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Substrate-shielding and hydrolytic reaction in hydrolases

Authors

  • Yusuke Kanematsu,

    1. Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan
    2. Department of Nanosystem Science, Graduate School of Nanobiosciences, Yokohama City University, Yokohama 236-0027, Japan
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  • Ryotaro Koike,

    1. Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan
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  • Takayuki Amemiya,

    1. Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan
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  • Motonori Ota

    Corresponding author
    1. Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan
    • Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan
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Abstract

In general, transferases undergo large structural changes and sequester substrate molecules, to shield them from water. By contrast, hydrolases exhibit only small structural changes, and expose substrate molecules to water. However, some hydrolases deeply bury their substrates within the proteins. To clarify the relationship between substrate-shielding and enzymatic functions, we investigated 70 representative hydrolase structures, and examined the relative accessible surface areas of their substrates. As compared to the hydrolases employing the single displacement reaction, the hydrolases employing the double displacement reaction bury the substrate within the proteins. The exo hydrolases display significantly more substrate-shielding from water than the endo hydrolases. It suggests that the substrate-shielding is related to the chemical reaction mechanism of the hydrolases and the substrate specificity. Proteins 2013; © 2012 Wiley Periodicals, Inc.

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