Computer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase
Barrozo, Alexandre ; Liao, Qinghua ; Esguerra, Mauricio ; Marloie, Gaël ; Florián, Jan ; Williams, Nicholas H and Kamerlin, Shina Caroline Lynn LU
(2018)
In Organic and Biomolecular Chemistry
16(12).
p.2060-2073
- Abstract
β-Phosphoglucomutase (β-PGM) has served as an important model system for understanding biological phosphoryl transfer. This enzyme catalyzes the isomerization of β-glucose-1-phosphate to β-glucose-6-phosphate in a two-step process proceeding via a bisphosphate intermediate. The conventionally accepted mechanism is that both steps are concerted processes involving acid-base catalysis from a nearby aspartate (D10) side chain. This argument is supported by the observation that mutation of D10 leaves the enzyme with no detectable activity. However, computational studies have suggested that a substrate-assisted mechanism is viable for many phosphotransferases. Therefore, we carried out empirical valence bond (EVB) simulations to address the... (More)
β-Phosphoglucomutase (β-PGM) has served as an important model system for understanding biological phosphoryl transfer. This enzyme catalyzes the isomerization of β-glucose-1-phosphate to β-glucose-6-phosphate in a two-step process proceeding via a bisphosphate intermediate. The conventionally accepted mechanism is that both steps are concerted processes involving acid-base catalysis from a nearby aspartate (D10) side chain. This argument is supported by the observation that mutation of D10 leaves the enzyme with no detectable activity. However, computational studies have suggested that a substrate-assisted mechanism is viable for many phosphotransferases. Therefore, we carried out empirical valence bond (EVB) simulations to address the plausibility of this mechanistic alternative, including its role in the abolished catalytic activity of the D10S, D10C and D10N point mutants of β-PGM. In addition, we considered both of these mechanisms when performing EVB calculations of the catalysis of the wild type (WT), H20A, H20Q, T16P, K76A, D170A and E169A/D170A protein variants. Our calculated activation free energies confirm that D10 is likely to serve as the general base/acid for the reaction catalyzed by the WT enzyme and all its variants, in which D10 is not chemically altered. Our calculations also suggest that D10 plays a dual role in structural organization and maintaining electrostatic balance in the active site. The correct positioning of this residue in a catalytically competent conformation is provided by a functionally important conformational change in this enzyme and by the extensive network of H-bonding interactions that appear to be exquisitely preorganized for the transition state stabilization.
(Less)
- author
- Barrozo, Alexandre
; Liao, Qinghua
; Esguerra, Mauricio
; Marloie, Gaël
; Florián, Jan
; Williams, Nicholas H
and Kamerlin, Shina Caroline Lynn
LU
- publishing date
- 2018-03-28
- type
- Contribution to journal
- publication status
- published
- keywords
- Animals, Catalysis, Catalytic Domain, Computer Simulation, Humans, Hydrogen Bonding, Intramolecular Transferases/metabolism, Mutant Proteins/genetics, Phosphoglucomutase/genetics, Protein Conformation, Static Electricity, Substrate Specificity, Thermodynamics
- in
- Organic and Biomolecular Chemistry
- volume
- 16
- issue
- 12
- pages
- 14 pages
- publisher
- Royal Society of Chemistry
- external identifiers
-
- pmid:29508879
- scopus:85044263364
- ISSN
- 1477-0539
- DOI
- 10.1039/c8ob00312b
- language
- English
- LU publication?
- no
- id
- a2031c9f-04a6-45b2-9e83-0e675311b7e8
- date added to LUP
- 2025-01-11 21:17:49
- date last changed
- 2025-04-06 11:20:16
@article{a2031c9f-04a6-45b2-9e83-0e675311b7e8,
abstract = {{<p>β-Phosphoglucomutase (β-PGM) has served as an important model system for understanding biological phosphoryl transfer. This enzyme catalyzes the isomerization of β-glucose-1-phosphate to β-glucose-6-phosphate in a two-step process proceeding via a bisphosphate intermediate. The conventionally accepted mechanism is that both steps are concerted processes involving acid-base catalysis from a nearby aspartate (D10) side chain. This argument is supported by the observation that mutation of D10 leaves the enzyme with no detectable activity. However, computational studies have suggested that a substrate-assisted mechanism is viable for many phosphotransferases. Therefore, we carried out empirical valence bond (EVB) simulations to address the plausibility of this mechanistic alternative, including its role in the abolished catalytic activity of the D10S, D10C and D10N point mutants of β-PGM. In addition, we considered both of these mechanisms when performing EVB calculations of the catalysis of the wild type (WT), H20A, H20Q, T16P, K76A, D170A and E169A/D170A protein variants. Our calculated activation free energies confirm that D10 is likely to serve as the general base/acid for the reaction catalyzed by the WT enzyme and all its variants, in which D10 is not chemically altered. Our calculations also suggest that D10 plays a dual role in structural organization and maintaining electrostatic balance in the active site. The correct positioning of this residue in a catalytically competent conformation is provided by a functionally important conformational change in this enzyme and by the extensive network of H-bonding interactions that appear to be exquisitely preorganized for the transition state stabilization.</p>}},
author = {{Barrozo, Alexandre and Liao, Qinghua and Esguerra, Mauricio and Marloie, Gaël and Florián, Jan and Williams, Nicholas H and Kamerlin, Shina Caroline Lynn}},
issn = {{1477-0539}},
keywords = {{Animals; Catalysis; Catalytic Domain; Computer Simulation; Humans; Hydrogen Bonding; Intramolecular Transferases/metabolism; Mutant Proteins/genetics; Phosphoglucomutase/genetics; Protein Conformation; Static Electricity; Substrate Specificity; Thermodynamics}},
language = {{eng}},
month = {{03}},
number = {{12}},
pages = {{2060--2073}},
publisher = {{Royal Society of Chemistry}},
series = {{Organic and Biomolecular Chemistry}},
title = {{Computer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase}},
url = {{http://dx.doi.org/10.1039/c8ob00312b}},
doi = {{10.1039/c8ob00312b}},
volume = {{16}},
year = {{2018}},
}