It is a peptidoglycan, which is amphipathic and named for its bactoprenol hydrocarbon chain, which acts as a lipid anchor, embedding itself in the bacterial cell membrane.

It is formed when the MurG transferase catalyzes addition of N-acetylglucosamine (GlcNAc) to Lipid I, resulting in a complete disaccharide-pentapeptide monomer with a bactoprenol-pyrophosphate anchor.

Lipid II is then transported across the membrane by a flippase, to expose the disaccharide-pentapeptide monomer, which is the pentapeptide stem consisting of L-Ala-γ-D-Glu-m-DAP-D-Ala-D-Ala between GlcNAc and N-acetylmuramic acid (MurNAc), for polymerization and cross-linking into peptidoglycan.

[4] The discovery remains somewhat controversial as assay results are conflicting; FtsW (EC 2.4.1.129) was proposed as an alternative, with evidence strongly favoring the MurJ side since 2019.

These antibiotics fight bacteria by either directly inhibiting the peptidoglycan synthesis, or by binding to lipid II to form destructive pores in the cytoplasmic membrane.

Oritavancin also uses the D-Ala-D-Ala terminus, but in addition it uses the crossbridge and D-iso-glutamine in position 2 of the lipid II stem peptide, as present in a number of Gram-positive pathogens, like staphylococci and enterococci.

The increased binding of oritavancin through amidation of lipid II can compensate for the loss of a crucial hydrogen bond in vancomycin-resistant strains,[15] Lantibiotics recognize lipid-II by its pyrophosphate.