DNA specificity of the Cre recombinase resides in the 25 kDa carboxyl domain of the protein

J Mol Biol. 1990 Dec 20;216(4):873-82. doi: 10.1016/S0022-2836(99)80007-2.


The Cre protein of bacteriophage P1 is a 38.5 kDa site-specific recombinase that belongs to the Int family of recombination proteins. Cre acts by binding specifically to a 34 base-pair sequence, lox, where it carries out recombination. A limited chymotryptic digest of Cre resulted in two fragments of sizes 25 and 13.5 kDa, respectively. The sequence of the amino terminus of the purified 25 kDa peptide demonstrates that this peptide represents the carboxyl-terminal portion of the Cre protein. A truncated version of the cre gene was constructed which produces only the 25 kDa peptide. The 25 kDa peptide is capable of specific binding to the lox site, but binds at lower affinity than does wild-type Cre. Footprinting with Fe-EDTA indicates that the 25 kDa peptide protects the inverted repeats of the lox site but shows only partial protection of the spacer region. This is in contrast to the footprint obtained with wild-type Cre which protects the entire spacer region.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites
  • Cloning, Molecular
  • Coliphages / genetics*
  • DNA Nucleotidyltransferases / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Integrases*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Peptide Fragments / metabolism
  • Peptide Mapping
  • Recombination, Genetic*
  • Regulatory Sequences, Nucleic Acid
  • Structure-Activity Relationship
  • Viral Proteins*


  • DNA-Binding Proteins
  • Peptide Fragments
  • Viral Proteins
  • Cre recombinase
  • DNA Nucleotidyltransferases
  • Integrases