MraY–antibiotic complex reveals details of tunicamycin mode of action

Abstract

The rapid increase of antibiotic resistance has created an urgent need to develop novel antimicrobial agents. Here we describe the crystal structure of the promising bacterial target phospho-N-acetylmuramoyl-pentapeptide translocase (MraY) in complex with the nucleoside antibiotic tunicamycin. The structure not only reveals the mode of action of several related natural-product antibiotics but also gives an indication on the binding mode of the MraY UDP-MurNAc-pentapeptide and undecaprenyl-phosphate substrates.

Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design

“…Together these results confirmed our hypothesis that systematic ''lipid alteration'' could create tunicamycin analogues in which mammalian cytotoxicity is separated from antibacterial effects. A Molecular Explanation for Differences in TUN-X,X Analogue Binding to DPAGT1 and MraY Comparison of the structures of the complexes of tunicamycin with DPAGT1 and MraY (Hakulinen et al, 2017;Yoo et al, 2018; this work) gave an explanation for selectivity of analogues on MraY over DPAGT1. The MraY tunicamycin binding site has a more open, shallow surface than in DPAGT1; in the latter the lipid tail is completely enclosed by Trp122 adjacent to the active site ( Figure 6G).…”

N -Acetylglucosamine-1-Phosphate Transferase, WecA, as a Validated Drug Target in Mycobacterium tuberculosis

“…Although we were unable to purify mycobacterial WecA to homogeneity, we could, however, demonstrate WecA activity in the partially purified orthologue from M. thermoresistibile, which can serve as a starting point for efforts toward the structural characterization of WecA from mycobacteria. Several recent reports on detailed structures of translocase I (MraY) (40)(41)(42), which belongs to the same family of polyprenyl phosphate-N-acetyl-hexosamine-1-phosphate transferases, hold promise for similar success with WecA enzymes.…”

Mechanism of action of nucleoside antibacterial natural product antibiotics

“…The carboxyl terminus of the peptide chain is bound by Gln-305, a residue that is conserved in bacterial MraY homologues, and the epi-capreomycidine amino acid is bound by His-324 and His-325 [76]. In 2017 the structure of a complex of Clostridium boltae MraY with tunicamycin was published [77]. The overall conformation of the protein was similar to the MraY-muraymycin complex, but some similarities and differences in the enzyme-ligand binding interactions were observed [77,78].…”

“…In 2017 the structure of a complex of Clostridium boltae MraY with tunicamycin was published [77]. The overall conformation of the protein was similar to the MraY-muraymycin complex, but some similarities and differences in the enzyme-ligand binding interactions were observed [77,78]. As in the MraY-muraymycin complex, the uracil base was bound in a small cavity, interacting via stacking interactions to Phe-228 (see Figure 9B), and the 4-carbonyl group binding to Asn-221.…”

“…The HHH motif (His-290, His-291) are also involved in ligand binding, in this case to the GlcNAc 4'-and 6'-hydroxyl groups. However, unlike the MraY-muraymycin complex, tunicamycin was found to interact with the catalytic Asp residues, with the tunicamine 9'hydroxyl group interacting with Asp-231, but in the absence of Mg 2+ [77] and E287A MraY mutant enzymes [81], suggesting that parts of the antibiotic structure somehow aid the targetting of MraY in vivo, perhaps aiding uptake into the cell via a hydrophobic channel present in the structure of MraY [75], as shown in Figure 10. This hypothesis might explain how these agents of molecular weight 600-1200 Da are able to access the MraY active site on the inner face of the cytoplasmic membrane, and also why it has proved difficult to design small analogues of these nucleoside antibiotics that retain both MraY inhibition and antimicrobial activity.…”