8YXK

X-ray structure of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.

Summary for 8YXK

• Entry DOI: 10.2210/pdb8yxk/pdb
• Descriptor: Phage cell wall hydrolase (2 entities in total)
• Functional Keywords: clostridioides difficile, endolysin, hydrolase
• Biological source: Clostridioides difficile (strain 630) (Peptoclostridium difficile)
• Total number of polymer chains: 2
• Total formula weight: 44794.12

Authors

Kamitori, S.,Tamai, E. (deposition date: 2024-04-02, release date: 2024-05-15)

Primary citation

Sekiya, H.,Nonaka, Y.,Kamitori, S.,Miyaji, T.,Tamai, E.
X-ray structure and mutagenesis analyses of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.
Biochem.Biophys.Res.Commun., 715:149957-149957, 2024

PubMed Abstract: Clostridioides difficile endolysin (Ecd09610) consists of an unknown domain at its N terminus, followed by two catalytic domains, a glucosaminidase domain and endopeptidase domain. X-ray structure and mutagenesis analyses of the Ecd09610 catalytic domain with glucosaminidase activity (Ecd09610CD53) were performed. Ecd09610CD53 was found to possess an α-bundle-like structure with nine helices, which is well conserved among GH73 family enzymes. The mutagenesis analysis based on X-ray structures showed that Glu405 and Asn470 were essential for enzymatic activity. Ecd09610CD53 may adopt a neighboring-group mechanism for a catalytic reaction in which Glu405 acted as an acid/base catalyst and Asn470 helped to stabilize the oxazolinium ion intermediate. Structural comparisons with the newly identified Clostridium perfringens autolysin catalytic domain (AcpCD) in the P1 form and a zymography analysis demonstrated that AcpCD was 15-fold more active than Ecd09610CD53. The strength of the glucosaminidase activity of the GH73 family appears to be dependent on the depth of the substrate-binding groove.

PubMed: 38688057
DOI: 10.1016/j.bbrc.2024.149957

Experimental method

X-RAY DIFFRACTION (1.87 Å)