8yxk: Difference between revisions
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==X-ray structure of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.== | |||
<StructureSection load='8yxk' size='340' side='right'caption='[[8yxk]], [[Resolution|resolution]] 1.87Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8yxk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridioides_difficile_630 Clostridioides difficile 630]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8YXK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8YXK FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.87Å</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8yxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8yxk OCA], [https://pdbe.org/8yxk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8yxk RCSB], [https://www.ebi.ac.uk/pdbsum/8yxk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8yxk ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q183Y3_CLOD6 Q183Y3_CLOD6] | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:38688057</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8yxk" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Clostridioides difficile 630]] | |||
[[Category: Large Structures]] | |||
[[Category: Kamitori S]] | |||
[[Category: Tamai E]] | |||
Latest revision as of 05:28, 15 May 2024
X-ray structure of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain.
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