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

Journal Article · · Nature Communications
 [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]
  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)
+ Show Author Affiliations

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.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
Huaiyin Normal Univ.; Australian Research Council; Suranaree Univ. of Technology; Thailand Research Fund
Grant/Contract Number:
DP120100900; BRG5980015
OSTI ID:
1523534
Journal Information:
Nature Communications, Vol. 10, Issue 1; ISSN 2041-1723
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
ENGLISH
Citation Metrics:
Cited by: 15 works
Citation information provided by
Web of Science

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Cited By (1)

GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm
  • Sánchez-Aparicio, José-Emilio; Sciortino, Giuseppe; Herrmannsdoerfer, Daniel Viladrich
  • International Journal of Molecular Sciences, Vol. 20, Issue 13 https://doi.org/10.3390/ijms20133155
journal June 2019

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Computational chemistry
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NMR spectroscopy
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