3WOJ: Crystal Structure Of The Dap Bii

The dipeptidyl aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the molecular mechanism of the exopeptidase activity of family S46 peptidase is unknown. Here, we report crystal structures of DAP BII. DAP BII contains a peptidase domain including a typical double beta-barrel fold and previously unreported alpha-helical domain. The structures of peptide complexes revealed that the alpha-helical domain covers the active-site cleft and the side chain of Asn330 in the domain forms hydrogen bonds with the N-terminus of the bound peptide. These observations indicate that the alpha-helical domain regulates the exopeptidase activity of DAP BII. Because S46 peptidases are not found in mammals, we expect that our study will be useful for the design of specific inhibitors of S46 peptidases from pathogens.
PDB ID: 3WOJDownload
MMDB ID: 122806
PDB Deposition Date: 2013/12/29
Updated in MMDB: 2014/09
Experimental Method:
x-ray diffraction
Resolution: 2.2  Å
Source Organism:
Similar Structures:
Biological Unit for 3WOJ: dimeric; determined by author and by software (PISA)
Molecular Components in 3WOJ
Label Count Molecule
Proteins (2 molecules)
Dipeptidyl Aminopeptidase BII
Molecule annotation
Chemicals (10 molecules)
* Click molecule labels to explore molecular sequence information.

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