Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa

• Published in: Scientific Reports Vol. 6; no. 1; p. 32822
• Main Authors: Okada, Chiaki, Wakabayashi, Hiroko, Kobayashi, Momoko, Shinoda, Akira, Tanaka, Isao, Yao, Min
• Format: Journal Article
• Language: English
• Published: London Springer Science and Business Media LLC 09.09.2016; Nature Publishing Group UK; Nature Publishing Group
• Subjects: 631/535/1266; 631/92/173; 82/80; 82/83; Antibiotics; Bacteria; Bacterial Proteins; Bacterial Proteins - chemistry; Binding sites; Biosynthesis; Catalytic Domain; Crystallography, X-Ray; Embedding; Endotoxins; Enzymes; Glycolipids; Glycolipids - metabolism; Gram-negative bacteria; Humanities and Social Sciences; Hydrophobic and Hydrophilic Interactions; Hydrophobicity; Lipid A; Lipid A - biosynthesis; Lipids; Lipopolysaccharides; Models, Molecular; multidisciplinary; Mutation; Protein Binding; Protein Conformation; Pseudomonas aeruginosa; Pseudomonas aeruginosa - chemistry; Pseudomonas aeruginosa - enzymology; Pseudomonas aeruginosa - genetics; Pyrophosphatases; Pyrophosphatases - chemistry; Pyrophosphatases - genetics; Pyrophosphatases - metabolism; Science
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep32822

Lipid A (also known as endotoxin) is the hydrophobic portion of lipopolysaccharides. It is an essential membrane component required for the viability of gram-negative bacteria. The enzymes involved in its biosynthesis are attractive targets for the development of novel antibiotics. LpxH catalyzes the fourth step of the lipid A biosynthesis pathway and cleaves the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP. Here we present the structures of LpxH from Pseudomonas aeruginosa (Pa LpxH). Pa LpxH consists of two domains: a catalytic domain that is homologous to the metallophosphoesterases and a helical insertion domain. Lipid X was captured in the crevice between these two domains, with its phosphate group facing the dinuclear metal (Mn 2+ ) center and two acyl chains buried in the hydrophobic cavity. The structures reveal that a large conformational change occurs at the lipid X binding site surface upon the binding/release of the product molecule. Based on these observations, we propose a novel model for lipid X embedding, which involves the scissor-like movement of helix α6, resulting in the release of lipid X into the lipid bilayer.