Transposition of Tn5 requires the binding of the transposase protein to the transposon outside end (OE) DNA sequences. Transposase mutants that increase the transposition frequency result in the formation of two distinct transposase/OE DNA complexes, observed by gel retardation analysis. The slower migrating complex I, also formed by wild-type transposase, contains protein oligomers of transposase and transposase related proteins. The faster migrating, novel complex II is caused by the binding of monomeric, proteolytic transposase fragments gamma and delta that have lost the carboxy-terminus of the protein. Transposase gamma and delta bind OE DNA with a high apparent affinity but are unable to promote transposition in vivo. We propose that the transposase protein is functionally unstable and can undergo a conformational change that reduces the activity but protects the protein from proteolysis. The transposase mutants favor the more active but proteolytically hypersensitive protein conformation.