PROSITE documentation PDOC51192

Superfamilies 1 and 2 helicase domain profiles

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]. For the two largest groups, commonly referred to as SF1 and SF2, a total of seven characteristic motifs has been identified [2]. These two superfamilies encompass a large number of DNA and RNA helicases from archaea, eubacteria, eukaryotes and viruses that seem to be active as monomers or dimers. RNA and DNA helicases are considered to be enzymes that catalyze the separation of double-stranded nucleic acids in an energy-dependent manner [3].

The various structures of SF1 and SF2 helicases present a common core with two α-β RecA-like domains (see for example <PDB:1FUU>) [3,4]. The structural homology with the RecA recombination protein covers the five contiguous parallel β strands and the tandem α helices. ATP binds to the amino proximal α-β domain, where the Walker A (motif I) and Walker B (motif II) are found. The N-terminal domain also contains motif III (S-A-T) which was proposed to participate in linking ATPase and helicase activities. The carboxy-terminal α-β domain is structurally very similar to the proximal one even though it is bereft of an ATP-binding site, suggesting that it may have originally arisen through gene duplication of the first one.

Some members of helicase superfamilies 1 and 2 are listed below:

• DEAD-box RNA helicases (see <PDOC00039>). The prototype of DEAD-box proteins is the translation initiation factor eIF4A. The eIF4A protein is an RNA-dependent ATPase which functions together with eIF4B as an RNA helicases [5].
• DEAH-box RNA helicases (see <PDOC00039>). Mainly pre-mRNA-splicing factor ATP-dependent RNA helicases [5].
• Eukaryotic DNA repair helicase RAD3/ERCC-2, an ATP-dependent 5'-3' DNA helicase involved in nucleotide excision repair of UV-damaged DNA.
• Eukaryotic TFIIH basal transcription factor complex helicase XPB subunit. An ATP-dependent 3'-5' DNA helicase which is a component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. It acts by opening DNA either around the RNA transcription start site or the DNA.
• Eukaryotic ATP-dependent DNA helicase Q. A DNA helicase that may play a role in the repair of DNA that is damaged by ultraviolet light or other mutagens.
• Eukaryotic ATP-dependent helicase SNF2/RAD54. A group of ATP-dependent remodelling factors frequently found associated with histone deacetylases.
• Bacterial and eukaryotic antiviral SKI2-like helicase. SKI2 has a role in the 3'-mRNA degradation pathway. It represses dsRNA virus propagation by specifically blocking translation of viral mRNAs, perhaps recognizing the absence of CAP or poly(A).
• Bacterial DNA-damage-inducible protein G (DinG). A probable helicase involved in DNA repair and perhaps also replication.
• Bacterial primosomal protein N' (PriA). PriA protein is one of seven proteins that make up the restart primosome, an apparatus that promotes assembly of replisomes at recombination intermediates and stalled replication forks.
• Bacterial ATP-dependent DNA helicase recG. It has a critical role in recombination and DNA repair. It helps process Holliday junction intermediates to mature products by catalyzing branch migration. It has a DNA unwinding activity characteristic of a DNA helicase with a 3' to 5' polarity.
• ssRNA positive-strand flaviviruses and potyviruses RNA helicase.
• dsDNA viruses early transcription factor 70 kDa subunit.
• dsDNA viruses nucleoside triphosphatase I (NPH I) protein. It serves two roles in transcription; it acts in concert with viral termination factor/capping enzyme to catalyze release of UUUUUNU-containing nascent RNA from the elongation complex, and it acts by itself as a polymerase elongation factor to facilitate readthrough of intrinsic pause sites.
• Poxviruses transcript release DNA helicase. It prevents virus-induced breakdown of RNA. It acts as a negative transcription elongation factor. It is involved in an ATP-dependent manner in release of nascent RNA.

To recognize helicase Superfamilies 1 and 2 we have developed two profiles. The first one recognizes all classical SF1 and SF2 helicases except bacterial DinG protein and eukaryotic Rad3 which belong to the same subfamily and which differ from other SF1-SF2 helicases by the presence of a large insert after the Walker A [6]. Our second profile recognizes specifically this subfamily.