Functions as a protein modifier covalently attached to lysine residues of substrate proteins. The protein modification process is termed sampylation and involves the formation of an isopeptide bond between the SAMP3 C-terminal glycine carboxylate and the epsilon-amino group of lysine residues on target proteins. Seems to be able to form polymeric chains with itself at Lys-18, Lys-55 and Lys-62, similar to ubiquitin and other ubiquitin-like proteins. SAMP3 appears not to serve as a proteolytic signal in the cell to target proteins for degradation by proteasomes. May regulate molybdenum cofactor (MoCo) biosynthesis by inhibiting the activity of MPT synthase MoaE under aerobic conditions, providing a hierarchy of oxygen use prior to that of alternative electron acceptors such as DMSO.