PROSITE documentation PDOC51195

DEAD-box RNA helicase Q motif profile




Description

RNA helicases from the DEAD-box family are found in almost all organisms and have important roles in RNA metabolism such as splicing, RNA transport, ribosome biogenesis, translation and RNA decay. They are enzyme that unwind double-stranded RNA molecules in an energy dependent fashion through the hydrolysis of NTP. DEAD-box RNA helicases belong to superfamily 2 (SF2) of helicases. As other SF1 and SF2 members they contain seven conserved motifs which are characteristic of these two superfamilies (see <PDOC51192>) [1,E1]. DEAD-box is named after the amino acids of motif II or Walker B (Mg2+-binding aspartic acid). Besides these seven motifs, DEAD-box RNA helicases contain a conserved cluster of nine amino-acids (the Q motif) with an invariant glutamine located N-terminally of motif I. An additional highly conserved but isolated aromatic residue is also found upstream of these nine residues [2]. The Q motif is characteristic of and unique to DEAD box family of helicases. It is supposed to control ATP binding and hydrolysis, and therefore it represents a potential mechanism for regulating helicase activity.

Several structural analyses of DEAD-box RNA helicases have been reported (see <PDB:1HV8>) [3,4]. The Q motif is located in close proximity to motif I. The conserved glutamine and aromatic residues interact with the ADP molecule.

Some proteins known to contain a Q motif:

  • Eukaryotic initiation factor 4A (eIF4A). An ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and required for mRNA binding to ribosome.
  • Various eukaryotic helicases involved in ribosome biogenesis (DBP3, DRS1, SPB4, MAK5, DBP6, DBP7, DBP9, DBP10).
  • Eukaryotic DEAD-box proteins involved in pre-mRNA splicing (Prp5p, Prp28p and Sub2p).
  • DEAD-box proteins required for mitochondrial genome expression (MSS116 and MRH4).
  • Fungi ATP-dependent RNA helicase DHH1. It is required for decapping and turnover of mRNA.
  • Fungi ATP-dependent RNA helicase DBP5. It is involved in nucleo-cytoplasmic transport of poly(A) RNA.
  • Bacterial ATP-dependent RNA helicase rhlB. It is involved in the RNA degradosome, a multi-enzyme complex important in RNA processing and messenger RNA degradation.
  • Bacterial cold-shock DEAD box protein A.

The profile we developed stretches from the conserved aromatic residue to one amino acid after the glutamine of the Q motif.

Last update:

April 2006 / First entry.

Technical section

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

Q_MOTIF, PS51195; DEAD-box RNA helicase Q motif profile  (MATRIX)


References

1AuthorsKoonin E.V., Gorbalenya A.E.
TitleAutogenous translation regulation by Escherichia coli ATPase SecA may be mediated by an intrinsic RNA helicase activity of this protein.
SourceFEBS. Lett. 298:6-8(1992).
PubMed ID1531961

2AuthorsTanner N.K., Cordin O., Banroques J., Doere M., Linder P.
TitleThe Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis.
SourceMol. Cell 11:127-138(2003).
PubMed ID12535527

3AuthorsStory R.M., Li H., Abelson J.N.
TitleCrystal structure of a DEAD box protein from the hyperthermophile Methanococcus jannaschii.
SourceProc. Natl. Acad. Sci. U.S.A. 98:1465-1470(2001).
PubMed ID11171974
DOI10.1073/pnas.98.4.1465

4AuthorsBenz J., Trachsel H., Baumann U.
TitleCrystal structure of the ATPase domain of translation initiation factor 4A from Saccharomyces cerevisiae--the prototype of the DEAD box protein family.
SourceStructure 7:671-679(1999).
PubMed ID10404596

E1Sourcehttp://medweb2.unige.ch/~linder/RNA_helicases.html



PROSITE is copyright. It is produced by the SIB Swiss Institute Bioinformatics. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement. For information about the licensing scheme send an email to
Prosite License or see: prosite_license.html.

Miscellaneous

View entry in original PROSITE document format
View entry in raw text format (no links)