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9v8i
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure for YxiD-YxxD toxin-immunity protein complex from Bacillus subtilis 6633.== | |
| + | <StructureSection load='9v8i' size='340' side='right'caption='[[9v8i]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[9v8i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._spizizenii_ATCC_6633_=_JCM_2499 Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9V8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9V8I 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]] 1.7Å</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=9v8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9v8i OCA], [https://pdbe.org/9v8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9v8i RCSB], [https://www.ebi.ac.uk/pdbsum/9v8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9v8i ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A0A9Q4H945_BACSC A0A9Q4H945_BACSC] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Polymorphic toxin systems (PTS) are widespread and play an important role in bacterial competition and shaping communities. However, these systems are less studied in Gram-positive bacteria. Here, we structurally and functionally characterized YxiD-YxxD, a predicted member of PTS from Bacillus subtilis 6633. Using growth curve assays, we established that YxiD-YxxD codes for a toxin-immunity protein pair. We determined a 1.7 A resolution crystal structure of the YxiDCTDH528A (C-terminal domain of YxiD) toxin bound to its cognate immunity protein YxxD. Structure revealed that the toxin adopts a Barnase/EndoU/colicin/RelE (BECR) fold, a characteristic of RNase toxins and the immunity protein sterically occludes binding of the molecular substrate to neutralize the toxin. Structural and other biophysical studies revealed that YxiDCTD-YxxD forms a stable 1:1 stoichiometric complex with KD of approximately 9.4 nM. RNA Sequencing experiments revealed that expression of toxin results in downregulation of several tRNAs and essential genes involved in cell wall biosynthesis, resulting in cellular toxicity. We further demonstrate that YxiDCTD is a metal ion-dependent tRNase that cleaves several tRNAs. Taken together, our study provides the structural basis for YxiD neutralization by cognate immunity protein YxxD and establishes YxiDCTD toxin as a metal-dependent tRNase. | ||
| - | + | The yxiD gene from Bacillus subtilis 6633 encodes a polymorphic toxin with tRNase activity and is neutralized by the cognate immunity protein YxxD.,Rohilla R, Kaundal S, Thakur KG Nucleic Acids Res. 2025 Nov 26;53(22):gkaf1321. doi: 10.1093/nar/gkaf1321. PMID:41385326<ref>PMID:41385326</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 9v8i" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Rohilla R]] | ||
| + | [[Category: Thakur KG]] | ||
Current revision
Crystal structure for YxiD-YxxD toxin-immunity protein complex from Bacillus subtilis 6633.
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