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Title: Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)

Abstract

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 reactionsmore » 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.« less

Authors:
ORCiD logo [1]; ORCiD logo [2];  [1]; ORCiD logo [2]; ORCiD logo [1]
  1. The Chinese Univ. of Hong Kong (China). Dept. of Physics
  2. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Biology; Whitehead Inst. for Biomedical Research, Cambridge, MA (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1480350
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS Computational Biology (Online)
Additional Journal Information:
Journal Volume: 14; Journal Issue: 10; Journal ID: ISSN 1553-7358
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; Arginine; Enzymes; Crystal structure; Enzyme metabolism; Crystallization; Molecular dynamics; Salt bridges; Enzyme structure

Citation Formats

Chiang, Ying-Chih, Levsh, Olesya, Lam, Chun Kei, Weng, Jing-Ke, and Wang, Yi. Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT). United States: N. p., 2018. Web. doi:10.1371/journal.pcbi.1006511.
Chiang, Ying-Chih, Levsh, Olesya, Lam, Chun Kei, Weng, Jing-Ke, & Wang, Yi. Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT). United States. doi:10.1371/journal.pcbi.1006511.
Chiang, Ying-Chih, Levsh, Olesya, Lam, Chun Kei, Weng, Jing-Ke, and Wang, Yi. Fri . "Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)". United States. doi:10.1371/journal.pcbi.1006511. https://www.osti.gov/servlets/purl/1480350.
@article{osti_1480350,
title = {Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)},
author = {Chiang, Ying-Chih and Levsh, Olesya and Lam, Chun Kei and Weng, Jing-Ke and Wang, Yi},
abstractNote = {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.},
doi = {10.1371/journal.pcbi.1006511},
journal = {PLoS Computational Biology (Online)},
issn = {1553-7358},
number = 10,
volume = 14,
place = {United States},
year = {2018},
month = {10}
}

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