Home | Contact

Helicases have been classified in 5 superfamilies (SF1-SF5) [1]. All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) (see <PDOC00017>) and Walker B (Mg2+-binding aspartic acid) motifs [1]. Superfamily 3 consists of helicases encoded mainly by small RNA and DNA viruses and some large nucleocytoplasmic DNA viruses [2,3]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small DNA viruses is associated with an origin-binding domain. By pairing a domain that recognizes 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, lenght. In addition to the A and B motifs this family is caracterized 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 [4].

Several structure of SF3 helicases have been solved (see <PDB:1N25>) [5]. They all possess the same core α/β fold, consisting of a five-stranded parallel β sheet flanked on both sides by several α helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the α/β core domain is that of AAA+ proteins [6]. 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.
• ssRNA positive strand viruses RNA1 polyprotein.

To recognize this domain we have developed two profiles. The first one is directed against DNA viruses SF3 helicase and the second one is specific for ssRNA positive-strand viruses SF3 helicase.

June 2006 / Text revised; profile added.

PROSITE methods (with tools and information) covered by this documentation:

SF3_HELICASE_1, PS51206; Superfamily 3 helicase of DNA viruses domain profile  (MATRIX)

Sequences known to belong to this class detected by the profile: ALL Other sequence(s) detected in Swiss-Prot: NONE

• Domain architecture view of Swiss-Prot proteins matching PS51206 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS51206 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51206 • Scan Swiss-Prot/TrEMBL entries against PS51206 • view ligand binding statistics

Matching PDB structures: 1N25 1S9H 1SVL 1SVM ... [ALL]

SF3_HELICASE_2, PS51218; Superfamily 3 helicase of positive ssRNA viruses domain profile  (MATRIX)

• Domain architecture view of Swiss-Prot proteins matching PS51218 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS51218 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51218 • Scan Swiss-Prot/TrEMBL entries against PS51218 • view ligand binding statistics

1	Authors	Gorbalenya A.E., and Koonin E.V. .
	Title	Helicases: amino acid sequence comparisons and structure-function relationships.
	Source	Curr. Opin. Struct. Biol. 3:419-429(1993).

2	Authors	Iyer L.M., Aravind L., Koonin E.V.
	Title	Common origin of four diverse families of large eukaryotic DNA viruses.
	Source	J. Virol. 75:11720-11734(2001).
	PubMed ID	11689653
	DOI	10.1128/JVI.75.23.11720-11734.2001

3	Authors	Iyer L.M., Leipe D.D., Koonin E.V., Aravind L.
	Title	Evolutionary history and higher order classification of AAA+ ATPases.
	Source	J. Struct. Biol. 146:11-31(2004).
	PubMed ID	15037234
	DOI	10.1016/j.jsb.2003.10.010

4	Authors	Gorbalenya A.E., Koonin E.V., Wolf Y.I.
	Title	A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses.
	Source	FEBS Lett. 262:145-148(1990).
	PubMed ID	2156730

5	Authors	Li D., Zhao R., Lilyestrom W., Gai D., Zhang R., DeCaprio J.A., Fanning E., Jochimiak A., Szakonyi G., Chen X.S.
	Title	Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen.
	Source	Nature 423:512-518(2003).
	PubMed ID	12774115
	DOI	10.1038/nature01691

6	Authors	Hickman A.B., Dyda F.
	Title	Binding and unwinding: SF3 viral helicases.
	Source	Curr. Opin. Struct. Biol. 15:77-85(2005).
	PubMed ID	15718137
	DOI	10.1016/j.sbi.2004.12.001

PROSITE is copyright. It is produced by the SIB Swiss Institute Bioinformatics. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement. For information about the licensing scheme send an email to

Prosite License or see: prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)

SIB Swiss Institute of Bioinformatics | Disclaimer