Structure
Cre Recombinase consists of 343 amino acids that form two distinct domains. The amino terminal domain encompasses residues 20−129 and this domain contains 5 alpha helical segments linked by a series of short loops. Helices A & E are involved in the formation of the recombinase tetramer with the C terminus region of helix E known to form contacts with the C terminal domain of adjacent subunits. Helices B & D form direct contacts with the major groove of the loxP DNA. These two helices are thought to make three direct contacts to DNA bases at the loxP site. The carboxy terminal domain of the enzyme consists of amino acids 132-341 and it harbours the active site of the enzyme. The overall structure of this domain shares a great deal of structural resemblance to the catalytic domain of other enzymes of the same family such as λ Integrase and HP1 Integrase. This domain is predominantly helical in structure with 9 distinct helices (F−N). The terminal helix (N) protrudes from the main body of the carboxy domain and this helix is reputed to play a role in mediating interactions with other subunits. Crystal structures demonstrate that this terminal N helix buries its hydrophobic surface into an acceptor pocket of an adjacent Cre subunit.
The effect of the two-domain structure is to form a C-shaped clamp that grasps the DNA from opposite sides.
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