9EXH | pdb_00009exh

Cryo-EM structure of the Apo E. coli BrxX methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb9EXH/pdb
• EM Map EMD-50038: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2024-04-08 Released: 2025-03-05 
• Deposition Author(s): Adams, M.C., Ghilarov, D.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 39979294 
• DOI: https://doi.org/10.1038/s41467-025-57006-2
• Primary Citation 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.

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Organizational Affiliation: 
• Skolkovo Institute of Science and Technology, Moscow, Russia.
Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
Department of Biosciences, Durham University, Durham, UK.
Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia. [e-mail].
Waksman Institute of Microbiology, Piscataway, NJ, USA. [e-mail].
Department of Molecular Microbiology, John Innes Centre, Norwich, UK. [e-mail].
Skolkovo Institute of Science and Technology, Moscow, Russia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 138.13 kDa 
• Atom Count: 9,728 
• Modeled Residue Count: 1,205 
• Deposited Residue Count: 1,205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine-specific methyltransferase BrxX	A	1,205	Escherichia coli	Mutation(s): 0  Gene Names: pglX, brxX, EcHS_A0339 EC: 2.1.1.72
UniProt
Find proteins for P0DUF9 (Escherichia coli O9:H4 (strain HS)) Explore P0DUF9  Go to UniProtKB:  P0DUF9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Adams, M.C., Ghilarov, D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	221868/Z/20/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/X01/097X/1

Revision History  

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