9NV3 | pdb_00009nv3

Hybrid model of a complex of BREX proteins BrxB and PglZ from Salmonella typhimurium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB.

Readshaw, J.J.Doyle, L.A.Puiu, M.Kelly, A.Nelson, A.Kaiser, A.J.McGuire, S.F.Peralta Acosta, J.Smith, D.L.Stoddard, B.L.Kaiser, B.K.Blower, T.R.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf540
  • Primary Citation of Related Structures:  
    9NV3

  • PubMed Abstract: 

    BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The varied BREX Types harbour multiple protein subunits (between four and eight) and all encode a conserved putative phosphatase, PglZ, and an equally conserved, putative ATPase, BrxC. Almost all BREX systems also contain a site-specific methyltransferase, PglX. Despite having determined the structure and fundamental biophysical and biochemical behaviours of several BREX factors (including the PglX methyltransferase, the BrxL effector, the BrxA DNA-binding protein, and a commonly-associated transcriptional regulator, BrxR), the mechanism by which BREX impedes phage replication remains largely undetermined. In this study, we identified a stable BREX sub-complex of PglZ:BrxB, generated and validated a structural model of that protein complex, and assessed the biochemical activity of PglZ from BREX, revealing it to be a metal-dependent nuclease. PglZ can cleave cyclic oligonucleotides, linear oligonucleotides, plasmid DNA and both non-modified and modified linear phage genomes. PglZ nuclease activity has no obvious role in BREX-dependent methylation, but does contribute to BREX phage defence. BrxB binding does not impact PglZ nuclease activity. These data contribute to our growing understanding of BREX phage defence.


  • Organizational Affiliation

    Department of Biosciences, Durham University, Stockton Road, DurhamDH1 3LE, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF1788 domain-containing protein199Salmonella enterica subsp. enterica serovar Typhimurium str. D23580Mutation(s): 0 
Gene Names: STMMW_44421
UniProt
Find proteins for A0A6C7ILK3 (Salmonella typhimurium (strain D23580))
Explore A0A6C7ILK3 
Go to UniProtKB:  A0A6C7ILK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6C7ILK3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PglZ domain-containing proteinB [auth C]887Salmonella enterica subsp. enterica serovar Typhimurium str. D23580Mutation(s): 0 
Gene Names: STMMW_44371
UniProt
Find proteins for A0A6C7IK08 (Salmonella typhimurium (strain D23580))
Explore A0A6C7IK08 
Go to UniProtKB:  A0A6C7IK08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6C7IK08
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/Y003659/1
The Lister Institute of Preventive MedicineUnited Kingdom--
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T008695/1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R35GM148166
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140375
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5 P30 CA015704-49
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection, Database references