8yxk

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

spinqualitylabelsall models 8yxk, resolution 1.87Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8yxk is a 2 chain structure with sequence from Clostridioides difficile 630. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.87Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q183Y3_CLOD6 Publication Abstract from PubMed 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 alpha-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. X-ray structure and mutagenesis analyses of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.,Sekiya H, Nonaka Y, Kamitori S, Miyaji T, Tamai E Biochem Biophys Res Commun. 2024 Jun 30;715:149957. doi: , 10.1016/j.bbrc.2024.149957. Epub 2024 Apr 16. PMID:38688057 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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