{PDOC52020}
{PS52020; CRESS_DNA_REP}
{BEGIN}
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* CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile *
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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-terminus and a superfamily 3
(SF3) helicase  domain  at  the  C-terminus.  The  Rep  endonuclease domain is
responsible for   initiating,   progressing,  and  completing  rolling  circle
replication (RCR)  of the genome. The Rep endonuclease domain is characterized
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 [1,2,3,4,5].

The CRESS-DNA  Rep  endonuclease  domain  consists  of  a  central  5-stranded
antiparallel beta-sheet  covered  on  one side by an alpha-helix and irregular
loops and  on  the  other,  more  open  side  of the domain, by an alpha-helix
containing the   catalytic   tyrosine   residue  (the  catalytic  helix)  (see
<PDB:2HWO>) [5].

The profile we developed covers the entire CRESS-DNA Rep endonuclease domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: March 2023 / First entry.

[ 1] Castrignano S.B., Nagasse-Sugahara T.K., Garrafa P., Monezi T.A.,
     Barrella K.M., Mehnert D.U.
     "Identification of circo-like virus-Brazil genomic sequences in raw
     sewage from  the metropolitan area of Sao Paulo: evidence of
     circulation two and three years  after the first detection."
     Mem. Inst. Oswaldo. Cruz. 112:175-181(2017).
     PubMed=28146157; DOI=10.1590/0074-02760160312
[ 2] Zhao L., Rosario K., Breitbart M., Duffy S.
     "Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA)
     Viruses:  Ubiquitous Viruses With Small Genomes and a Diverse Host
     Range."
     Adv. Virus. Res. 103:71-133(2019).
     PubMed=30635078; DOI=10.1016/bs.aivir.2018.10.001
[ 3] Tarasova E., Dhindwal S., Popp M., Hussain S., Khayat R.
     "Mechanism of DNA Interaction and Translocation by the Replicase of a
     Circular  Rep-Encoding Single-Stranded DNA Virus."
     mBio 12:E0076321-E0076321(2021).
     PubMed=34311576; DOI=10.1128/mBio.00763-21
[ 4] Kazlauskas D., Varsani A., Koonin E.V., Krupovic M.
     "Multiple origins of prokaryotic and eukaryotic single-stranded DNA
     viruses from  bacterial and archaeal plasmids."
     Nat. Commun. 10:3425-3425(2019).
     PubMed=31366885; DOI=10.1038/s41467-019-11433-0
[ 5] Vega-Rocha S., Byeon I.-J.L., Gronenborn B., Gronenborn A.M.,
     Campos-Olivas R.
     "Solution structure, divalent metal and DNA binding of the
     endonuclease domain  from the replication initiation protein from
     porcine circovirus 2."
     J. Mol. Biol. 367:473-487(2007).
     PubMed=17275023; DOI=10.1016/j.jmb.2007.01.002

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