3HPV

Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28

3HPV の概要

• エントリーDOI: 10.2210/pdb3hpv/pdb
• 分子名称: Catechol 2,3-dioxygenase, FE (II) ION (3 entities in total)
• 機能のキーワード: repeated motifs, aromatic hydrocarbons catabolism, dioxygenase, iron, oxidoreductase
• 由来する生物種: Pseudomonas sp.
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 140713.82

構造登録者

Cho, J.-H.,Rhee, S. (登録日: 2009-06-05, 公開日: 2009-10-20, 最終更新日: 2023-11-01)

主引用文献

Cho, J.-H.,Jung, D.-K.,Lee, K.,Rhee, S.
Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas
J.Biol.Chem., 284:34321-34330, 2009

PubMed Abstract: LapB is a non-heme Fe(II)-dependent 2,3-dioxygenase that catalyzes the second step of a long-chain alkylphenol (lap) degradation pathway in Pseudomonas sp. KL28 and belongs to the superfamily of type I extradiol dioxygenases. In this study, the crystal structures of substrate-free LapB and its complexes with a substrate or product were determined, along with a functional analysis of the active site residues. Structural features of the homotetramer are similar to those of other type I extradiol dioxygenases. In particular, the active site is located in the C-domain of each monomer, with a 2-His-1-carboxylate motif as the first coordination shell to iron ion. A comparison of three different structures in the catalytic cycle indicated catalysis-related local conformational changes in the active site. Specifically, the active site loop containing His-248 exhibits positional changes upon binding of the substrate and establishes a hydrogen-bonding network with Tyr-257, which is near the hydroxyl group of the substrate. Kinetic analysis of the mutant enzymes H248A, H248N, and Y257F showed that these three mutant enzymes are inactive, suggesting that this hydrogen-bonding network plays a crucial role in catalysis by deprotonating the incoming substrate and leaving it in a monoanionic state. Additional functional analysis of His-201, by using H201A and H201N mutants, near the dioxygen-binding site also supports its role as base and acid catalyst in the late stage of catalysis. We also noticed a disordered-to-ordered structural transition in the C-terminal region, resulting in the opening or closing of the active site. These results provide detailed insights into the structural and functional features of an extradiol dioxygenase that can accommodate a wide range of alkylcatechols.

PubMed: 19828456
DOI: 10.1074/jbc.M109.031054

実験手法

X-RAY DIFFRACTION (2.3 Å)