9FRT

Crystal structure of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3

Summary for 9FRT

• Entry DOI: 10.2210/pdb9frt/pdb
• Descriptor: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase, GLYCEROL, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: hydratase, aldolase, lyase
• Biological source: Pseudomonas fluorescens
• Total number of polymer chains: 8
• Total formula weight: 309358.13

Authors

Milani, M. (deposition date: 2024-06-19, release date: 2025-06-25)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.96 Å)