3WOM

Crystal structure of the DAP BII dipeptide complex II

3WOM の概要

• エントリーDOI: 10.2210/pdb3wom/pdb
• 関連するPDBエントリー: 3WOI 3WOJ 3WOK 3WOL 3WON 3WOO 3WOP 3WOQ 3WOR
• 分子名称: dipeptidyl aminopeptidase BII, VALINE, TYROSINE, ... (6 entities in total)
• 機能のキーワード: chymotrypsin fold, hydrolase
• 由来する生物種: Pseudoxanthomonas mexicana
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 154555.81

構造登録者

Sakamoto, Y.,Suzuki, Y.,Iizuka, I.,Tateoka, C.,Roppongi, S.,Fujimoto, M.,Nonaka, T.,Ogasawara, W.,Tanaka, N. (登録日: 2013-12-29, 公開日: 2014-09-03, 最終更新日: 2023-11-08)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.86 Å)