Helicase, superfamily 3, single-stranded DNA/RNA virus (IPR000605)

Short name: Helicase_SF3_ssDNA/RNA_vir

Overlapping homologous superfamilies

Domain relationships


Helicases have been classified in 5 superfamilies (SF1-SF5). All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [PMID: 11689653, PMID: 15037234]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated.

In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues [PMID: 2156730].

Several structures of SF3 helicases have been solved [PMID: 12774115]. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins [PMID: 15718137]. The SF3 helicase proteins assemble into a hexameric ring.

Some proteins known to contain an SF3 helicase domain are listed below:

  • Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication.
  • Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication.
  • Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication.
  • Poxviridae and other large DNA viruses D5 protein.
  • Bacteriophage DNA primase/helicase protein.
  • Bacterial prophage DNA primase/helicase protein.

The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0003723 RNA binding
GO:0003724 RNA helicase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.