Figure 1
Nucleotides and amino acids at the protein-DNA interface of Cre/loxP and Dre/rox recombinase systems. (a) Sequences of loxP and rox target sites. The three nucleotides that differ between loxP and rox are highlighted in color. The numbering of the individual bases is provided for the upper and lower DNA strand, respectively. (b) Protein amino acids facing the altered DNA bases of loxP and rox. (c) Snapshot of the cleaving monomer of the Cre/loxP complex (PDB 1Q3U). The recognition regions at the protein-DNA interface are displayed in magenta (helix B), orange (helix D), green (helix J) and purple (beta 4). The area of interest in this study (i.e. PDIBJ area; the protein-DNA interface formed by amino acids of helix B and J and nucleotides 10/66, 11/65, and 12/64) is zoomed in, and relevant bases and amino acids are labeled. The numbering used is based on the Cre/loxP crystal structure (for details see Fig. S1). Figure generated using Pymol (version 2.1, https://pymol.org/).
