7ZGE | pdb_00007zge

BrxA, BREX phage defence protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.265 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the BREX phage defence protein BrxA.

Beck, I.N.Picton, D.M.Blower, T.R.

(2022) Curr Res Struct Biol 4: 211-219

  • DOI: https://doi.org/10.1016/j.crstbi.2022.06.001
  • Primary Citation Related Structures: 
    7ZGE

  • PubMed Abstract: 

    Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multitudinous and varied resistance mechanisms. Bacteriophage Exclusion (BREX) systems protect from phage infection by generating methylation patterns at non-palindromic 6 bp sites in host bacterial DNA, to distinguish and block replication of non-self DNA. Type 1 BREX systems are comprised of six conserved core genes. Here, we present the first reported structure of a BREX core protein, BrxA from the phage defence island of Escherichia fergusonii ATCC 35469 plasmid pEFER, solved to 2.09 ​Å. BrxA is a monomeric protein in solution, with an all α-helical globular fold. Conservation of surface charges and structural homology modelling against known phage defence systems highlighted that BrxA contains two helix-turn-helix motifs, juxtaposed by 180°, positioned to bind opposite sides of a DNA major groove. BrxA was subsequently shown to bind dsDNA. This new understanding of BrxA structure, and first indication of BrxA biological activity, suggests a conserved mode of DNA-recognition has become widespread and implemented by diverse phage defence systems.


  • Organizational Affiliation
    • Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK.

Macromolecule Content 

  • Total Structure Weight: 68.31 kDa 
  • Atom Count: 4,865 
  • Modeled Residue Count: 583 
  • Deposited Residue Count: 597 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BrxA, BREX phage defence protein
A, B, C
199Escherichia fergusonii ATCC 35469Mutation(s): 0 
Gene Names: EFER_p0021
UniProt
Find proteins for B7L3Y4 (Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CCUG 18766 / IAM 14443 / JCM 21226 / LMG 7866 / NBRC 102419 / NCTC 12128 / CDC 0568-73))
Explore B7L3Y4 
Go to UniProtKB:  B7L3Y4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7L3Y4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.265 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.424α = 90
b = 42.539β = 102.744
c = 86.839γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-03-20
    Changes: Structure summary
  • Version 1.4: 2026-03-11
    Changes: Database references, Structure summary