4Y06

Crystal structure of the DAP BII (G675R) dipeptide complex

4Y06 の概要

• エントリーDOI: 10.2210/pdb4y06/pdb
• 関連するPDBエントリー: 4XZY 4Y01 4Y02 4Y04
• 分子名称: Dipeptidyl aminopeptidase BII, LEUCINE, GLUTAMIC ACID, ... (6 entities in total)
• 機能のキーワード: 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: 159949.67

構造登録者

Sakamoto, Y.,Iizuka, I.,Tateoka, C.,Roppongi, S.,Fujimoto, M.,Nonaka, T.,Ogasawara, W.,Tanaka, N. (登録日: 2015-02-05, 公開日: 2015-07-15, 最終更新日: 2024-11-06)

主引用文献

Sakamoto, Y.,Suzuki, Y.,Iizuka, I.,Tateoka, C.,Roppongi, S.,Fujimoto, M.,Inaka, K.,Tanaka, H.,Yamada, M.,Ohta, K.,Gouda, H.,Nonaka, T.,Ogasawara, W.,Tanaka, N.
Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.
Sci Rep, 5:11151-11151, 2015

PubMed Abstract: The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double β-barrel fold and a recently identified regulatory α-helical domain. Crystal structure analyses, docking studies, and biochemical studies revealed that the side chain of Arg673 in the S1 subsite is essential for recognition of the Asp/Glu side chain at the P1 position of the bound substrate. Because S46 peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we anticipate that DPP11s could be utilised as targets for antibiotics. In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms.

PubMed: 26057589
DOI: 10.1038/srep11151

実験手法

X-RAY DIFFRACTION (2.18 Å)