
- Abstract
Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a noncatalytic residue in the WPD-loops of YopH and PTP1B result in shifted pH-rate profiles from an altered kinetic pK a of the nucleophilic cysteine. Compared to wild type, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Changes in the corresponding PTP1B T177G variant are more modest and in the opposite direction, with a narrowed pH profile and less activity in the most acidic range. Crystal structures of the... (More)
Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a noncatalytic residue in the WPD-loops of YopH and PTP1B result in shifted pH-rate profiles from an altered kinetic pK a of the nucleophilic cysteine. Compared to wild type, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Changes in the corresponding PTP1B T177G variant are more modest and in the opposite direction, with a narrowed pH profile and less activity in the most acidic range. Crystal structures of the variants show no structural perturbations but suggest an increased preference for the WPD-loop-closed conformation. Computational analysis confirms a shift in loop conformational equilibrium in favor of the closed conformation, arising from a combination of increased stability of the closed state and destabilization of the loop-open state. Simulations identify the origins of this population shift, revealing differences in the flexibility of the WPD-loop and neighboring regions. Our results demonstrate that changes to the pH dependency of catalysis by PTPs can result from small changes in amino acid composition in their WPD-loops affecting only loop dynamics and conformational equilibrium. The perturbation of kinetic pK a values of catalytic residues by nonchemical processes affords a means for nature to alter an enzyme's pH dependency by a less disruptive path than altering electrostatic networks around catalytic residues themselves.
(Less)
- author
- Shen, Ruidan
; Crean, Rory M
; Johnson, Sean J
; Kamerlin, Shina C L
LU
and Hengge, Alvan C
- publishing date
- 2021-05-24
- type
- Contribution to journal
- publication status
- published
- in
- JACS Au
- volume
- 1
- issue
- 5
- pages
- 14 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- pmid:34308419
- scopus:85110477952
- ISSN
- 2691-3704
- DOI
- 10.1021/jacsau.1c00054
- language
- English
- LU publication?
- no
- additional info
- © 2021 The Authors. Published by American Chemical Society.
- id
- 0ee13daa-4ff4-4e48-9bc4-8312ffd8d5c0
- date added to LUP
- 2025-01-11 18:50:21
- date last changed
- 2025-07-28 09:30:19
@article{0ee13daa-4ff4-4e48-9bc4-8312ffd8d5c0,
abstract = {{<p>Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a noncatalytic residue in the WPD-loops of YopH and PTP1B result in shifted pH-rate profiles from an altered kinetic pK a of the nucleophilic cysteine. Compared to wild type, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Changes in the corresponding PTP1B T177G variant are more modest and in the opposite direction, with a narrowed pH profile and less activity in the most acidic range. Crystal structures of the variants show no structural perturbations but suggest an increased preference for the WPD-loop-closed conformation. Computational analysis confirms a shift in loop conformational equilibrium in favor of the closed conformation, arising from a combination of increased stability of the closed state and destabilization of the loop-open state. Simulations identify the origins of this population shift, revealing differences in the flexibility of the WPD-loop and neighboring regions. Our results demonstrate that changes to the pH dependency of catalysis by PTPs can result from small changes in amino acid composition in their WPD-loops affecting only loop dynamics and conformational equilibrium. The perturbation of kinetic pK a values of catalytic residues by nonchemical processes affords a means for nature to alter an enzyme's pH dependency by a less disruptive path than altering electrostatic networks around catalytic residues themselves.</p>}},
author = {{Shen, Ruidan and Crean, Rory M and Johnson, Sean J and Kamerlin, Shina C L and Hengge, Alvan C}},
issn = {{2691-3704}},
language = {{eng}},
month = {{05}},
number = {{5}},
pages = {{646--659}},
publisher = {{The American Chemical Society (ACS)}},
series = {{JACS Au}},
title = {{Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases}},
url = {{http://dx.doi.org/10.1021/jacsau.1c00054}},
doi = {{10.1021/jacsau.1c00054}},
volume = {{1}},
year = {{2021}},
}