PROSITE documentation PDOC00039 [for PROSITE entry PS00039]

DEAD and DEAH box families ATP-dependent helicases signatures




Description

A number of eukaryotic and prokaryotic proteins have been characterized [1,2,3] on the basis of their structural similarity. They all seem to be involved in ATP-dependent, nucleic-acid unwinding. Proteins currently known to belong to this family are:

  • Initiation factor eIF-4A. Found in eukaryotes, this protein is a subunit of a high molecular weight complex involved in 5'cap recognition and the binding of mRNA to ribosomes. It is an ATP-dependent RNA-helicase.
  • PRP5 and PRP28. These yeast proteins are involved in various ATP-requiring steps of the pre-mRNA splicing process.
  • Pl10, a mouse protein expressed specifically during spermatogenesis.
  • An3, a Xenopus putative RNA helicase, closely related to Pl10.
  • SPP81/DED1 and DBP1, two yeast proteins probably involved in pre-mRNA splicing and related to Pl10.
  • Caenorhabditis elegans helicase glh-1.
  • MSS116, a yeast protein required for mitochondrial splicing.
  • SPB4, a yeast protein involved in the maturation of 25S ribosomal RNA.
  • p68, a human nuclear antigen. p68 has ATPase and DNA-helicase activities in vitro. It is involved in cell growth and division.
  • Rm62 (p62), a Drosophila putative RNA helicase related to p68.
  • DBP2, a yeast protein related to p68.
  • DHH1, a yeast protein.
  • DRS1, a yeast protein involved in ribosome assembly.
  • MAK5, a yeast protein involved in maintenance of dsRNA killer plasmid.
  • ROK1, a yeast protein.
  • ste13, a fission yeast protein.
  • Vasa, a Drosophila protein important for oocyte formation and specification of of embryonic posterior structures.
  • Me31B, a Drosophila maternally expressed protein of unknown function.
  • dbpA, an Escherichia coli putative RNA helicase.
  • deaD, an Escherichia coli putative RNA helicase which can suppress a mutation in the rpsB gene for ribosomal protein S2.
  • rhlB, an Escherichia coli putative RNA helicase.
  • rhlE, an Escherichia coli putative RNA helicase.
  • srmB, an Escherichia coli protein that shows RNA-dependent ATPase activity. It probably interacts with 23S ribosomal RNA.
  • Caenorhabditis elegans hypothetical proteins T26G10.1, ZK512.2 and ZK686.2.
  • Yeast hypothetical protein YHR065c.
  • Yeast hypothetical protein YHR169w.
  • Fission yeast hypothetical protein SpAC31A2.07c.
  • Bacillus subtilis hypothetical protein yxiN.

All these proteins share a number of conserved sequence motifs. Some of them are specific to this family while others are shared by other ATP-binding proteins or by proteins belonging to the helicases `superfamily' [4]. One of these motifs, called the 'D-E-A-D-box', represents a special version of the B motif of ATP-binding proteins.

Some other proteins belong to a subfamily which have His instead of the second Asp and are thus said to be 'D-E-A-H-box' proteins [3,5,6]. Proteins currently known to belong to this subfamily are:

  • PRP2, PRP16, PRP22 and PRP43. These yeast proteins are all involved in various ATP-requiring steps of the pre-mRNA splicing process.
  • Fission yeast prh1, which my be involved in pre-mRNA splicing.
  • Male-less (mle), a Drosophila protein required in males, for dosage compensation of X chromosome linked genes.
  • RAD3 from yeast. RAD3 is a DNA helicase involved in excision repair of DNA damaged by UV light, bulky adducts or cross-linking agents. Fission yeast rad15 (rhp3) and mammalian DNA excision repair protein XPD (ERCC-2) are the homologs of RAD3.
  • Yeast CHL1 (or CTF1), which is important for chromosome transmission and normal cell cycle progression in G(2)/M.
  • Yeast TPS1.
  • Yeast hypothetical protein YKL078w.
  • Caenorhabditis elegans hypothetical proteins C06E1.10 and K03H1.2.
  • Poxviruses' early transcription factor 70 Kd subunit which acts with RNA polymerase to initiate transcription from early gene promoters.
  • I8, a putative vaccinia virus helicase.
  • hrpA, an Escherichia coli putative RNA helicase.

We have developed signature patterns for both subfamilies.

Note:

Proteins belonging to this family also contain a copy of the ATP/GTP- binding motif 'A' (P-loop) (see the relevant entry <PDOC00017>).

Expert(s) to contact by email:

Linder P.

Last update:

July 1999 / Text revised.

Technical section

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

DEAD_ATP_HELICASE, PS00039; DEAD-box subfamily ATP-dependent helicases signature  (PATTERN)

DEAH_ATP_HELICASE, PS00690; DEAH-box subfamily ATP-dependent helicases signature  (PATTERN)


References

1AuthorsSchmid S.R., Linder P.
TitleD-E-A-D protein family of putative RNA helicases.
SourceMol. Microbiol. 6:283-291(1992).
PubMed ID1552844

2AuthorsLinder P., Lasko P.F., Ashburner M., Leroy P., Nielsen P.J., Nishi K., Schnier J., Slonimski P.P.
TitleBirth of the D-E-A-D box.
SourceNature 337:121-122(1989).
PubMed ID2563148
DOI10.1038/337121a0

3AuthorsWassarman D.A., Steitz J.A.
TitleRNA splicing. Alive with DEAD proteins.
SourceNature 349:463-464(1991).
PubMed ID1825133
DOI10.1038/349463a0

4AuthorsHodgman T.C.
TitleA new superfamily of replicative proteins.
SourceNature 333:22-23(1988) and Nature 333:578-578(1988) (Errata).
PubMed ID3362205
DOI10.1038/333022b0

5AuthorsHarosh I., Deschavanne P.
TitleThe RAD3 gene is a member of the DEAH family RNA helicase-like protein.
SourceNucleic Acids Res. 19:6331-6331(1991).
PubMed ID1956796

6AuthorsKoonin E.V., Senkevich T.G.
TitleVaccinia virus encodes four putative DNA and/or RNA helicases distantly related to each other.
SourceJ. Gen. Virol. 73:989-993(1992).
PubMed ID1321883



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