8C45

PglX methyltransferase from the Salmonella BREX phage defence system (aka BrxX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence.

Went, S.C.Picton, D.M.Morgan, R.D.Nelson, A.Brady, A.Mariano, G.Dryden, D.T.F.Smith, D.L.Wenner, N.Hinton, J.C.D.Blower, T.R.

(2024) Nat Commun 15: 7236-7236

  • DOI: https://doi.org/10.1038/s41467-024-51629-7
  • Primary Citation of Related Structures:  
    8C45, 8Q56

  • PubMed Abstract: 

    Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognise and methylate 6 bp non-palindromic motifs within the host genome, and prevent replication of non-methylated phage DNA that encodes these same motifs. How BREX recognises cognate motifs has not been fully understood. In this study we characterise BREX from pathogenic Salmonella and present X-ray crystallographic structures of the conserved BREX protein, PglX. The PglX N-terminal domain encodes the methyltransferase, whereas the C-terminal domain is for motif recognition. We also present the structure of PglX bound to the phage-derived DNA mimic, Ocr, an inhibitor of BREX activity. Our analyses propose modes for DNA-binding by PglX and indicate that both methyltransferase activity and defence require larger BREX complexes. Through rational engineering of PglX we broaden both the range of phages targeted, and the host motif sequences that are methylated by BREX. Our data demonstrate that PglX is used to recognise specific DNA sequences for BREX activity, contributing to motif recognition for both phage defence and host methylation.


  • Organizational Affiliation

    Department of Biosciences, Durham University, South Road, Durham, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
site-specific DNA-methyltransferase (adenine-specific)
A, B
1,225Salmonella enterica subsp. enterica serovar Typhimurium str. D23580Mutation(s): 0 
Gene Names: STMMW_44401
EC: 2.1.1.72
UniProt
Find proteins for A0A6C7IK61 (Salmonella typhimurium (strain D23580))
Explore A0A6C7IK61 
Go to UniProtKB:  A0A6C7IK61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6C7IK61
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.266 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.539α = 90
b = 138.539β = 90
c = 407.956γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2.multiplexdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references, Structure summary