5DG3

Structure of Pseudomonas aeruginosa LpxA in complex with UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc

Summary for 5DG3

• Entry DOI: 10.2210/pdb5dg3/pdb
• Related: 5DEM 5DEP
• Descriptor: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase, uridine-5'-diphosphate-3-O-(R-3-hydroxydecanoyl)-N-acetyl-D-glucosamine, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: acyltransferases, catalytic domain, udp-glcnac, fatty acids, lipid a, substrate specificity, uridine diphosphate n-acetylglucosamine, hydrocarbon rulers, transferase
• Biological source: Pseudomonas aeruginosa (strain PA7)
• Cellular location: Cytoplasm : A6V1E4
• Total number of polymer chains: 6
• Total formula weight: 171497.76

Authors

Smith, E.W.,Chen, Y. (deposition date: 2015-08-27, release date: 2015-09-16, Last modification date: 2024-03-06)

Primary citation

Smith, E.W.,Zhang, X.,Behzadi, C.,Andrews, L.D.,Cohen, F.,Chen, Y.
Structures of Pseudomonas aeruginosa LpxA Reveal the Basis for Its Substrate Selectivity.
Biochemistry, 54:5937-5948, 2015

PubMed Abstract: In Gram-negative bacteria, the first step of lipid A biosynthesis is catalyzed by UDP-N-acetylglucosamine acyltransferase (LpxA) through the transfer of a R-3-hydroxyacyl chain from the acyl carrier protein (ACP) to the 3-hydroxyl group of UDP-GlcNAc. Previous studies suggest that LpxA is a critical determinant of the acyl chain length found in lipid A, which varies among species of bacteria. In Escherichia coli and Leptospira interrogans, LpxA prefers to incorporate longer R-3-hydroxyacyl chains (C14 and C12, respectively), whereas in Pseudomonas aeruginosa, the enzyme is selective for R-3-hydroxydecanoyl, a 10-hydrocarbon long acyl chain. We now report three P. aeruginosa LpxA crystal structures: apo protein, substrate complex with UDP-GlcNAc, and product complex with UDP-3-O-(R-3-hydroxydecanoyl)-GlcNAc. A comparison between the apo form and complexes identifies key residues that position UDP-GlcNAc appropriately for catalysis and supports the role of catalytic His121 in activating the UDP-GlcNAc 3-hydroxyl group for nucleophilic attack during the reaction. The product-complex structure, for the first time, offers structural insights into how Met169 serves to constrain the length of the acyl chain and thus functions as the so-called hydrocarbon ruler. Furthermore, compared with ortholog LpxA structures, the purported oxyanion hole, formed by the backbone amide group of Gly139, displays a different conformation in P. aeruginosa LpxA, which suggests flexibility of this structural feature important for catalysis and the potential need for substrate-induced conformational change in catalysis. Taken together, the three structures provide valuable insights into P. aeruginosa LpxA catalysis and substrate specificity as well as templates for future inhibitor discovery.

PubMed: 26352800
DOI: 10.1021/acs.biochem.5b00720

Experimental method

X-RAY DIFFRACTION (2.3 Å)