Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site
| Autor: | Jean-Didier Maréchal, José-Emilio Sánchez-Aparicio, Igor Tvaroška, Jose N. Varghese, Maria Hrmova, José M. Lluch, Sukanya Luang, V.A. Streltsov, A. Peisley, Marcel Hijnen, Jesús Jiménez-Barbero, Ana Ardá, J.R. Ketudat Cairns, Laura Tiessler-Sala, Carme Rovira, Fernanda Mendoza, Mercedes Alfonso-Prieto, Jaime Rodríguez-Guerra, Sébastien Fort, Laura Masgrau |
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| Přispěvatelé: | Centre de Recherches sur les Macromolécules Végétales (CERMAV ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institute of Chemistry, Centre for Glycomics, Slovak Academy of Science [Bratislava] (SAS), Catalytic Spectroscopy Laboratory (CSIC), Institute of Catalysis and Petroleum Chemistry, Departament de Quimica Fisica and Institut de Quimica Teorica i Computacional (IQTCUB), Universitat de Barcelona (UB), Universitat Autònoma de Barcelona (UAB) |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Models Molecular Computational chemistry Science General Physics and Astronomy 02 engineering and technology Molecular Dynamics Simulation Crystallography X-Ray General Biochemistry Genetics and Molecular Biology Article Catalysis Substrate Specificity 03 medical and health sciences Molecular dynamics NMR spectroscopy Catalytic Domain Hydrolase [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Glycosides lcsh:Science Nuclear Magnetic Resonance Biomolecular Alkyl ComputingMilieux_MISCELLANEOUS Enzyme Assays Plant Proteins X-ray crystallography chemistry.chemical_classification Multidisciplinary biology Active site Substrate (chemistry) Hordeum General Chemistry 021001 nanoscience & nanotechnology Recombinant Proteins 030104 developmental biology Enzyme chemistry Biocatalysis Seedlings Enzyme mechanisms biology.protein Biophysics lcsh:Q Molecular modelling 0210 nano-technology Glucosidases |
| Zdroj: | Dipòsit Digital de Documents de la UAB Universitat Autònoma de Barcelona Nature Communications, Vol 10, Iss 1, Pp 1-17 (2019) Nature Communications Nature Communications, Nature Publishing Group, 2019, 10 (1), ⟨10.1038/s41467-019-09691-z⟩ |
| ISSN: | 2041-1723 |
| Popis: | 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. Enzyme substrates and products often diffuse too rapidly to assess the catalytic implications of these movements. Here, the authors characterise the structural basis of product and substrate diffusion for an exo-hydrolase and discover a substrate-product assisted processive catalytic mechanism. |
| Databáze: | OpenAIRE |
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