A site-specific recombination reaction. (a) The reaction proceeds within a tetramer of identical recombinase subunits. The subunits bind to the recombination site and catalyze the recombination in several steps, as described in the text. The light gray subunits are the active subunits, with the active-site Tyr residue either poised to react or covalently linked to the DNA. The darker gray subunits are in an inactive conformation in which the active-site Tyr residues are too distant from their DNA substrates to function. Isomerization (step 3) switches the conformations of both sets of subunits so that the inactive subunits (dark gray) become active (light gray) and the active-site Tyr residues are now properly positioned to promote the reaction. (b) A surface contour model of Flp recombinase, showing the four subunits bound to a Holliday intermediate; this is equivalent to the product of step 2 in (a). The protein is made transparent so that the bound DNA is visible.