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

Research output: Contribution to journalArticle

15 Citations (Scopus)

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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Substrates
Iron
Oxygen
Aromatic Hydrocarbons
Substrate Specificity
Mutagenesis
Hydroxyl Radical
Catalytic Domain
Water
Enzymes
extradiol dioxygenase
3-methylcatechol
Molecular oxygen
Crystal structure
Degradation
catechol

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., ... 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
Cho, Hyo Je ; Kim, Kyungsun ; Sohn, Seo Yean ; Cho, Ha Yeon ; Kim, Kyung Jin ; Kim, Myung Hee ; Kim, Dockyu ; Kim, Eungbin ; Kang, Beom Sik. / Substrate binding mechanism of a type I extradiol dioxygenase. In: Journal of Biological Chemistry. 2010 ; Vol. 285, No. 45. pp. 34643-34652.
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Cho, HJ, Kim, K, Sohn, SY, Cho, HY, Kim, KJ, Kim, MH, Kim, D, Kim, E & Kang, BS 2010, 'Substrate binding mechanism of a type I extradiol dioxygenase', Journal of Biological Chemistry, vol. 285, no. 45, pp. 34643-34652. https://doi.org/10.1074/jbc.M110.130310

Substrate binding mechanism of a type I extradiol dioxygenase. / Cho, Hyo Je; Kim, Kyungsun; Sohn, Seo Yean; Cho, Ha Yeon; Kim, Kyung Jin; Kim, Myung Hee; Kim, Dockyu; Kim, Eungbin; Kang, Beom Sik.

In: Journal of Biological Chemistry, Vol. 285, No. 45, 05.11.2010, p. 34643-34652.

Research output: Contribution to journalArticle

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Cho HJ, Kim K, Sohn SY, Cho HY, Kim KJ, Kim MH et al. Substrate binding mechanism of a type I extradiol dioxygenase. Journal of Biological Chemistry. 2010 Nov 5;285(45):34643-34652. https://doi.org/10.1074/jbc.M110.130310