8DK3

CryoEM structure of Pseudomonas aeruginosa PA14 JetC ATPase domain bound to DNA and cWHD domain of JetA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA.

Deep, A.Gu, Y.Gao, Y.Q.Ego, K.M.Herzik Jr., M.A.Zhou, H.Corbett, K.D.

(2022) Mol Cell 82: 4145

  • DOI: https://doi.org/10.1016/j.molcel.2022.09.008
  • Primary Citation of Related Structures:  
    7TIL, 8DK1, 8DK2, 8DK3

  • PubMed Abstract: 

    Self versus non-self discrimination is a key element of innate and adaptive immunity across life. In bacteria, CRISPR-Cas and restriction-modification systems recognize non-self nucleic acids through their sequence and their methylation state, respectively. Here, we show that the Wadjet defense system recognizes DNA topology to protect its host against plasmid transformation. By combining cryoelectron microscopy with cross-linking mass spectrometry, we show that Wadjet forms a complex similar to the bacterial condensin complex MukBEF, with a novel nuclease subunit similar to a type II DNA topoisomerase. Wadjet specifically cleaves closed-circular DNA in a reaction requiring ATP hydrolysis by the structural maintenance of chromosome (SMC) ATPase subunit JetC, suggesting that the complex could use DNA loop extrusion to sense its substrate's topology, then specifically activate the nuclease subunit JetD to cleave plasmid DNA. Overall, our data reveal how bacteria have co-opted a DNA maintenance machine to specifically recognize and destroy foreign DNAs through topology sensing.


  • Organizational Affiliation

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
JetC
A, B
1,119Pseudomonas aeruginosa PA14Mutation(s): 0 
Gene Names: IPC1494_27645IPC1595_14260IPC607_32065
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
JetA517Pseudomonas aeruginosa PA14Mutation(s): 0 
Gene Names: PA14_03250
UniProt
Find proteins for A0A0H2ZJP9 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZJP9 
Go to UniProtKB:  A0A0H2ZJP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZJP9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (26-MER)D [auth P]26synthetic construct
Sequence Annotations
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (26-MER)E [auth Q]26synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 GM104141
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI148814

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2022-11-16
    Changes: Database references
  • Version 1.3: 2024-06-12
    Changes: Data collection