9U8D

5hmC specific restriction endonuclease Escherichia coli O157:H7 PD-T4-3 in complex with 5-Hydroxymethyl-dCTP

This is a non-PDB format compatible entry.

Summary for 9U8D

• Entry DOI: 10.2210/pdb9u8d/pdb
• Descriptor: GIY-YIG domain-containing protein, [[(2R,3S,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (3 entities in total)
• Functional Keywords: restriction endonuclease, defense system, giy-yig, pd-t4-3, dna binding protein
• Biological source: Escherichia coli O157:H7
• Total number of polymer chains: 4
• Total formula weight: 118426.78

Authors

Yu, Y.,Liu, R. (deposition date: 2025-03-26, release date: 2026-02-11, Last modification date: 2026-03-04)

Primary citation

Liu, R.,Tang, D.,Niu, M.,Lei, S.,Zong, Z.,Chen, Q.,Yu, Y.
A bacterial defense system targeting modified cytosine of phage genomic DNA.
Nat Commun, 17:-, 2026

PubMed Abstract: 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 ‌a 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 ‌R‌estriction 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.

PubMed: 41571690
DOI: 10.1038/s41467-026-68792-8

Experimental method

X-RAY DIFFRACTION (3.002 Å)