PROSITE documentation PDOC00039
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{PDOC00039}
{PS00039; DEAD_ATP_HELICASE}
{PS00690; DEAH_ATP_HELICASE}
{BEGIN}
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* DEAD and DEAH box families ATP-dependent helicases signatures *
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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 <PDOC00017>).
-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).
PubMed=1321883
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