6DWV

Crystal structure of the LigJ Hydratase in the Apo state

6DWV の概要

• エントリーDOI: 10.2210/pdb6dwv/pdb
• 分子名称: 4-oxalomesaconate hydratase, ZINC ION (3 entities in total)
• 機能のキーワード: hydratase, lignin degradation, lyase
• 由来する生物種: Sphingobium sp. SYK-6
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 152635.28

構造登録者

Mabanglo, M.F.,Raushel, F.M. (登録日: 2018-06-28, 公開日: 2018-10-03, 最終更新日: 2024-03-13)

主引用文献

Hogancamp, T.N.,Mabanglo, M.F.,Raushel, F.M.
Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway.
Biochemistry, 57:5841-5850, 2018

PubMed Abstract: LigJ from the soil bacterium Sphingobium sp. SYK-6 catalyzes the reversible hydration of (3 Z)-2-keto-4-carboxy-3-hexenedioate (KCH) to 4-carboxy-4-hydroxy-2-oxoadipate (CHA) in the degradation of lignin in the protocatechuate 4,5-cleavage pathway. LigJ is a member of the amidohydrolase superfamily and an enzyme in cog2159. The three-dimensional crystal structure of wild-type LigJ was determined in the presence [Protein Data Bank (PDB) entry 6DXQ ] and absence of the product CHA (PDB entry 6DWV ). The protein folds as a distorted (β/α)-barrel, and a single zinc ion is bound in the active site at the C-terminal end of the central β-barrel. The product CHA is ligated to the zinc ion in the active site via the displacement of a single water molecule from the coordination shell of the metal center in LigJ. The product-bound structure reveals that the enzyme catalyzes the hydration of KCH with the formation of a chiral center at C4 with S stereochemistry. The E284Q mutant was unable to catalyze the hydration of KCH to CHA, and the structure of this mutant was determined in the presence of the substrate KCH (PDB entry 6DXS ). On the basis of the structure of LigJ in the presence of KCH and CHA, it is proposed that the side chain carboxylate of Glu-284 functions as a general base in the abstraction of a proton from a bound water molecule for nucleophilic attack at C4 of the substrate. The reaction is facilitated by the delocalization of the negative charge to the metal center via the carbonyl group at C2 of the substrate. C3 of the substrate is subsequently protonated by Glu-284 functioning as a general acid. The overall reaction occurs by the syn addition of water to the double bond between C4 and C3 of the substrate KCH. The kinetic constants for the hydration of KCH to CHA by LigJ at pH 8.0 are 25 s ( k) and 2.6 × 10 M s ( k/ K).

PubMed: 30207699
DOI: 10.1021/acs.biochem.8b00713

実験手法

X-RAY DIFFRACTION (2.2 Å)