The pink to light reddish-pigmented bacterium Rubellimicrobium mesophilum strain MSL-20T contains a BLUF coupled endonuclease III of unknown function. A purified recombinant triple mutated sample of the BLUF coupled endonuclease III (F5Y, N27H, A87W) named RmPAE (Rubellimicrobium mesophilum Photo-Activated Endonuclease) was produced and characterized by optical spectroscopic methods. The BLUF domain photo-cycling dynamics occurred with high efficient blue-light induced signaling state formation (quantum yield of signaling state formation φs ≈ 0.6), small spectral red-shift (δλs,r ≈ 5.4 nm), and slow thermal activated dark recovery to the receptor state (τrec ≈ 20 min at room temperature). An apparent RmPAE melting temperature of ϑm ≈ 63 °C was determined by stepwise sample heating and absorption spectrum analysis. The photo-degradation of RmPAE in the signaling state was determined by prolonged intense blue-light exposure. An irreversible flavin photo-degradation occurred with quantum yield of φD ≈ 2.6×10-5. Schemes of the photo-cycling and the photo-degradation dynamics are presented. Engineered RmPAE may find application as light guided DNA cutter in optogenetic applications.