3NB6

Crystal structure of Aquifex aeolicus peptidoglycan glycosyltransferase in complex with Methylphosphoryl Neryl Moenomycin

Summary for 3NB6

• Entry DOI: 10.2210/pdb3nb6/pdb
• Related: 2OQO 3D3H 3NB7
• Descriptor: Penicillin-binding protein 1A (1 entity in total)
• Functional Keywords: glycosyltransferases, peptidoglycan glycosyltransferase, polysaccharides, cell wall, antibiotics, moenomycin, transferase
• Biological source: Aquifex aeolicus
• Cellular location: Cell inner membrane; Single-pass type II membrane protein (By similarity): O66874
• Total number of polymer chains: 1
• Total formula weight: 22884.38

Authors

Sliz, P.,Yuan, Y.,Walker, S.,Kahne, D. (deposition date: 2010-06-02, release date: 2011-05-18, Last modification date: 2023-09-06)

Primary citation

Fuse, S.,Tsukamoto, H.,Yuan, Y.,Wang, T.S.,Zhang, Y.,Bolla, M.,Walker, S.,Sliz, P.,Kahne, D.
Functional and structural analysis of a key region of the cell wall inhibitor moenomycin.
Acs Chem.Biol., 5:701-711, 2010

PubMed Abstract: Moenomycin A (MmA) belongs to a family of natural products that inhibit peptidoglycan biosynthesis by binding to the peptidoglycan glycosyltransferases, the enzymes that make the glycan chains of peptidoglycan. MmA is remarkably potent, but its clinical utility has been hampered by poor physicochemical properties. Moenomycin contains three structurally distinct regions: a pentasaccharide, a phosphoglycerate, and a C25 isoprenyl (moenocinyl) lipid tail that gives the molecule its name. The phosphoglycerate moiety links the pentasaccharide to the moenocinyl chain. This moiety contains two negatively charged groups, a phosphoryl group and a carboxylate. Both the phosphoryl group and the carboxylate have previously been implicated in target binding but the role of the carboxylate has not been explored in detail. Here we report the synthesis of six MmA analogues designed to probe the importance of the phosphoglycerate. These analogues were evaluated for antibacterial and enzyme inhibitory activity; the specific contacts between the phosphoglycerate and the protein target were assessed by X-ray crystallography in conjunction with molecular modeling. Both the phosphoryl group and the carboxylate of the phosphoglycerate chain play roles in target binding. The negative charge of the carboxylate, and not its specific structure, appears to be the critical feature in binding since replacing it with a negatively charged acylsulfonamide group produces a more active compound than replacing it with the isosteric amide. Analysis of the ligand-protein contacts suggests that the carboxylate makes a critical contact with an invariant lysine in the active site. The reported work provides information and validated computational methods critical for the design of analogues based on moenomycin scaffolds.

PubMed: 20496948
DOI: 10.1021/cb100048q

Experimental method

X-RAY DIFFRACTION (2.7 Å)