ONIOM Study of the Mechanism of the Enzymatic Hydrolysis of Biodegradable Plastics

• Sakae Yoshitake

  Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University

• Matsubara Toshiaki

  Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University

• Aida Misako

  Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University

• Kondo Hidemasa

  Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology

• Masaki Kazuo

  National Research Institute of Brewing

• Iefuji Haruyuki

  National Research Institute of Brewing

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.

Journal

• Bulletin of the Chemical Society of Japan

  Bulletin of the Chemical Society of Japan 82 (3), 338-346, 2009

  The Chemical Society of Japan

Keywords

• General Chemistry

Details

• CRID: 1390282679120772864
• NII Article ID: 130004058956
• NII Article ID: 10025116578
• NII Book ID: AA00580132
• DOI: 10.1246/bcsj.82.338
• COI: 1:CAS:528:DC%2BD1MXjvFagt7k%3D
• ISSN: 13480634
• ISSN: 00092673
• NDL BIB ID: 10178702
• Web Site: https://ndlsearch.ndl.go.jp/books/R000000004-I10178702
• Web Site: https://academic.oup.com/bcsj/article-pdf/82/3/338/56270212/bcsj.82.338.pdf
• Text Lang: en
• Data Source:
  • JaLC
  • NDL
  • Crossref
  • CiNii Articles
  • KAKEN
• Abstract License Flag: Disallowed