7R08

Abortive infection DNA polymerase Abi-P2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of protein-primed template-independent DNA synthesis by Abi polymerases.

Figiel, M.Gapinska, M.Czarnocki-Cieciura, M.Zajko, W.Sroka, M.Skowronek, K.Nowotny, M.

(2022) Nucleic Acids Res 50: 10026-10040

  • DOI: https://doi.org/10.1093/nar/gkac772
  • Primary Citation of Related Structures:  
    7R06, 7R07, 7R08, 7Z0Z

  • PubMed Abstract: 

    Abortive infection (Abi) is a bacterial antiphage defense strategy involving suicide of the infected cell. Some Abi pathways involve polymerases that are related to reverse transcriptases. They are unique in the way they combine the ability to synthesize DNA in a template-independent manner with protein priming. Here, we report crystal and cryo-electron microscopy structures of two Abi polymerases: AbiK and Abi-P2. Both proteins adopt a bilobal structure with an RT-like domain that comprises palm and fingers subdomains and a unique helical domain. AbiK and Abi-P2 adopt a hexameric and trimeric configuration, respectively, which is unprecedented for reverse transcriptases. Biochemical experiments showed that the formation of these oligomers is required for the DNA polymerization activity. The structure of the AbiK-DNA covalent adduct visualized interactions between the 3' end of DNA and the active site and covalent attachment of the 5' end of DNA to a tyrosine residue used for protein priming. Our data reveal a structural basis of the mechanism of highly unusual template-independent protein-priming polymerases.


  • Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse transcriptase
A, B, C, D, E
A, B, C, D, E, F
541Escherichia phage P2Mutation(s): 0 
UniProt
Find proteins for Q2P9X6 (Enterobacteria phage P2-EC30)
Explore Q2P9X6 
Go to UniProtKB:  Q2P9X6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2P9X6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.334α = 90
b = 88.359β = 103.18
c = 161.094γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Polish SciencePolandPOIR.04.04.00-00-20E7/16-00
European Regional Development FundEuropean UnionPOIG.02.02.00-14-024/08-00

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2022-10-05
    Changes: Database references