8YXK image
Entry Detail
PDB ID:
8YXK
Keywords:
Title:
X-ray structure of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.
Biological Source:
PDB Version:
Deposition Date:
2024-04-02
Release Date:
2024-05-15
Method Details:
Experimental Method:
Resolution:
1.87 Å
R-Value Free:
0.28
R-Value Work:
0.24
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Phage cell wall hydrolase
Chain IDs:A, B
Chain Length:201
Number of Molecules:2
Biological Source:Clostridioides difficile (strain 630)
Primary Citation
X-ray structure and mutagenesis analyses of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.
Biochem.Biophys.Res.Commun. 715 149957 149957 (2024)
PMID: 38688057 DOI: 10.1016/j.bbrc.2024.149957

Abstact

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.

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