1DRG

CRYSTAL STRUCTURE OF TRIMERIC CRE RECOMBINASE-LOX COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.186 

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This is version 1.4 of the entry. See complete history. 


Literature

Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction

Woods, K.C., Martin, S.S., Chu, V.C., Baldwin, E.P.

(2001) J Mol Biol 313: 49-69

  • DOI: 10.1006/jmbi.2001.5012
  • Primary Citation of Related Structures:  
    1DRG, 1F44

  • PubMed Abstract: 

    • The crystal structure of a novel Cre-Lox synapse was solved using phases from multiple isomorphous replacement and anomalous scattering, and refined to 2.05 A resolution. In this complex, a symmetric protein trimer is bound to a Y-shaped three-way DNA junction, a marked departure from the pseudo-4-fold symmetrical tetramer associated with Cre-mediated LoxP recombination ...

    The crystal structure of a novel Cre-Lox synapse was solved using phases from multiple isomorphous replacement and anomalous scattering, and refined to 2.05 A resolution. In this complex, a symmetric protein trimer is bound to a Y-shaped three-way DNA junction, a marked departure from the pseudo-4-fold symmetrical tetramer associated with Cre-mediated LoxP recombination. The three-way DNA junction was accommodated by a simple kink without significant distortion of the adjoining DNA duplexes. Although the mean angle between DNA arms in the Y and X structures was similar, adjacent Cre trimer subunits rotated 29 degrees relative to those in the tetramers. This rotation was accommodated at the protein-protein and DNA-DNA interfaces by interactions that are "quasi-equivalent" to those in the tetramer, analogous to packing differences of chemically identical viral subunits at non-equivalent positions in icosahedral capsids. This structural quasi-equivalence extends to function as Cre can bind to, cleave and perform strand transfer with a three-way Lox substrate. The structure explains the dual recognition of three and four-way junctions by site-specific recombinases as being due to shared structural features between the differently branched substrates and plasticity of the protein-protein interfaces. To our knowledge, this is the first direct demonstration of quasi-equivalence in both the assembly and function of an oligomeric enzyme.

    Organizational Affiliation: 

    Section of Molecular and Cellular Biology, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CRE RECOMBINASEC [auth A]323Escherichia virus P1Mutation(s): 1 
Gene Names: cre
UniProt
Find proteins for P06956 (Escherichia phage P1)
Explore P06956 
Go to UniProtKB:  P06956
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06956
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3'A [auth B]16N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3'B [auth C]19N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.186 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.99α = 90
b = 160.99β = 90
c = 160.99γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2021-11-03
    Changes: Database references