Most eukaryotic endopeptidases (Merops Family A1) are synthesised with signal and propeptides. The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide. The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residues in the propeptide. This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions [1,2].

1: The high-resolution crystal structure of porcine pepsinogen. Hartsuck JA, Koelsch G, Remington SJ; Proteins 1992;13:1-25. PMID:1594574

2: Refined structure of porcine pepsinogen at 1.8 A resolution. Sielecki AR, Fujinaga M, Read RJ, James MN; J Mol Biol 1991;219:671-692. PMID:2056534