Bulletin of the Chemical Society of Japan
Online ISSN : 1348-0634
Print ISSN : 0009-2673
ISSN-L : 0009-2673
ONIOM Study of the Mechanism of the Enzymatic Hydrolysis of Biodegradable Plastics
Yoshitake SakaeToshiaki MatsubaraMisako AidaHidemasa KondoKazuo MasakiHaruyuki Iefuji
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2009 Volume 82 Issue 3 Pages 338-346

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Abstract

A cutinase-like enzyme (CLE), which is purified experimentally from the yeast Cryptococcus sp. strain S-2, has been recently found to degrade biodegradable plastics very efficiently. In this study, we theoretically examine the mechanism of hydrolysis of biodegradable plastics by the CLE by means of the ONIOM method. We optimize all the intermediates and the transition states involved in the considered enzymatic reaction and determine the energy surface of the entire catalytic cycle. The calculations show that the amino acid residues inside the pocket of the active site, Thr17 and Gln86, which stabilize the tetrahedral intermediates, and Gly115 in addition to Ser85, His180, and Asp165, which compose the catalytic triad, significantly contribute to the catalytic reaction. This is similar to the case of serine protease reported to date. Moreover, we have newly found that the energy barrier of the catalytic cycle is significantly lowered by the electronic effect of the OH group in the side-chain of Thr17 and bound water. The calculated potential energy surface of the reaction shows that the cleavage of the ester bond is a rate-determining step.

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© 2009 The Chemical Society of Japan
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