{PDOC51195}
{PS51195; Q_MOTIF}
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* DEAD-box RNA helicase Q motif profile *
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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].
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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: April 2006 / First entry.

[ 1] Koonin E.V., Gorbalenya A.E.
     "Autogenous translation regulation by Escherichia coli ATPase SecA may
     be mediated by an intrinsic RNA helicase activity of this protein."
     FEBS. Lett. 298:6-8(1992).
     PubMed=1531961
[ 2] Tanner N.K., Cordin O., Banroques J., Doere M., Linder P.
     "The Q motif: a newly identified motif in DEAD box helicases may
     regulate ATP binding and hydrolysis."
     Mol. Cell 11:127-138(2003).
     PubMed=12535527
[ 3] Story R.M., Li H., Abelson J.N.
     "Crystal structure of a DEAD box protein from the hyperthermophile
     Methanococcus jannaschii."
     Proc. Natl. Acad. Sci. U.S.A. 98:1465-1470(2001).
     PubMed=11171974; DOI=10.1073/pnas.98.4.1465
[ 4] Benz J., Trachsel H., Baumann U.
     "Crystal structure of the ATPase domain of translation initiation
     factor 4A from Saccharomyces cerevisiae--the prototype of the DEAD box
     protein family."
     Structure 7:671-679(1999).
     PubMed=10404596

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