Fig. 1

Analysis of TTV1 nucleocapsid protein TP1. a Genome map of TTV1 with the four genes encoding capsid proteins highlighted in red. The newly annotated open reading frame (ORF7), which encodes a putative protein corresponding to the C-terminal part of the Cas4 nuclease, is shown in cyan. b Multiple sequence alignment of TTV1 TP1 (upper block) and gp7 (bottom block) with Cas4 nucleases from archaea and their viruses. Sequences are indicated with GenBank or PDB identifiers. Red ellipses and blue arrows above the alignment respectively correspond to α-helices and β-strands experimentally determined for Cas4 protein (Sso0001) from S. solfataricus [26]. The four conserved cysteine residues coordinating the Fe-S cluster are indicated with stars, whereas amino acid residues conserved in the RecB-like nucleases and shown to be important for catalysis [26, 27] are indicated with blue circles. The conserved motifs are also highlighted under the alignment. c X-ray structure of the Cas4 nuclease from S. solfataricus (left) was used as a template to build a model of TTV1 TP1 (middle and right). In the Cas4 structure, the region shared with TP1 is colored green, whereas the C-terminal domain which corresponds to TTV1 gp7 is in red. Models in the middle and on the right are depicted using ribbon and surface rendering, respectively. The latter is colored according to the electrostatic surface potential following Coulomb’s law. The color scale is from −7 (red) to +7 (blue) kcal/(mol·e)