Initiates and terminates the replication only of its own subviral DNA molecule. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the intergenic region of the genome, thereby initiating the rolling circle replication (RCR). Following cleavage, binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication. Displays origin-specific DNA cleavage, nucleotidyl transferase, ATPase and helicase activities. ATP + H2O = ADP + H(+) + phosphate Divalent metal cations, possibly Mg(2+) or Mn(2+). Homooligomer (Potential). Rep binds to repeated DNA motifs (iterons) (By similarity). There are 3 rolling circle replication (RCR) motifs. RCR-2 is probably involved in metal coordination. RCR-3 is required for phosphodiester bond cleavage for initiation of RCR. The genome of nanoviruses is composed of six to eight segments. In addition, some isolates contain subviral DNAs. Belongs to the nanoviridea/circoviridae replication-associated protein family. This protein is encoded by a subviral DNA that is not present in all isolates of the virus.