Overview of hDNPEP structure. (A) hDNPEP protomer organizes into the dimerization (blue) and proteolytic domains, the latter is further comprised of subdomain A (orange) and subdomain B (magenta). Zinc ions are shown as blue spheres and the ABH ligand as yellow sticks. (B) Sequence alignment of DNPEP (human, h; bovine, b) and M18 aminopeptidases from yeast Saccharomyces cerevisiae Lap4 (Sc LAP4), yeast Ape4 (Sc Ape4) and two bacterial enzymes (Pseudomonas aeruginosa Pa ApeB and Thermotoga maritima Tm ApeA). Secondary structure elements, catalytic residues (yellow) and residues in the P1 substrate pocket (cyan) of hDNPEP are highlighted. Structural superimposition of hDNPEP with bacterial M18 APs (C) and with M20, M28 and M42 representatives from the MH clan (D) reveals highly conserved topology of the proteolytic domain. The superimposed structures include M18 APs: Thermotoga maritima ApeA (Tm ApeA), Clostridium acetobutylicum ApeA (Ca ApeA), Borrelia burgdorferi ApeA (Bb ApeA), Pseudomonas aeruginosa ApeB (Pa ApeB); M20 APs: Pseudomonas CPG2 (PsCPG2), Lactobacillus delbrueckii PepV (LdPepV), Legionella pneumophila DapE (Lp DapE); M28; Aeromonas proteolytica LAP (Ap LAP), Streptomyces griseus Ap (Sg ApS); and M42: Pyrococcus horikoshii TET1 and TET2 (Ph TET1, Ph TET2), Streptococcus pneumonia PepA (Sp PepA). PDB IDs of all structures are given.