title: Substrate binding mechanism of a type I extradiol dioxygenase.
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.
authors.affiliation: From the School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Korea.
authors.forename: Hyo Je
authors.initials: HJ
authors.lastname: Cho
authors.forename: Kyungsun
authors.initials: K
authors.lastname: Kim
authors.forename: Seo Yean
authors.initials: SY
authors.lastname: Sohn
authors.forename: Ha Yeon
authors.initials: HY
authors.lastname: Cho
authors.forename: Kyung Jin
authors.initials: KJ
authors.lastname: Kim
authors.forename: Myung Hee
authors.initials: MH
authors.lastname: Kim
authors.forename: Dockyu
authors.initials: D
authors.lastname: Kim
authors.forename: Eungbin
authors.initials: E
authors.lastname: Kim
authors.forename: Beom Sik
authors.initials: BS
authors.lastname: Kang
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002396:Catechols / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D010105:Oxygenases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012240:Rhodococcus / Q000201:enzymology* / Q000235:genetics; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D002396:Catechols; C031136:3-methylcatechol; D010105:Oxygenases; C439587:extradiol dioxygenase
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