Catalyzes the phospholipid dependent N-acylation of the N-terminal cysteine of apolipoprotein, the last step in lipoprotein maturation. a glycerophospholipid + N-terminal S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[lipoprotein] = a 2-acyl-sn-glycero-3-phospholipid + H(+) + N-acyl-S-1,2-diacyl-sn-glyceryl-L-cysteinyl-[lipoprotein] Protein modification; lipoprotein biosynthesis (N-acyl transfer). Belongs to the CN hydrolase family. Apolipoprotein N-acyltransferase subfamily.