CRESS-DNA virus replication initiator protein, endonuclease domain (CRESS_DNA_REP)
Type: Domain

Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses, such as circoviruses, nanoviruses, and geminiviruses, are eukaryotic viruses with small circular single-stranded DNA (ssDNA) genomes encoding a replication initiator protein (Rep) with a distinctive two functional domain organization, containing an endonuclease domain toward the N-terminal and a superfamily 3 (SF3) helicase domain at the C-terminal. The Rep endonuclease domain is responsible for initiating, progressing, and completing rolling circle replication (RCR) of the genome. The Rep endonuclease domain is characterised by RCR motifs I through III, which are important for RCR initiation and termination. Motif I, UUTU (U denotes hydrophobic residues), is thought to be involved in the recognition of the origin of replication. Motif II, HU(H/Q), is involved in the coordination of divalent metal ions, Mg+2 or Mn+2, which are essential for endonuclease activity at the origin of replication. Motif III (YxxK, where x is any amino acid) is involved in dsDNA cleavage and subsequent covalent attachment of the Rep through the catalytic tyrosine residue to the 5' end of the cleaved product .

This entry represents the CRESS-DNA Rep endonuclease domain which consists of a central 5-stranded antiparallel β-sheet covered on one side by an α-helix and irregular loops and on the other, more open side of the domain, by an α-helix containing the catalytic tyrosine residue (the catalytic helix) .

The replication initiator protein (Rep) of geminiviruses is a replicon-specific initiator enzyme and is an essential component of the replisome . In geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer . It is found in association with

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Proteins in this entry are essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication introducing an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3'.
This initiates rolling circle replication (RCR). Following cleavage, the protein 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.

Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name . Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) . Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants.

Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship . Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions . Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus and Miscanthus streak virus (MiSV) , reveal high levels of similarity.