9u8d: Difference between revisions
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==5hmC specific restriction endonuclease Escherichia coli O157:H7 PD-T4-3 in complex with 5-Hydroxymethyl-dCTP== | |||
<StructureSection load='9u8d' size='340' side='right'caption='[[9u8d]], [[Resolution|resolution]] 3.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9u8d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9U8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9U8D 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]] 3.002Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1EOD:[[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+phosphono+hydrogen+phosphate'>A1EOD</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=9u8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9u8d OCA], [https://pdbe.org/9u8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9u8d RCSB], [https://www.ebi.ac.uk/pdbsum/9u8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9u8d ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A9Q7EI50_ECO57 A0A9Q7EI50_ECO57] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The evolutionary arms race between bacteria and phages drives the development of bacterial antiviral defense systems and phage counter-defense strategies. Restriction-modification (RM) systems protect bacteria by methylating 'self' DNA and cleaving unmodified phage DNA. Phages like T-even coliphages evade RM systems by substituting cytosine with 5-hydroxymethyl cytosine (5hmC) or 5-glucosylated hmC (5ghmC). Here, we characterize âa single-component antiviral defense system featuring a GIY-YIG endonuclease domain. Biochemical and structural analyses demonstrate that this defense system is a type IV modification-dependent restriction endonuclease that specifically degrades 5hmC- or 5ghmC-modified DNA, and we accordingly name it CMoRE (Cytosine Modification âRâestriction Endonuclease). The crystal structures reveal an N-terminal GIY-YIG nuclease domain and a C-terminal modification-sensing domain. Unique features, including a 'GIYxY-YIG' motif and an inhibitory negatively charged loop, distinguish CMoRE as an additional member of the GIY-YIG family. This system not only highlights the evolutionary interplay between phages and bacteria but also presents CMoRE as a potential tool for precise genomic detection of 5hmC in mammals, with implications for epigenetics research and disease diagnostics. | |||
A bacterial defense system targeting modified cytosine of phage genomic DNA.,Liu R, Tang D, Niu M, Lei S, Zong Z, Chen Q, Yu Y Nat Commun. 2026 Jan 22. doi: 10.1038/s41467-026-68792-8. PMID:41571690<ref>PMID:41571690</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 9u8d" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli O157:H7]] | |||
[[Category: Large Structures]] | |||
[[Category: Liu R]] | |||
[[Category: Yu Y]] | |||
Latest revision as of 07:29, 11 February 2026
5hmC specific restriction endonuclease Escherichia coli O157:H7 PD-T4-3 in complex with 5-Hydroxymethyl-dCTP
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