Structure of replication initiator protein unites diverse viruses causing tomato leaf curl disease (ToLCD)

Abstract

The complete nucleotide sequence of the replication initiator (Rep) gene of tomato leaf curl New Delhi virus-IARI (ToLCNDV-IARI), a whitefly transmitted geminivirus, was determined. The replication initiator protein gene is composed of 1086 nucleotide coding for 361 amino acids. The functional domains of Rep protein responsible for Rep oligomerization (amino acids 121–181), DNA binding (amino acids 1–181), and DNA cleavage (amino acids 1–120) have been mapped. Extended alignment of ToLCNDV-IARI Rep protein sequence with those of other viruses causing tomato leaf curl disease (ToLCD) reveals conservation of sequences within the -helix, involved in DNA cleavage, three motifs and P-loop for ATP binding, despite high variability at extreme N- and C-terminal. The modeled structure of the catalytic domain of Rep protein is composed of a central five stranded antiparallel -sheets and two -helices. The 3D model indicates a presence of DNA-binding cleft containing the catalytic residue at Tyr103, a positively charged domain for DNA binding, and a specificity determinant (SPD).