Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination

EMBO J. 1998 Jul 15;17(14):4175-87. doi: 10.1093/emboj/17.14.4175.

Abstract

We have determined the X-ray crystal structures of two DNA Holliday junctions (HJs) bound by Cre recombinase. The HJ is a four-way branched structure that occurs as an intermediate in genetic recombination pathways, including site-specific recombination by the lambda-integrase family. Cre recombinase is an integrase family member that recombines 34 bp loxP sites in the absence of accessory proteins or auxiliary DNA sequences. The 2.7 A structure of Cre recombinase bound to an immobile HJ and the 2.5 A structure of Cre recombinase bound to a symmetric, nicked HJ reveal a nearly planar, twofold-symmetric DNA intermediate that shares features with both the stacked-X and the square conformations of the HJ that exist in the unbound state. The structures support a protein-mediated crossover isomerization of the junction that acts as the switch responsible for activation and deactivation of recombinase active sites. In this model, a subtle isomerization of the Cre recombinase-HJ quaternary structure dictates which strands are cleaved during resolution of the junction via a mechanism that involves neither branch migration nor helical restacking.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Substitution
  • Binding Sites
  • Crystallography, X-Ray
  • DNA / chemistry*
  • Integrases / chemistry*
  • Isomerism
  • Models, Molecular
  • Mutation
  • Nucleic Acid Conformation*
  • Oligodeoxyribonucleotides / chemical synthesis
  • Oligodeoxyribonucleotides / chemistry
  • Protein Conformation
  • Recombination, Genetic*
  • Repetitive Sequences, Nucleic Acid
  • Viral Proteins*

Substances

  • Oligodeoxyribonucleotides
  • Viral Proteins
  • DNA
  • Cre recombinase
  • Integrases

Associated data

  • PDB/2CRX
  • PDB/3CRX