3NZK

Structure of LpxC from Yersinia enterocolitica Complexed with CHIR090 Inhibitor

Summary for 3NZK

• Entry DOI: 10.2210/pdb3nzk/pdb
• Descriptor: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase, N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide, ZINC ION, ... (5 entities in total)
• Functional Keywords: deacetylase, endotoxin, metal-binding, hydrolase
• Biological source: Yersinia enterocolitica
• Total number of polymer chains: 2
• Total formula weight: 70903.72

Authors

Cole, K.E.,Christianson, D.W. (deposition date: 2010-07-16, release date: 2011-01-05, Last modification date: 2023-09-06)

Primary citation

Cole, K.E.,Gattis, S.G.,Angell, H.D.,Fierke, C.A.,Christianson, D.W.
Structure of the Metal-Dependent Deacetylase LpxC from Yersinia enterocolitica Complexed with the Potent Inhibitor CHIR-090 .
Biochemistry, 50:258-262, 2010

PubMed Abstract: The first committed step of lipid A biosynthesis is catalyzed by UDP-(3-O-((R)-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase, a metal-dependent deacetylase also known as LpxC. Because lipid A is essential for bacterial viability, the inhibition of LpxC is an appealing therapeutic strategy for the treatment of Gram-negative bacterial infections. Here we report the 1.79 Å resolution X-ray crystal structure of LpxC from Yersinia enterocolitica (YeLpxC) complexed with the potent hydroxamate inhibitor CHIR-090. This enzyme is a nearly identical orthologue of LpxC from Yersinia pestis (99.7% sequence identity), the pathogen that causes bubonic plague. Similar to the inhibition of LpxC from Escherichia coli, CHIR-090 inhibits YeLpxC via a two-step slow, tight-binding mechanism with an apparent K(i) of 0.54 ± 0.14 nM followed by conversion of the E·I to E·I* species with a rate constant of 0.11 ± 0.01 min(-1). The structure of the LpxC complex with CHIR-090 shows that the inhibitor hydroxamate group chelates the active site zinc ion, and the "tail" of the inhibitor binds in the hydrophobic tunnel in the active site. This hydrophobic tunnel is framed by a βαβ subdomain that exhibits significant conformational flexibility as it accommodates inhibitor binding. CHIR-090 displays a 27 mm zone of inhibition against Y. enterocolitica in a Kirby-Bauer antibiotic assay, which is comparable to its reported activity against other Gram-negative species including E. coli and Pseudomonas aeruginosa. This study demonstrates that the inhibition of LpxC should be explored as a potential therapeutic and/or prophylatic response to infection by weaponized Yersinia species.

PubMed: 21171638
DOI: 10.1021/bi101622a

Experimental method

X-RAY DIFFRACTION (1.8 Å)