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Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase

Gamiz-Arco, Gloria ; Gutierrez-Rus, Luis I ; Risso, Valeria A ; Ibarra-Molero, Beatriz ; Hoshino, Yosuke ; Petrović, Dušan ; Justicia, Jose ; Cuerva, Juan Manuel ; Romero-Rivera, Adrian and Seelig, Burckhard , et al. (2021) In Nature Communications 12(1).
Abstract

Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme... (More)

Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.

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publishing date
type
Contribution to journal
publication status
published
keywords
Allosteric Regulation, Amino Acid Sequence/genetics, Bacteria/enzymology, Crystallography, X-Ray, Eukaryota/enzymology, Glycoside Hydrolases/genetics, Heme/metabolism, Molecular Dynamics Simulation, Phylogeny, Protein Structure, Secondary, Sequence Homology, Amino Acid
in
Nature Communications
volume
12
issue
1
article number
380
publisher
Nature Publishing Group
external identifiers
  • pmid:33452262
  • scopus:85099457586
ISSN
2041-1723
DOI
10.1038/s41467-020-20630-1
language
English
LU publication?
no
id
4bc706d9-dcf0-4a36-9b82-85ee1c847ede
date added to LUP
2025-01-11 18:51:55
date last changed
2025-06-16 04:34:31
@article{4bc706d9-dcf0-4a36-9b82-85ee1c847ede,
  abstract     = {{<p>Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.</p>}},
  author       = {{Gamiz-Arco, Gloria and Gutierrez-Rus, Luis I and Risso, Valeria A and Ibarra-Molero, Beatriz and Hoshino, Yosuke and Petrović, Dušan and Justicia, Jose and Cuerva, Juan Manuel and Romero-Rivera, Adrian and Seelig, Burckhard and Gavira, Jose A and Kamerlin, Shina C L and Gaucher, Eric A and Sanchez-Ruiz, Jose M}},
  issn         = {{2041-1723}},
  keywords     = {{Allosteric Regulation; Amino Acid Sequence/genetics; Bacteria/enzymology; Crystallography, X-Ray; Eukaryota/enzymology; Glycoside Hydrolases/genetics; Heme/metabolism; Molecular Dynamics Simulation; Phylogeny; Protein Structure, Secondary; Sequence Homology, Amino Acid}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature Communications}},
  title        = {{Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase}},
  url          = {{http://dx.doi.org/10.1038/s41467-020-20630-1}},
  doi          = {{10.1038/s41467-020-20630-1}},
  volume       = {{12}},
  year         = {{2021}},
}