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

J Mol Biol. 2001 Oct 12;313(1):49-69. doi: 10.1006/jmbi.2001.5012.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Attachment Sites, Microbiological / genetics*
  • Base Sequence
  • Binding Sites
  • Catalysis
  • Crystallography, X-Ray
  • DNA, Bacterial / chemistry*
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Integrases / chemistry*
  • Integrases / metabolism*
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Protein Binding
  • Protein Structure, Quaternary
  • Protein Subunits
  • Recombination, Genetic*
  • Rotation
  • Structure-Activity Relationship
  • Viral Proteins / chemistry*
  • Viral Proteins / metabolism*


  • DNA, Bacterial
  • DNA-Binding Proteins
  • Protein Subunits
  • Viral Proteins
  • Cre recombinase
  • Integrases

Associated data

  • PDB/1DRG
  • PDB/1F44
  • PDB/4CRX