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

BMC Structural Biology

Wyatt W Yue²  Udo Oppermann³  Catherine Vénien-Bryan¹  Kathryn L Kavanagh²  Frank von Delft²  Antonio De Riso¹  Ewa S Pilka²  Apirat Chaikuad² 

[1] Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford, OX1 3QU, UK;Structural Genomics Consortium, Old Road Research Campus Building, Oxford OX3 7DQ, UK;Botnar Research Centre, Oxford Biomedical Research Unit, Oxford, OX3 7LD, UK

关键词: Domain swapping;    Metalloprotease;    M18 peptidase;    Dodecameric tetrahedron;    Aspartyl aminopeptidase;   

Others  :  1092182
DOI  :  10.1186/1472-6807-12-14

 received in 2012-03-22, accepted in 2012-05-29,  发布年份 2012

【 摘 要 】

Backround

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.

Results

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.

Conclusions

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.

【 授权许可】

   
2012 Chaikuad et al.; licensee BioMed Central Ltd.

【 图 表 】

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