Four photoreceptor families have been found from plants including phytochrome, cryptochrome, phototropin, and ADO/ FKF/LKP/ZTL family proteins. Among them, phototropin and ADO/FKF/LKP/ZTL use a common light-sensing domain, LOV domain (1). The LOV domain was found as the lightsensing domain of the phototropin (PHOT1 and PHOT2) (2-4) and has been well characterized (1, 5-7). LOV domaincontaining proteins are distributed not only in plants but also in many other organisms. For example, WC-1 and VVD are found in the ascomycete fungus Neurospora crassa (8), aureochrome in the alga Vaucheria frigida (9), and bacterial histidine kinases in the animal pathogenic bacterium Brucella abortus (10) and in the stalked bacterium Caulobacter crescentus (11). These proteins have all been shown to function as photoreceptors.Six genes encoding LOV domain-containing proteins are found in the genome of Arabidopsis thaliana. Among them, two encode phototropins, and three encode the ADO/FKF/ LKP/ZTL family proteins, proteins involved in circadian clock and photoperiod-dependent flowering functions (12-15). All of the LOV domains of phototropins and ADO/FKF/LKP/ZTL family proteins are shown to bind FMN (2,4,15,16). In addition to those above, there exists a unique LOV domain-containing protein, referred to as PAS/LOV protein (PLP), 2 which contains a PAS domain followed by a LOV domain (1, 17).Ogura et al. (18) screened for proteins interacting with A. thaliana PLP using the yeast two-hybrid system. They isolated VTC2 (vitamin C defective 2), VTC2L (VTC2-like), and BLH10A and BLH10B (BEL1-like homeodomain 10 A and B proteins) as interacting proteins in yeast cells. The molecular interactions between PLP and VTC2L, BLH10A, or BLH10B in yeast were dependent on blue light irradiation, suggesting that PLP may function as a photoreceptor (18). Blue light treatment diminished the interaction. However, the flavin binding and photochemical properties of the A. thaliana PLP are unclear because the recombinant protein expressed in Escherichia coli did not show absorption spectra of flavin-binding proteins (18).In this study, we isolate cDNAs coding for PLP homologs from tomato (Solanum lycopersicum) and the moss Physcomitrella patens, and phylogenetic analysis shows that the PAS domains of the homologs, even the PAS domain of A. thaliana PLP, are closely related to the LOV domain. Thus, we propose that the isolated LOV domain-containing protein should be referred to as LOV/LOV protein (LLP), instead of PLP. Here, we analyze chromophore binding and photochemical properties of LLP from S. lycopersicum using wild-type and mutant proteins expressed in E. coli. We also examine both LOV domains of both PpLLPs for FMN binding and photochemical properties.