Substrate binding mechanism of a type I extradiol dioxygenase.
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.
Cho
Hyo Je
HJ
From the School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Korea.
Kim
Kyungsun
K
Sohn
Seo Yean
SY
Cho
Ha Yeon
HY
Kim
Kyung Jin
KJ
Kim
Myung Hee
MH
Kim
Dockyu
D
Kim
Eungbin
E
Kang
Beom Sik
BS
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
D001426:Bacterial Proteins; D002396:Catechols; C031136:3-methylcatechol; D010105:Oxygenases; C439587:extradiol dioxygenase
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