- EMDB-31339: Cryo-EM structure of the Gp168-beta-clamp complex -
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Entry
Database: EMDB / ID: EMD-31339
Title
Cryo-EM structure of the Gp168-beta-clamp complex
Map data
Cryo-EM structure of the Gp168-beta-clamp complex
Sample
Complex: Gp168-beta-clamp complex
Complex: Beta sliding clamp 2
Protein or peptide: Beta sliding clamp
Complex: Gp168
Protein or peptide: Sliding clamp inhibitor
Keywords
gp168 / DNA beta-clamp / cross-species inhibitor / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information
DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function
DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit Similarity search - Domain/homology
National Natural Science Foundation of China (NSFC)
81871662
China
Citation
Journal: Nucleic Acids Res / Year: 2021 Title: Bacteriophage Twort protein Gp168 is a β-clamp inhibitor by occupying the DNA sliding channel. Authors: Bing Liu / Shanshan Li / Yang Liu / Huan Chen / Zhenyue Hu / Zhihao Wang / Yimin Zhao / Lei Zhang / Biyun Ma / Hongliang Wang / Steve Matthews / Yawen Wang / Kaiming Zhang / 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 ...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.
History
Deposition
May 21, 2021
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Header (metadata) release
Feb 16, 2022
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Map release
Feb 16, 2022
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Update
Jun 5, 2024
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Current status
Jun 5, 2024
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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