A key feature of the copy control in the 2 micron circle plasmid of Saccharomyces cerevisiae is its ability to amplify when the copy number drops below the steady state value. The Flp protein encoded by the plasmid is an essential component of the amplification mechanism. A central regulatory event in amplification involves the phosphorylation/dephosphorylation of Tyr-343 of Flp. Tyrosine phosphorylation is achieved by a transesterification mechanism involving a specific phosphodiester within the 2 micron circle. The dephosphorylation is also a transesterification reaction that uses a specific 5'-OH (generated during tyrosine phosphorylation) as the phosphoryl acceptor. A sum of four phosphorylation/dephosphorylation reactions, coordinated in sets of two, is thought to invert the relative directions of a pair of replication forks. This allows more than one copy of the plasmid to be made from a single replication initiation event. In this paper we discuss the structural features of the Flp active site that control and coordinate the transesterification reactions required for amplification.