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Title: Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site

Abstract

Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.

Authors:
 [1];  [2]; ORCiD logo [1];  [1]; ORCiD logo [3]; ORCiD logo [4];  [5];  [6];  [7];  [7]; ORCiD logo [8]; ORCiD logo [9]; ORCiD logo [10];  [11]; ORCiD logo [11]; ORCiD logo [12]; ORCiD logo [11];  [11]; ORCiD logo [11]; ORCiD logo [13]
+ Show Author Affiliations
  1. Commonwealth Scientific and Industrial Research Organisation, Parkville, VIC (Australia)
  2. Food and Wine, Univ. of Adelaide, Glen Osmond South Australia (Australia)
  3. Suranaree Univ. of Technology, Nakhon Ratchasima (Thailand)
  4. Univ. Grenoble Alpes, Grenoble cedex (France)
  5. GE Healthcare Life Sciences, Paramatta NSW (Australia)
  6. Slovak Academy of Sciences, Bratislava (Slovak Republic)
  7. Centre for Cooperative Research in Biosciences, Derio-Bizkaia (Spain)
  8. Univ. de Barcelona (Spain)
  9. Univ. de Barcelona (Spain); Inst. Catalana de Recerca i Estudis Avançats, Barcelona (Spain)
  10. Univ. Andrés Bello, Talcahuano (Chile); Univ. Autònoma de Barcelona, Bellaterra (Spain)
  11. Univ. Autònoma de Barcelona, Bellaterra (Spain)
  12. Univ. Autònoma de Barcelona, Bellaterra (Spain); The Barcelona Inst. of Science and Technology, Tarragona (Spain)
  13. Univ. of Adelaide, Glen Osmond South Australia (Australia); Huaiyin Normal Univ., Huaian (China)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
Huaiyin Normal Univ.; Australian Research Council; Suranaree Univ. of Technology; Thailand Research Fund
OSTI Identifier:
1523534
Grant/Contract Number:  
DP120100900; BRG5980015
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Computational chemistry; Enzyme mechanisms; Molecular modelling; NMR spectroscopy; X-ray crystallography

Citation Formats

Streltsov, Victor A., Luang, Sukanya, Peisley, Alys, Varghese, Joseph N., Ketudat Cairns, James R., Fort, Sebastien, Hijnen, Marcel, Tvaroška, Igor, Ardá, Ana, Jiménez-Barbero, Jesús, Alfonso-Prieto, Mercedes, Rovira, Carme, Mendoza, Fernanda, Tiessler-Sala, Laura, Sánchez-Aparicio, José-Emilio, Rodríguez-Guerra, Jaime, Lluch, José M., Maréchal, Jean-Didier, Masgrau, Laura, and Hrmova, Maria. Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. United States: N. p., 2019. Web. doi:10.1038/s41467-019-09691-z.
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Streltsov, Victor A., Luang, Sukanya, Peisley, Alys, Varghese, Joseph N., Ketudat Cairns, James R., Fort, Sebastien, Hijnen, Marcel, Tvaroška, Igor, Ardá, Ana, Jiménez-Barbero, Jesús, Alfonso-Prieto, Mercedes, Rovira, Carme, Mendoza, Fernanda, Tiessler-Sala, Laura, Sánchez-Aparicio, José-Emilio, Rodríguez-Guerra, Jaime, Lluch, José M., Maréchal, Jean-Didier, Masgrau, Laura, & Hrmova, Maria. Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. United States. https://doi.org/10.1038/s41467-019-09691-z
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Streltsov, Victor A., Luang, Sukanya, Peisley, Alys, Varghese, Joseph N., Ketudat Cairns, James R., Fort, Sebastien, Hijnen, Marcel, Tvaroška, Igor, Ardá, Ana, Jiménez-Barbero, Jesús, Alfonso-Prieto, Mercedes, Rovira, Carme, Mendoza, Fernanda, Tiessler-Sala, Laura, Sánchez-Aparicio, José-Emilio, Rodríguez-Guerra, Jaime, Lluch, José M., Maréchal, Jean-Didier, Masgrau, Laura, and Hrmova, Maria. Mon . "Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site". United States. https://doi.org/10.1038/s41467-019-09691-z. https://www.osti.gov/servlets/purl/1523534.
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@article{osti_1523534,
title = {Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site},
author = {Streltsov, Victor A. and Luang, Sukanya and Peisley, Alys and Varghese, Joseph N. and Ketudat Cairns, James R. and Fort, Sebastien and Hijnen, Marcel and Tvaroška, Igor and Ardá, Ana and Jiménez-Barbero, Jesús and Alfonso-Prieto, Mercedes and Rovira, Carme and Mendoza, Fernanda and Tiessler-Sala, Laura and Sánchez-Aparicio, José-Emilio and Rodríguez-Guerra, Jaime and Lluch, José M. and Maréchal, Jean-Didier and Masgrau, Laura and Hrmova, Maria},
abstractNote = {Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.},
doi = {10.1038/s41467-019-09691-z},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {Mon May 20 00:00:00 EDT 2019},
month = {Mon May 20 00:00:00 EDT 2019}
}
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    GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm
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    • Sánchez-Aparicio, José-Emilio; Sciortino, Giuseppe; Herrmannsdoerfer, Daniel Viladrich
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    GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm
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    • Sánchez-Aparicio, José-Emilio; Sciortino, Giuseppe; Herrmannsdoerfer, Daniel Viladrich
    • International Journal of Molecular Sciences, Vol. 20, Issue 13
    • DOI: 10.3390/ijms20133155
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