3EH0

Crystal Structure of LpxD from Escherichia coli

Summary for 3EH0

• Entry DOI: 10.2210/pdb3eh0/pdb
• Descriptor: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (2 entities in total)
• Functional Keywords: lpxd, acyltransferase, left-handed parallel beta helix, acyl carrier protein, antibiotic resistance, lipid a biosynthesis, lipid synthesis, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 108136.04

Authors

Bartling, C.M.,Raetz, C.R.H. (deposition date: 2008-09-11, release date: 2009-08-18, Last modification date: 2023-08-30)

Primary citation

Bartling, C.M.,Raetz, C.R.
Crystal structure and acyl chain selectivity of Escherichia coli LpxD, the N-acyltransferase of lipid A biosynthesis
Biochemistry, 48:8672-8683, 2009

PubMed Abstract: LpxD catalyzes the third step of lipid A biosynthesis, the R-3-hydroxyacyl-ACP-dependent N-acylation of UDP-3-O-(acyl)-alpha-D-glucosamine, and is a target for new antibiotic development. Here we report the 2.6 A crystal structure of the Escherichia coli LpxD homotrimer (EcLpxD). As is the case in Chlamydia trachomatis LpxD (CtLxpD), each EcLpxD chain consists of an N-terminal uridine-binding region, a left-handed parallel beta-helix (LbetaH), and a C-terminal alpha-helical domain. The backbones of the LbetaH domains of the two enzymes are similar, as are the positions of key active site residues. The N-terminal nucleotide binding domains are oriented differently relative to the LbetaH regions, but are similar when overlaid on each other. The orientation of the EcLpxD tripeptide (residues 303-305), connecting the distal end of the LbetaH and the proximal end of the C-terminal helical domains, differs from its counterpart in CtLpxD (residues 311-312); this results in a 120 degrees rotation of the C-terminal domain relative to the LbetaH region in EcLpxD versus CtLpxD. M290 of EcLpxD appears to cap the distal end of a hydrophobic cleft that binds the acyl chain of the R-3-hydroxyacyl-ACP donor substrate. Under standard assay conditions, wild-type EcLpxD prefers R,S-3-hydroxymyristoyl-ACP over R,S-3-hydroxypalmitoyl-ACP by a factor of 3, whereas the M290A mutant has the opposite selectivity. Both wild-type and M290A EcLpxD rescue the conditional lethality of E. coli RL25, a temperature-sensitive strain harboring point mutations in lpxD. Complementation with wild-type EcLpxD restores normal lipid A containing only N-linked hydroxymyristate to RL25 at 42 degrees C, as judged by mass spectrometry, whereas the M290A mutant generates multiple lipid A species containing one or two longer hydroxy fatty acids in place of the usual R-3-hydroxymyristate at positions 2 and 2'.

PubMed: 19655786
DOI: 10.1021/bi901025v

Experimental method

X-RAY DIFFRACTION (2.6 Å)