The unlinked galR gene encodes the repressor for this system. A tetrameric GalR repressor binds to 2 operators, one located at +55 and one located at -60 relative to the PG1 start site. Looping of the DNA blocks the access of RNA polymerase to promoters and/or inhibits formation of the open complex. This looping requires the presence of the histone-like protein, HU to facilitate the formation of the structure and allow for proper repression. When GalR binds as a dimer to the -60 site only, the promoter PG2 is activated, not repressed, allowing basal levels of GalE to be produced. In this state, the PG1 promoter is inactivated through interactions with the alpha subunit of RNA polymerase. Activity of this repressor protein is controlled based on the levels of D-galactose in the cell. Increased levels of this sugar inhibit the activity of the repressor by binding allosterically, resulting in a conformational change of the protein, which suppresses its interactions with RNA polymerase and DNA. This induces the activity of the operon, which will increase the rate of galactose metabolism.
The gal operon is also controlled by CRP-cAMP, similarly to the lac operon. CRP-cAMP binds to the -35 region, promoting transcription from PG1 but inhibiting transcription from PG2. This is accomplished due to the location of the activation sequence. When CRP-cAMP binds the activating sequence, it blocks RNA polymerase from establishing an open complex with PG2, but enhances a closed complex with RNA polymerase at PG1. This represses the activity of the PG2 promoter, and increases the activity of the PG1 promoter. When cells are grown in glucose, basal level transcription occurs from PG2.