2WL9
Crystal structure of catechol 2,3-dioxygenase
Summary for 2WL9
| Entry DOI | 10.2210/pdb2wl9/pdb |
| Related | 2WL3 |
| Descriptor | CATECHOL 2,3-DIOXYGENASE, FE (III) ION, MAGNESIUM ION, ... (6 entities in total) |
| Functional Keywords | aromatic hydrocarbons catabolism, iron, oxidoreductase |
| Biological source | RHODOCOCCUS SP. DK17 |
| Total number of polymer chains | 4 |
| Total formula weight | 137044.98 |
| Authors | Cho, H.J.,Kim, K.J.,Kang, B.S. (deposition date: 2009-06-23, release date: 2010-09-01, Last modification date: 2023-12-13) |
| Primary citation | Cho, H.J.,Kim, K.,Sohn, S.Y.,Cho, H.Y.,Kim, K.J.,Kim, M.H.,Kim, D.,Kim, E.,Kang, B.S. Substrate-Binding Mechanism of a Type I Extradiol Dioxygenase. J.Biol.Chem., 285:34643-, 2010 Cited by PubMed 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. PubMed: 20810655DOI: 10.1074/JBC.M110.130310 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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