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Structure paper

TitleMolecular basis of foreign DNA recognition by BREX anti-phage immunity system.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 1825, Year 2025
Publish dateFeb 20, 2025
AuthorsAlena Drobiazko / Myfanwy C Adams / Mikhail Skutel / Kristina Potekhina / Oksana Kotovskaya / Anna Trofimova / Mikhail Matlashov / Daria Yatselenko / Karen L Maxwell / Tim R Blower / Konstantin Severinov / Dmitry Ghilarov / Artem Isaev /
PubMed AbstractAnti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I ...Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-Å cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.
External linksNat Commun / PubMed:39979294 / PubMed Central
MethodsEM (single particle)
Resolution2.22 - 3.9 Å
Structure data

50027

9ewz

EMDB-50027, PDB-9ewz:
Cryo-EM structure of the E. coli BrxX methyltransferase in complex with DNA
Method: EM (single particle) / Resolution: 2.22 Å

EMDB-50028: Focused map for NTD and MTD domains of the phage immunity methyltransferase protein BrxX.
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-50029: Consensus map for the phage immunity methyltransferase protein BrxX
Method: EM (single particle) / Resolution: 2.91 Å

50032

9ex7

EMDB-50032, PDB-9ex7:
Cryo-EM structure of the E. coli BrxX methyltransferase in complex with Ocr
Method: EM (single particle) / Resolution: 2.91 Å

50038

9exh

EMDB-50038, PDB-9exh:
Cryo-EM structure of the Apo E. coli BrxX methyltransferase
Method: EM (single particle) / Resolution: 3.9 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-SAM:
S-ADENOSYLMETHIONINE

Source
  • escherichia coli (E. coli)
  • escherichia phage t7 (virus)
KeywordsTRANSFERASE / Methyltransferase / phage defense / BREX / DNA-binding / DNA binding

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