Poster Presentation 9th General Meeting of the International Proteolysis Society 2015

First structures of Family S46 peptidase reveal exo-peptidase activity in Clan PA peptidases. (#132)

Ippei Iizuka 1 , Yasumitsu Sakamoto 2 , Yoshiyuki Suzuki 3 , Chika Tateoka 2 , Saori Roppongi 2 , Mayu Fujimoto 2 , Koji Inaka 4 , Hiroaki Tanaka 5 , Mika Masaki 6 , Kazunori Ohta 6 , Hirofumi Okada 3 , Takamasa Nonaka 2 , Yasushi Morikawa 3 , Kazuo T. Nakamura 7 , Wataru Ogasawara 3 , Nobutada Tanaka 7
  1. School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
  2. School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate, Japan
  3. Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
  4. Maruwa Foods and Biosciences Inc., 170-1 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
  5. Confocal Science Inc., 2-12-2 Iwamoto-cho, Chiyoda-ku, Tokyo 101-0032, Japan
  6. Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305- 8505, Japan
  7. School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan

 Asaccharolytic gram-negative bacteria, such as Stenotrophomonas  maltophiliia (multidrug-resistant opportunistic pathogen) and Porphyromonas gingivalis (a periodontal pathogen), utilizes peptides or protein as an energy source instead of carbohydrate. Inner membrane of these bacteria preferentially transports not amino acids, but dipeptides. Thus, production of dipeptide by dipeptidyl peptidases (DPPs), which exists in periplasm region are very important for growth of these bacteria. DPPs of these bacteria are classified into Clan SC Family S9 (DPP4, POP) and Clan PA Family S46 (DPP7), peptidases belonging to Family S46 are not found in mammals. In addition, Family S46 peptides play mainly dipeptides production, so the peptides are promising as target for antibiotics.

At this time, we determined the three-dimensional structure of DAP BII (Bacterial DPP7) from Pseudoxanthomonas mexicana WO24. This is the first structure example as peptidase belonging to Family S46 peptidases. The overall structure of DAP BII reveals that it comprised of a chymotrypsin fold catalytic domain and α-helical domain. The enzymes belonging to Clan PA contain chymotrypsin fold and are endopeptidase except for S46 peptidases. Structure analysis of apo and peptide-bound forms of DAP BII reveal that the Asn330 in α-helical domain involved in recognition of the N-terminus of the substrate peptide. Furthermore, it reveals the residues comprising an S1 pocket of DAP BII and the substrate recognition mode of the peptide. Development of new inhibitors, which is target to metabolic pathway of peptides for asaccharolytic gram-negative bacteria is expected by this structural studies.

  1. Suzuki Y. et al. Identification of the Catalytic Triad of Family S46 Exopeptidases, Closely Related to Clan PA Endopeptidases. Sci. Rep. 4:4292 (2014)
  2. Sakamoto Y. et al. S46 Peptidases are the First Exopeptidases to be Members of Clan PA Sci. Rep. 4:4977 (2014)