7f5i

X-ray structure of Clostridium perfringens-specific amidase endolysin

spinqualitylabelsall models 7f5i, resolution 1.65Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7f5i is a 1 chain structure with sequence from Clostridium perfringens str. 13. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.65Å Ligands: GLU, NA, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q8XLA4_CLOPE Publication Abstract from PubMed 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 A resolution. Psa-CD has a typical Amidase_2 domain structure, consisting of a spherical structure with a central beta-sheet surrounded by two alpha-helix groups. Furthermore, there is a Zn(2+) 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(2+)-mediated catalytic reaction mechanism for the Amidase_2 family, in which tyrosine constitutes part of the catalytic reaction site. Structural and biochemical characterization of the Clostridium perfringens-specific Zn(2+)-dependent amidase endolysin, Psa, catalytic domain.,Sekiya H, Kamitori S, Nariya H, Matsunami R, Tamai E Biochem Biophys Res Commun. 2021 Oct 22;576:66-72. doi:, 10.1016/j.bbrc.2021.08.085. Epub 2021 Aug 30. PMID:34482025 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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