{PDOC00039} {PS00039; DEAD_ATP_HELICASE} {PS00690; DEAH_ATP_HELICASE} {BEGIN} ***************************************************************** * 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. -Consensus pattern: [LIVMF](2)-D-E-A-D-[RKEN]-x-[LIVMFYGSTN] -Sequences known to belong to this class detected by the pattern: ALL, except for YHR169w. -Other sequence(s) detected in Swiss-Prot: 14. -Consensus pattern: [GSAH]-x-[LIVMF](3)-D-E-[ALIV]-H-[NECR] -Sequences known to belong to this class detected by the pattern: ALL, except for hrpA. -Other sequence(s) detected in Swiss-Prot: 6. -Note: Proteins belonging to this family also contain a copy of the ATP/GTP- binding motif 'A' (P-loop) (see the relevant entry ). -Expert(s) to contact by email: Linder P.; linder@medecine.unige.ch -Last update: July 1999 / Text revised. [ 1] Schmid S.R., Linder P. "D-E-A-D protein family of putative RNA helicases." Mol. Microbiol. 6:283-291(1992). PubMed=1552844 [ 2] Linder P., Lasko P.F., Ashburner M., Leroy P., Nielsen P.J., Nishi K., Schnier J., Slonimski P.P. "Birth of the D-E-A-D box." Nature 337:121-122(1989). PubMed=2563148; DOI=10.1038/337121a0 [ 3] Wassarman D.A., Steitz J.A. "RNA splicing. Alive with DEAD proteins." Nature 349:463-464(1991). PubMed=1825133; DOI=10.1038/349463a0 [ 4] Hodgman T.C. "A new superfamily of replicative proteins." Nature 333:22-23(1988) and Nature 333:578-578(1988) (Errata). PubMed=3362205; DOI=10.1038/333022b0 [ 5] Harosh I., Deschavanne P. "The RAD3 gene is a member of the DEAH family RNA helicase-like protein." Nucleic Acids Res. 19:6331-6331(1991). PubMed=1956796 [ 6] Koonin E.V., Senkevich T.G. "Vaccinia virus encodes four putative DNA and/or RNA helicases distantly related to each other." J. Gen. Virol. 73:989-993(1992). 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