8y1k
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | The | + | ==The cryo-EM structure of TdpAB in complex with AMPPNP and PT-DNA== |
| + | <StructureSection load='8y1k' size='340' side='right'caption='[[8y1k]], [[Resolution|resolution]] 3.10Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[8y1k]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus Thermus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8Y1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8Y1K FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.1Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene></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=8y1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8y1k OCA], [https://pdbe.org/8y1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8y1k RCSB], [https://www.ebi.ac.uk/pdbsum/8y1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8y1k ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | In prokaryotes, the non-bridging oxygen in the DNA sugar-phosphate backbone can be enzymatically replaced by a sulfur atom, resulting in phosphorothioate (PT) modification. However, the mechanism underlying the oxygen-to-sulfur substitution remains enigmatic. In this study, we discovered a hypercompact DNA phosphorothioation system, TdpABC, in extreme thermophiles. This DNA sulfuration process occurs through two sequential steps: an initial activation step by ATP to form an adenylated intermediate, followed by a substitution step where the adenyl group is replaced with a sulfur atom. Together with the TdpA-TdpB, the TdpABC system provides anti-phage defense by degrading PT-free phage DNA. Cryogenic electron microscopy structural analysis revealed that the TdpA hexamer binds one strand of encircled duplex DNA via hydrogen bonds arranged in a spiral staircase conformation. Nevertheless, the TdpAB-DNA interaction was sensitive to the hydrophobicity of the PT sulfur. PTs inhibit ATP-driven translocation and nuclease activity of TdpAB on self-DNA, thereby preventing autoimmunity. | ||
| - | + | A DNA phosphorothioation pathway via adenylated intermediate modulates Tdp machinery.,An T, Tan Q, Jiang L, Liu L, Jiang X, Liu L, Chang X, Tian X, Deng Z, Gao S, Wang L, Chen S Nat Chem Biol. 2025 Jan 16. doi: 10.1038/s41589-024-01832-w. PMID:39820821<ref>PMID:39820821</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 8y1k" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Thermus]] | ||
| + | [[Category: Chen TA]] | ||
| + | [[Category: Qian T]] | ||
Current revision
The cryo-EM structure of TdpAB in complex with AMPPNP and PT-DNA
| |||||||||||
