Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)
Substrate permissiveness has long been regarded as the raw materials for the evolution of new enzymatic functions. In land plants, hydroxycinnamoyltransferase (HCT) is an essential enzyme of the phenylpropanoid metabolism. Although essential enzymes are normally associated with high substrate specif...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020
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| Online Access: | https://hdl.handle.net/1721.1/124937 |
| _version_ | 1811077401940066304 |
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| author | Levsh, Olesya Weng, Jing-Ke |
| author2 | Whitehead Institute for Biomedical Research |
| author_facet | Whitehead Institute for Biomedical Research Levsh, Olesya Weng, Jing-Ke |
| author_sort | Levsh, Olesya |
| collection | MIT |
| description | Substrate permissiveness has long been regarded as the raw materials for the evolution of new enzymatic functions. In land plants, hydroxycinnamoyltransferase (HCT) is an essential enzyme of the phenylpropanoid metabolism. Although essential enzymes are normally associated with high substrate specificity, HCT can utilize a variety of non-native substrates. To examine the structural and dynamic basis of substrate permissiveness in this enzyme, we report the crystal structure of HCT from Selaginella moellendorffii and molecular dynamics (MD) simulations performed on five orthologous HCTs from several major lineages of land plants. Through altogether 17-μs MD simulations, we demonstrate the prevalent swing motion of an arginine handle on a submicrosecond timescale across all five HCTs, which plays a key role in native substrate recognition by these intrinsically promiscuous enzymes. Our simulations further reveal how a non-native substrate of HCT engages a binding site different from that of the native substrate and diffuses to reach the catalytic center and its co-substrate. By numerically solving the Smoluchowski equation, we show that the presence of such an alternative binding site, even when it is distant from the catalytic center, always increases the reaction rate of a given substrate. However, this increase is only significant for enzyme-substrate reactions heavily influenced by diffusion. In these cases, binding non-native substrates ‘off-center’ provides an effective rationale to develop substrate permissiveness while maintaining the native functions of promiscuous enzymes. |
| first_indexed | 2024-09-23T10:42:26Z |
| format | Article |
| id | mit-1721.1/124937 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T10:42:26Z |
| publishDate | 2020 |
| publisher | Public Library of Science (PLoS) |
| record_format | dspace |
| spelling | mit-1721.1/1249372022-09-30T22:25:02Z Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT) Levsh, Olesya Weng, Jing-Ke Whitehead Institute for Biomedical Research Massachusetts Institute of Technology. Department of Biology Ecology Modelling and Simulation Computational Theory and Mathematics Genetics Ecology, Evolution, Behavior and Systematics Molecular Biology Cellular and Molecular Neuroscience Substrate permissiveness has long been regarded as the raw materials for the evolution of new enzymatic functions. In land plants, hydroxycinnamoyltransferase (HCT) is an essential enzyme of the phenylpropanoid metabolism. Although essential enzymes are normally associated with high substrate specificity, HCT can utilize a variety of non-native substrates. To examine the structural and dynamic basis of substrate permissiveness in this enzyme, we report the crystal structure of HCT from Selaginella moellendorffii and molecular dynamics (MD) simulations performed on five orthologous HCTs from several major lineages of land plants. Through altogether 17-μs MD simulations, we demonstrate the prevalent swing motion of an arginine handle on a submicrosecond timescale across all five HCTs, which plays a key role in native substrate recognition by these intrinsically promiscuous enzymes. Our simulations further reveal how a non-native substrate of HCT engages a binding site different from that of the native substrate and diffuses to reach the catalytic center and its co-substrate. By numerically solving the Smoluchowski equation, we show that the presence of such an alternative binding site, even when it is distant from the catalytic center, always increases the reaction rate of a given substrate. However, this increase is only significant for enzyme-substrate reactions heavily influenced by diffusion. In these cases, binding non-native substrates ‘off-center’ provides an effective rationale to develop substrate permissiveness while maintaining the native functions of promiscuous enzymes. University Grants Committee (Hong Kong, China) (Project 14323816) 2020-04-30T14:48:37Z 2020-04-30T14:48:37Z 2018-10-26 2020-02-03T17:55:33Z Article http://purl.org/eprint/type/JournalArticle 1553-7358 https://hdl.handle.net/1721.1/124937 Chiang, Ying-Chih et al. “Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).” PLOS computational biology 14 (2018): e1006511 © 2018 The Author(s) en 10.1371/journal.pcbi.1006511 PLOS computational biology Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science (PLoS) PLoS |
| spellingShingle | Ecology Modelling and Simulation Computational Theory and Mathematics Genetics Ecology, Evolution, Behavior and Systematics Molecular Biology Cellular and Molecular Neuroscience Levsh, Olesya Weng, Jing-Ke Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT) |
| title | Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT) |
| title_full | Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT) |
| title_fullStr | Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT) |
| title_full_unstemmed | Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT) |
| title_short | Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT) |
| title_sort | structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase hct |
| topic | Ecology Modelling and Simulation Computational Theory and Mathematics Genetics Ecology, Evolution, Behavior and Systematics Molecular Biology Cellular and Molecular Neuroscience |
| url | https://hdl.handle.net/1721.1/124937 |
| work_keys_str_mv | AT levsholesya structuralanddynamicbasisofsubstratepermissivenessinhydroxycinnamoyltransferasehct AT wengjingke structuralanddynamicbasisofsubstratepermissivenessinhydroxycinnamoyltransferasehct |