3WOM

Crystal structure of the DAP BII dipeptide complex II

Summary for 3WOM

• Entry DOI: 10.2210/pdb3wom/pdb
• Related: 3WOI 3WOJ 3WOK 3WOL 3WON 3WOO 3WOP 3WOQ 3WOR
• Descriptor: dipeptidyl aminopeptidase BII, VALINE, TYROSINE, ... (6 entities in total)
• Functional Keywords: chymotrypsin fold, hydrolase
• Biological source: Pseudoxanthomonas mexicana
• Total number of polymer chains: 2
• Total formula weight: 154555.81

Authors

Sakamoto, Y.,Suzuki, Y.,Iizuka, I.,Tateoka, C.,Roppongi, S.,Fujimoto, M.,Nonaka, T.,Ogasawara, W.,Tanaka, N. (deposition date: 2013-12-29, release date: 2014-09-03, Last modification date: 2023-11-08)

Primary citation

Sakamoto, Y.,Suzuki, Y.,Iizuka, I.,Tateoka, C.,Roppongi, S.,Fujimoto, M.,Inaka, K.,Tanaka, H.,Masaki, M.,Ohta, K.,Okada, H.,Nonaka, T.,Morikawa, Y.,Nakamura, K.T.,Ogasawara, W.,Tanaka, N.
S46 peptidases are the first exopeptidases to be members of clan PA
SCI REP, 4:4977-4977, 2014

PubMed Abstract: 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 β-barrel fold and previously unreported α-helical domain. The structures of peptide complexes revealed that the α-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 α-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.

PubMed: 24827749
DOI: 10.1038/srep04977

Experimental method

X-RAY DIFFRACTION (1.86 Å)