The putative synaptotagmin protein encoded by the SYT1 gene of the picoplanktonic alga Micromonas is a novel member of C2-domain containing proteins: evidence from in silico characterization and homology modeling

Synaptotagmin proteins are a class of membrane trafficking proteins and controls endocytosis and exocytosis of synaptic vesicles in animals. Increasing number of plant nucleotide and protein data shows they are also present in plants. Micromonas pusilla is a picophytoplanktonic alga belonging to Prasinophyceae which is believed to be the ancient member of green plant lineage and thus, very useful in various evolutionary studies. The SYT1 gene of this alga encodes a putative synaptotagmin which shows novel features. In this study, this protein has been characterized by several bioinformatic tools. The protein contains several novel motifs and domains besides the C2 domain. The three dimensional structure has been predicted in silico by homology modeling to gather knowledge about the structure of the ancient forms of the plant synaptotagmin protein. The C2 domain in this protein itself is somewhat different from the known structures. The spatial distribution of the active site amino acids around the calcium ion showed that some amino acids outside the C2 domain are also involved in calcium binding which is a novel feature of this protein.