Sequence and structural analysis of 4SNc-Tudor domain protein from Takifugu Rubripes

The fugu SN4TDR protein belongs to an evolutionarily conserved family, consisting of four repeat staphylococcal nuclease-like domains (SN1-SN4) at the N-terminus followed by Tudor and SN-like domains (TSN). Sequence analysis showed that the C-terminal TSN domain is composed of a complete SN-like domain interdigitated with a Tudor domain. In despite of low level of sequence identities, five SN-like domains have a few conserved amino acids that may play essential roles in the function of the protein. Computer modeling and secondary structural prediction of the SN-like domains revealed the presence of similar structural features of beta1-beta2-beta3-alpha1-beta4-beta5-alpha2-alpha3, which provides a structural basis for oligonucleotides binding. The loop region L(3alpha) for binding sites between beta3 and alpha1 of SN-like domains are different from human p100, implying the divergence in the structures of binding sites. These results indicate that fugu SN4TDR may bind methylated ligands and/or oligonucleotides through its distant domains.