The RusA protein of Escherichia coli is an endonuclease that can resolve Holliday intermediates and correct the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC. The structure of the rusA gene, its organisation in the genome, and its interaction with the Ruv and RecG proteins have been investigated. Recombinant plasmids carrying rusA were identified by their ability to make ruv mutants resistant to UV light. The gene was located to an open reading frame encoding a polypeptide of 120 amino acids. It forms the fifth gene in an operon containing a chain of short, interlinked open reading frames. A similar arrangement was found in the genome of the lambdoid bacteriophage, 82. The two rusA genes show 95% sequence identity. The E. coli operon forms part of the defective lambdoid prophage, DLP12, and is probably derived from a phage related to 82 and PA-2. rusA appears to be very poorly expressed in E. coli, but can be activated by insertion of IS2 or IS10 upstream of the coding sequence to promote transcription. These insertions arise spontaneously in ruv strains as suppressors of the mutant phenotype. Deletion of rusA from the chromosome of either wild-type or ruv mutant strains has no obvious effect on recombination or sensitivity to UV light. Multicopy plasmids expressing RusA alone make ruvA, ruvB, and ruvC mutants resistant to UV light. Suppression depends critically on RecG.