6P3K

Crystal structure of LigU(C100S)

6P3K の概要

• エントリーDOI: 10.2210/pdb6p3k/pdb
• 分子名称: (4E)-oxalomesaconate Delta-isomerase, CHLORIDE ION (3 entities in total)
• 機能のキーワード: lignin degradation, protocatechuate 4, 5-cleavage pathway, prpf superfamily, (4e)-oxalomesaconate isomerase mechanism, isomerase
• 由来する生物種: Novosphingobium sp. (strain KA1)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 76101.22

構造登録者

Cory, S.A.,Hogancamp, T.N.,Raushel, F.M.,Barondeau, D.P. (登録日: 2019-05-23, 公開日: 2019-07-31, 最終更新日: 2023-10-11)

主引用文献

Hogancamp, T.N.,Cory, S.A.,Barondeau, D.P.,Raushel, F.M.
Structure and Chemical Reaction Mechanism of LigU, an Enzyme That Catalyzes an Allylic Isomerization in the Bacterial Degradation of Lignin.
Biochemistry, 58:3494-3503, 2019

PubMed Abstract: LigU from sp. strain KA1 catalyzes the isomerization of (4)-oxalomesaconate (OMA) to (3)-2-keto-4-carboxy-3-hexenedioate (KCH) as part of the protocatechuate (PCA) 4,5-cleavage pathway during the degradation of lignin. The three-dimensional structure of the apo form of the wild-type enzyme was determined by X-ray crystallography, and the structure of the K66M mutant enzyme was determined in the presence of the substrate OMA. LigU is a homodimer requiring no cofactors or metal ions with a diaminopimelate epimerase structural fold, consisting of two domains with similar topologies. Each domain has a central α-helix surrounded by a β-barrel composed of antiparallel β-strands. The active site is at the cleft of the two domains. H nuclear magnetic resonance spectroscopy demonstrated that the enzyme catalyzes the exchange of the pro- hydrogen at C5 of KCH with DO during the isomerization reaction. Solvent-deuterium exchange experiments demonstrated that mutation of Lys-66 eliminated the isotope exchange at C5 and that mutation of C100 abolished exchange at C3. The positioning of these two residues in the active site of LigU is consistent with a reaction mechanism that is initiated by the abstraction of the pro- hydrogen at C3 of OMA by the thiolate anion of Cys-100 and the donation of a proton at C5 of the proposed enolate anion intermediate by the side chain of Lys-66 to form the product KCH. The 1,3-proton transfer is suprafacial.

PubMed: 31339729
DOI: 10.1021/acs.biochem.9b00549

実験手法

X-RAY DIFFRACTION (1.88 Å)