title: Crystal structure of A. aeolicus LpxC with bound product suggests alternate deacetylation mechanism.
abstract: UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is the first committed step to form lipid A, an essential component of the outer membrane of Gram-negative bacteria. As it is essential for the survival of many pathogens, LpxC is an attractive target for antibacterial therapeutics. Herein, we report the product-bound co-crystal structure of LpxC from the acheal Aquifex aeolicus solved to 1.6 Å resolution. We identified interactions by hydroxyl and hydroxymethyl substituents of the product glucosamine ring that may enable new insights to exploit waters in the active site for structure-based design of LpxC inhibitors with novel scaffolds. By using this product structure, we have performed quantum mechanical modeling on the substrate in the active site. Based on our results and published experimental data, we propose a new mechanism that may lead to a better understanding of LpxC catalysis and inhibition.
authors.affiliation: AstraZeneca R&D Boston, Infection Innovative Medicines Unit, Waltham, Massachusetts, 02451.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Miller
authors.affiliation: AstraZeneca R&D Boston, Discovery Sciences, Waltham, Massachusetts, 02451.
authors.forename: Ning
authors.initials: N
authors.lastname: Gao
authors.affiliation: AstraZeneca R&D Boston, Discovery Sciences, Waltham, Massachusetts, 02451.
authors.forename: Philip L
authors.initials: PL
authors.lastname: Ross
authors.affiliation: AstraZeneca R&D Cambridge-UK, Discovery Sciences, Cambridge, CB4 0FZ, United Kingdom.
authors.forename: Nelson B
authors.initials: NB
authors.lastname: Olivier
mesh_terms: D000107:Acetylation; D000581:Amidohydrolases / Q000737:chemistry* / Q000378:metabolism; D001419:Bacteria / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D055162:Biocatalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism; D005944:Glucosamine / Q000737:chemistry / Q000378:metabolism; D008050:Lipid A / Q000096:biosynthesis; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D013379:Substrate Specificity; D015032:Zinc / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; D008050:Lipid A; D000581:Amidohydrolases; C097307:UDP-3-O-acyl-N-acetylglucosamine deacetylase; D015032:Zinc; D005944:Glucosamine
keywords: LpxC; QM/MM; deacetylase; dynamics; lipid A; lipopolysaccharide; mechanism; natural product; transition state; zinc