7EVP

Cryo-EM structure of the Gp168-beta-clamp complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Bacteriophage Twort protein Gp168 is a beta-clamp inhibitor by occupying the DNA sliding channel.

Liu, B.Li, S.Liu, Y.Chen, H.Hu, Z.Wang, Z.Zhao, Y.Zhang, L.Ma, B.Wang, H.Matthews, S.Wang, Y.Zhang, K.

(2021) Nucleic Acids Res 49: 11367-11378

  • DOI: https://doi.org/10.1093/nar/gkab875
  • Primary Citation of Related Structures:  
    7EVP

  • PubMed Abstract: 

    Bacterial chromosome replication is mainly catalyzed by DNA polymerase III, whose beta subunits enable rapid processive DNA replication. Enabled by the clamp-loading complex, the two beta subunits form a ring-like clamp around DNA and keep the polymerase sliding along. Given the essential role of β-clamp, its inhibitors have been explored for antibacterial purposes. Similarly, β-clamp is an ideal target for bacteriophages to shut off host DNA synthesis during host takeover. The Gp168 protein of phage Twort is such an example, which binds to the β-clamp of Staphylococcus aureus and prevents it from loading onto DNA causing replication arrest. Here, we report a cryo-EM structure of the clamp-Gp168 complex at 3.2-Å resolution. In the structure of the complex, the Gp168 dimer occupies the DNA sliding channel of β-clamp and blocks its loading onto DNA, which represents a new inhibitory mechanism against β-clamp function. Interestingly, the key residues responsible for this interaction on the β-clamp are well conserved among bacteria. We therefore demonstrate that Gp168 is potentially a cross-species β-clamp inhibitor, as it forms complex with the Bacillus subtilis β-clamp. Our findings reveal an alternative mechanism for bacteriophages to inhibit β-clamp and provide a new strategy to combat bacterial drug resistance.


  • Organizational Affiliation

    MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta sliding clampA,
C [auth B]
377Staphylococcus aureusMutation(s): 0 
Gene Names: dnaN
UniProt
Find proteins for P0A024 (Staphylococcus aureus)
Explore P0A024 
Go to UniProtKB:  P0A024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A024
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sliding clamp inhibitorB [auth C],
D
74Twortvirus twortMutation(s): 0 
Gene Names: TwortDSMZ_173
UniProt
Find proteins for Q4Z971 (Staphylococcus phage Twort (strain DSM 17442 / HER 48))
Explore Q4Z971 
Go to UniProtKB:  Q4Z971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4Z971
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81871662

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release