7F5I

X-ray structure of Clostridium perfringens-specific amidase endolysin

Summary for 7F5I

• Entry DOI: 10.2210/pdb7f5i/pdb
• Descriptor: amidase, GLUTAMIC ACID, ZINC ION, ... (5 entities in total)
• Functional Keywords: endolysin, amidase, hydrolase
• Biological source: Clostridium perfringens (strain 13 / Type A)
• Total number of polymer chains: 1
• Total formula weight: 19350.05

Authors

Kamitori, S.,Tamai, E. (deposition date: 2021-06-22, release date: 2022-05-04, Last modification date: 2023-11-29)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.65 Å)