Structure of the Bacterial Deacetylase LpxC Bound to the Nucleotide Reaction Product Reveals Mechanisms of Oxyanion Stabilization and Proton Transfer

Abstract

Background: LpxC is a metal-dependent deacetylase essential for lipopolysaccharide biosynthesis. Results: The LpxC reaction product binds an extensive, conserved groove with the 2-amino group positioned in the active site. Conclusion: The product-bound LpxC structure reveals conserved ligand interactions and stabilization of a phosphate mimic of the oxyanion intermediate. Significance: LpxC structures are critical to elucidate the catalytic mechanism and design of novel antibiotics.

Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N′‐diacetylchitobiose deacetylase

“…The resulting tetrahedral oxyanion intermediate was mimicked by the phosphate ion that was observed in the crystal structure of Ph‐Dac (Figs D and A). The results of a recent study showed similar mimicking employed by the bacterial deacetylase LpxC . The tetrahedral oxyanion intermediate contains two oxygen atoms: one (O1) from the water molecule that attacked the acetyl group, and the other (O2) from the carbonyl oxygen.…”

The Inhibition of Lipid A Biosynthesis—The Antidote Against Superbugs?

“…[54][55][56][57] The most relevant examples are: i) the 4-(phenylethynyl)benzamide derivatives LPC-004 and CHIR-090, [58,59] the 4-(phenylbuta-1,3-diyn-1-yl)benzamide derivatives LPC-009 and LPC-011, [60] all of which were developed by Chiron and the University of Washington; ii) the difluoromethyl derivative LPC-058 developed by C. -J. Lee et al; [61] iii) the pyridine methylsulfone LpxC-4 (PF-5081090), [62,63] which was discovered by Pfizer; and iv) the cyclopropane derivative ACHN-975 [56] developed by Achaogen (Figure 5). Diverse crystal structures of the LpxC enzyme from different species, including P. aeruginosa, [59,63,[65][66][67][68][69] Aquifex aeolicus, [67,[70][71][72][73][74][75] Yersinia enterocolitica [76] and E. coli, [52,77] have been solved, either as an apo-form or in complex mainly with inhibitors and these structures provide a good understanding at the molecular level of the differences in the inhibitory potency observed experimentally. The identification of these lead compounds was the result of the synthesis of a very large number of compounds in which mainly diverse moieties that mimic the fatty acid chain of the substrate were explored.…”

Structure, inhibition, and regulation of essential lipid A enzymes

“…Several models of LpxC catalysis have been proposed based on metal substitution, mutagenesis, structural, and pH dependence studies [37-44]. The emerging view implicates E73 as the catalytic general base for deprotonation of the catalytic Zn 2+ -bound water ( Fig.…”