1Q3V

Crystal structure of a wild-type Cre recombinase-loxP synapse: phosphotyrosine covalent intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation

Ennifar, E.Meyer, J.E.W.Buchholz, F.Stewart, A.F.Suck, D.

(2003) Nucleic Acids Res 31: 5449-5460

  • DOI: 10.1093/nar/gkg732
  • Primary Citation of Related Structures:  
    1OUQ, 1Q3V, 1Q3U, 1NZB

  • PubMed Abstract: 
  • Escherichia coli phage P1 Cre recombinase catalyzes the site-specific recombination of DNA containing loxP sites. We report here two crystal structures of a wild-type Cre recombinase-loxP synaptic complex corresponding to two distinct reaction states ...

    Escherichia coli phage P1 Cre recombinase catalyzes the site-specific recombination of DNA containing loxP sites. We report here two crystal structures of a wild-type Cre recombinase-loxP synaptic complex corresponding to two distinct reaction states: an initial pre-cleavage complex, trapped using a phosphorothioate modification at the cleavable scissile bond that prevents the recombination reaction, and a 3'-phosphotyrosine protein-DNA intermediate resulting from the first strand cleavage. In contrast to previously determined Cre complexes, both structures contain a full tetrameric complex in the asymmetric unit, unequivocally showing that the anti-parallel arrangement of the loxP sites is an intrinsic property of the Cre-loxP recombination synapse. The conformation of the spacer is different to the one observed for the symmetrized loxS site: a kink next to the scissile phosphate in the top strand of the pre-cleavage complex leads to unstacking of the TpG step and a widening of the minor groove. This side of the spacer is interacting with a 'cleavage-competent' Cre subunit, suggesting that the first cleavage occurs at the ApT step in the top strand. This is further confirmed by the structure of the 3'-phosphotyrosine intermediate, where the DNA is cleaved in the top strands and covalently linked to the 'cleavage-competent' subunits. The cleavage is followed by a movement of the C-terminal part containing the attacking Y324 and the helix N interacting with the 'non-cleaving' subunit. This rearrangement could be responsible for the interconversion of Cre subunits. Our results also suggest that the Cre-induced kink next to the scissile phosphodiester activates the DNA for cleavage at this position and facilitates strand transfer.


    Organizational Affiliation

    Structural and Computational Biology Programme, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cre recombinaseA, B, E, F347Escherichia virus P1Mutation(s): 0 
Gene Names: cre
Find proteins for P06956 (Escherichia phage P1)
Explore P06956 
Go to UniProtKB:  P06956
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    loxP DNAC, G16N/A
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    (by identity cutoff)  |  Structure
    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    loxP DNAX, Y21N/A
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    (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    loxP DNAD, H37N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    IOD
    Query on IOD

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    C, F
    IODIDE ION
    I
    XMBWDFGMSWQBCA-UHFFFAOYSA-M
     Ligand Interaction
    MG
    Query on MG

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    A, D, F
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.91 Å
    • R-Value Free: 0.276 
    • R-Value Work: 0.247 
    • R-Value Observed: 0.247 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 108.938α = 90
    b = 164.16β = 90
    c = 194.759γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    AMoREphasing
    CNSrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2003-09-16
      Type: Initial release
    • Version 1.1: 2008-04-29
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance