9FTK

Crystal structure of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3 bound to substrate intermediate

9FTK の概要

• エントリーDOI: 10.2210/pdb9ftk/pdb
• 関連するPDBエントリー: 9FRT
• 分子名称: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase, (4R)-4-hydroxy-4-(2-hydroxyphenyl)butanoic acid, PHOSPHATE ION, ... (6 entities in total)
• 機能のキーワード: hydratase, aldolase, lyase
• 由来する生物種: Pseudomonas fluorescens
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 312349.52

構造登録者

Milani, M.,Ferrara, S. (登録日: 2024-06-24, 公開日: 2025-07-23)

主引用文献

Ferrara, S.,Braggiotti, B.,Mastrangelo, E.,Di Gennaro, P.,Bertoni, G.,Milani, M.
Structural snapshots of the aldol condensation reaction of the enzyme trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3.
Biochem.Biophys.Res.Commun., 747:151281-151281, 2025

PubMed Abstract: Aldolases are crucial enzymes that catalyze the formation of carbon-carbon bonds in the context of the anabolic and catabolic pathways of various metabolites. The bacterium Pseudomonas fluorescens N3 can use naphthalene as its sole carbon and energy source by using, among other enzymes, the trans-o-hydroxybenzylidenepyruvate (tHBP) hydratase-aldolase (HA), encoded by the nahE gene. In this study, we present the crystallographic structures of tHBP-HA in three different functional states: the apo enzyme with a phosphate ion in the active site, and the Schiff base adduct bound either to pyruvate or to the substitute with '(R)-4-hydroxy-4-(2-hydroxyphenyl)-2-oxobutanoate'(intermediate state). Our structures elucidate some of the phases of the aldol condensation reaction, proposing the role of a conserved water molecule (W2) in the deprotonation of the catalytic lysine. Moreover, our crystallographic data suggest potential pathways for substrate and product diffusion to and from the protein's active site. These insights advance our understanding of the molecular mechanisms of the aldolase function and can also be used for the design and optimization of new enzymes engineered for the chemical synthesis of different C-C adducts.

PubMed: 39793398
DOI: 10.1016/j.bbrc.2024.151281

実験手法

X-RAY DIFFRACTION (1.76 Å)