Computational Evidence for a Water-Assisted Proton-Transfer Mechanism in Uronate Isomerase from Bacillus Halodurans (Bh0493)
Jitonnom, Wijitra ; Oláh, Julianna ; Ryde, Ulf LU
and Jitonnom, Jitrayut
(2025)
In The journal of physical chemistry. B
129(49).
p.12675-12684
- Abstract
Uronate isomerase (EC 5.3.1.12; URI) catalyzes uronate sugar interconversion, a key step in bacterial metabolism, yet its reaction mechanism remains poorly understood. This study delineates the detailed mechanism for the isomerization of d-glucuronate to d-fructuronate catalyzed by a Zn2+-dependent URI enzyme (from Bacillus halodurans). Using quantum mechanical (QM) cluster calculations, three mechanistic pathways were evaluated, all involving Asp355 as the catalytic base but differing in the proton-shuttle mechanism. The most favorable mechanism features C5 deprotonation of the substrate, followed by a water-mediated 1,2-proton transfer via a stabilized cis-enediol intermediate, with the C2-C5 intramolecular transfer as the... (More)
Uronate isomerase (EC 5.3.1.12; URI) catalyzes uronate sugar interconversion, a key step in bacterial metabolism, yet its reaction mechanism remains poorly understood. This study delineates the detailed mechanism for the isomerization of d-glucuronate to d-fructuronate catalyzed by a Zn2+-dependent URI enzyme (from Bacillus halodurans). Using quantum mechanical (QM) cluster calculations, three mechanistic pathways were evaluated, all involving Asp355 as the catalytic base but differing in the proton-shuttle mechanism. The most favorable mechanism features C5 deprotonation of the substrate, followed by a water-mediated 1,2-proton transfer via a stabilized cis-enediol intermediate, with the C2-C5 intramolecular transfer as the rate-determining step. The calculated activation barrier (17.3 kcal mol- 1) aligns well with experimental data. Alternative pathways involving Tyr50 or a Tyr48-water relay were found to be less favorable due to higher net barriers (26-36 kcal mol- 1). A comparative analysis of d-glucuronate and d-galacturonate revealed that although both proceed through similar steps, d-glucuronate has ∼2 kcal mol- 1 lower overall barrier due to enhanced stabilization of late-stage intermediates. These findings clarify the roles of solvent and active-site residues in URI catalysis and contribute to a broader understanding of proton-transfer mechanisms in Zn2+-dependent enzymes across the amidohydrolase superfamily.
(Less)
- author
- Jitonnom, Wijitra
; Oláh, Julianna
; Ryde, Ulf
LU
and Jitonnom, Jitrayut
- organization
- publishing date
- 2025-12-11
- type
- Contribution to journal
- publication status
- published
- subject
- in
- The journal of physical chemistry. B
- volume
- 129
- issue
- 49
- pages
- 10 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- pmid:41327824
- scopus:105024729808
- ISSN
- 1520-5207
- DOI
- 10.1021/acs.jpcb.5c06862
- language
- English
- LU publication?
- yes
- id
- c4fc4adf-a362-4efb-b36f-576f176fdc28
- date added to LUP
- 2026-02-11 15:31:29
- date last changed
- 2026-02-12 03:02:16
@article{c4fc4adf-a362-4efb-b36f-576f176fdc28,
abstract = {{<p>Uronate isomerase (EC 5.3.1.12; URI) catalyzes uronate sugar interconversion, a key step in bacterial metabolism, yet its reaction mechanism remains poorly understood. This study delineates the detailed mechanism for the isomerization of d-glucuronate to d-fructuronate catalyzed by a Zn2+-dependent URI enzyme (from Bacillus halodurans). Using quantum mechanical (QM) cluster calculations, three mechanistic pathways were evaluated, all involving Asp355 as the catalytic base but differing in the proton-shuttle mechanism. The most favorable mechanism features C5 deprotonation of the substrate, followed by a water-mediated 1,2-proton transfer via a stabilized cis-enediol intermediate, with the C2-C5 intramolecular transfer as the rate-determining step. The calculated activation barrier (17.3 kcal mol- 1) aligns well with experimental data. Alternative pathways involving Tyr50 or a Tyr48-water relay were found to be less favorable due to higher net barriers (26-36 kcal mol- 1). A comparative analysis of d-glucuronate and d-galacturonate revealed that although both proceed through similar steps, d-glucuronate has ∼2 kcal mol- 1 lower overall barrier due to enhanced stabilization of late-stage intermediates. These findings clarify the roles of solvent and active-site residues in URI catalysis and contribute to a broader understanding of proton-transfer mechanisms in Zn2+-dependent enzymes across the amidohydrolase superfamily.</p>}},
author = {{Jitonnom, Wijitra and Oláh, Julianna and Ryde, Ulf and Jitonnom, Jitrayut}},
issn = {{1520-5207}},
language = {{eng}},
month = {{12}},
number = {{49}},
pages = {{12675--12684}},
publisher = {{The American Chemical Society (ACS)}},
series = {{The journal of physical chemistry. B}},
title = {{Computational Evidence for a Water-Assisted Proton-Transfer Mechanism in Uronate Isomerase from Bacillus Halodurans (Bh0493)}},
url = {{http://dx.doi.org/10.1021/acs.jpcb.5c06862}},
doi = {{10.1021/acs.jpcb.5c06862}},
volume = {{129}},
year = {{2025}},
}