9EWZ | pdb_00009ewz

Cryo-EM structure of the E. coli BrxX methyltransferase in complex with DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of foreign DNA recognition by BREX anti-phage immunity system.

Drobiazko, A.Adams, M.C.Skutel, M.Potekhina, K.Kotovskaya, O.Trofimova, A.Matlashov, M.Yatselenko, D.Maxwell, K.L.Blower, T.R.Severinov, K.Ghilarov, D.Isaev, A.

(2025) Nat Commun 16: 1825-1825

  • DOI: https://doi.org/10.1038/s41467-025-57006-2
  • Primary Citation of Related Structures:  
    9EWZ, 9EX7, 9EXH

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Skolkovo Institute of Science and Technology, Moscow, Russia.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenine-specific methyltransferase BrxXA [auth C]1,205Escherichia coliMutation(s): 0 
Gene Names: pglXbrxXEcHS_A0339
EC: 2.1.1.72
UniProt
Find proteins for P0DUF9 (Escherichia coli O9:H4 (strain HS))
Explore P0DUF9 
Go to UniProtKB:  P0DUF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DUF9
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (26-MER) with BREX binding site GGTAAG25Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (26-MER) with BREX binding site GGTAAGC [auth A]25Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom221868/Z/20/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/X01/097X/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection