Predicted 3D-structure of melanopsin, the non-rod, non-cone photopigment of the mammalian circadian clock, from Djungarian hamsters (Phodopus sungorus)

Melanopsin is the photopigment of the retinal ganglion cells, which are involved in the synchronization of the biological clock in the suprachiasmatic nucleus (SCN) of mammals with the exogenous photoperiod. So far, no information about the three-dimensional (3D) structure of melanopsin is available. Here we report the predicted structure based on the protein-coding region of the nucleotide sequence of the gene for melanopsin, originating from isolated mRNA from the eyes of Djungarian hamsters (Phodopus sungorus). The nucleotide sequence shares the largest homologies with melanopsin of mice and rats (each 89%) and humans (84%). Based on the amino-acid sequence, and in comparison with the known structure of bovine rhodopsin, the three-dimensional melanopsin protein structure was modeled by using automated homology modeling approaches that were subsequently refined. Melanopsin consists of highly conserved seven-transmembrane domains and a long cytoplasmatic tail with multiple putative phosphorylation sites. In the binding site of the chromophore, a 11-cis-retinal is likely to be bound to lysine at position 336 as Schiff's base. The modeling results may indicate different photoisomerization within the melanopsin molecule compared with bovine rhodopsin.