PROSITE documentation PDOC00039

DEAD and DEAH box families ATP-dependent helicases signatures

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.