Open Access Highly Accessed Research article

Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family

Apirat Chaikuad1, Ewa S Pilka1, Antonio De Riso2, Frank von Delft1, Kathryn L Kavanagh1, Catherine Vénien-Bryan2, Udo Oppermann13 and Wyatt W Yue1*

Author affiliations

1 Structural Genomics Consortium, Old Road Research Campus Building, Oxford OX3 7DQ, UK

2 Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford, OX1 3QU, UK

3 Botnar Research Centre, Oxford Biomedical Research Unit, Oxford, OX3 7LD, UK

For all author emails, please log on.

Citation and License

BMC Structural Biology 2012, 12:14  doi:10.1186/1472-6807-12-14

Published: 21 June 2012



Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated.


The crystal structure of human DNPEP complexed with zinc and a substrate analogue aspartate-β-hydroxamate reveals a dodecameric machinery built by domain-swapped dimers, in agreement with electron microscopy data. A structural comparison with bacterial homologues identifies unifying catalytic features among the poorly understood M18 enzymes. The bound ligands in the active site also reveal the coordination mode of the binuclear zinc centre and a substrate specificity pocket for acidic amino acids.


The DNPEP structure provides a molecular framework to understand its catalysis that is mediated by active site loop swapping, a mechanism likely adopted in other M18 and M42 metallopeptidases that form dodecameric complexes as a self-compartmentalization strategy. Small differences in the substrate binding pocket such as shape and positive charges, the latter conferred by a basic lysine residue, further provide the key to distinguishing substrate preference. Together, the structural knowledge will aid in the development of enzyme-/family-specific aminopeptidase inhibitors.

Aspartyl aminopeptidase; Dodecameric tetrahedron; M18 peptidase; Metalloprotease; Domain swapping