7F5I

X-ray structure of Clostridium perfringens-specific amidase endolysin

7F5I の概要

• エントリーDOI: 10.2210/pdb7f5i/pdb
• 分子名称: amidase, GLUTAMIC ACID, ZINC ION, ... (5 entities in total)
• 機能のキーワード: endolysin, amidase, hydrolase
• 由来する生物種: Clostridium perfringens (strain 13 / Type A)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 19350.05

構造登録者

Kamitori, S.,Tamai, E. (登録日: 2021-06-22, 公開日: 2022-05-04, 最終更新日: 2023-11-29)

主引用文献

Sekiya, H.,Kamitori, S.,Nariya, H.,Matsunami, R.,Tamai, E.
Structural and biochemical characterization of the Clostridium perfringens-specific Zn 2+ -dependent amidase endolysin, Psa, catalytic domain.
Biochem.Biophys.Res.Commun., 576:66-72, 2021

PubMed Abstract: Phage-derived endolysins, enzymes that degrade peptidoglycans, have the potential to serve as alternative antimicrobial agents. Psa, which was identified as an endolysin encoded in the genome of Clostridium perfringens st13, was shown to specifically lyse C. perfringens. Psa has an N-terminal catalytic domain that is homologous to the Amidase_2 domain (PF01510), and a novel C-terminal cell wall-binding domain. Here, we determined the X-ray structure of the Psa catalytic domain (Psa-CD) at 1.65 Å resolution. Psa-CD has a typical Amidase_2 domain structure, consisting of a spherical structure with a central β-sheet surrounded by two α-helix groups. Furthermore, there is a Zn at the center of Psa-CD catalytic reaction site, as well as a unique T-shaped substrate-binding groove consisting of two grooves on the molecule surface. We performed modeling study of the enzyme/substrate complex along with a mutational analysis, and demonstrated that the structure of the substrate-binding groove is closely related to the amidase activity. Furthermore, we proposed a Zn-mediated catalytic reaction mechanism for the Amidase_2 family, in which tyrosine constitutes part of the catalytic reaction site.

PubMed: 34482025
DOI: 10.1016/j.bbrc.2021.08.085

実験手法

X-RAY DIFFRACTION (1.65 Å)