Substrate binding mechanism of a type I extradiol dioxygenase

Hyo Je Cho, Kyungsun Kim, Seo Yean Sohn, Ha Yeon Cho, Kyung Jin Kim, Myung Hee Kim, Dockyu Kim, Eungbin Kim, Beom Sik Kang

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Abstract

A meta-cleavage pathway for the aerobic degradation of aromatic hydrocarbons is catalyzed by extradiol dioxygenases via a two-step mechanism: catechol substrate binding and dioxygen incorporation. The binding of substrate triggers the release of water, thereby opening a coordination site for molecular oxygen. The crystal structures of AkbC, a type I extradiol dioxygenase, and the enzyme substrate (3-methylcatechol) complex revealed the substrate binding process of extradiol dioxygenase. AkbC is composed of an N-domain and an active C-domain, which contains iron coordinated by a 2-His-1-carboxylate facial triad motif. The C-domain includes a β-hairpin structure and a C-terminal tail. In substrate-bound AkbC, 3-methylcatechol interacts with the iron via a single hydroxyl group, which represents an intermediate stage in the substrate binding process. Structure-based mutagenesis revealed that the C-terminal tail and β-hairpin form part of the substrate binding pocket that is responsible for substrate specificity by blocking substrate entry. Once a substrate enters the active site, these structural elements also play a role in the correct positioning of the substrate. Based on the results presented here, a putative substrate binding mechanism is proposed.

Original languageEnglish
Pages (from-to)34643-34652
Number of pages10
JournalJournal of Biological Chemistry
Volume285
Issue number45
DOIs
Publication statusPublished - 2010 Nov 5

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All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Cho, H. J., Kim, K., Sohn, S. Y., Cho, H. Y., Kim, K. J., Kim, M. H., Kim, D., Kim, E., & Kang, B. S. (2010). Substrate binding mechanism of a type I extradiol dioxygenase. Journal of Biological Chemistry, 285(45), 34643-34652. https://doi.org/10.1074/jbc.M110.130310