{PDOC50889}
{PS50889; S4}
{BEGIN}
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* S4 RNA-binding domain profile *
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The S4  domain  is  a  small  globular  domain  consisting of 60-65 amino acid
residues that is found in:

 - The ribosomal protein S4 family (see <PDOC00549>).
 - Tyrosyl-tRNA synthetases.
 - The rluA and rsuA families of pseudouridine synthases.
 - Several predicted RNA methylases.
 - A putative novel RNA editing enzyme.
 - A  number  of  uncharacterized,  small  proteins  that  may  be involved in
   translation regulation.

The S4  domain  typically  occurs  in  a  single  copy at various positions in
different proteins.  The  S4  domain  can  be  found alone as in several small
bacterial proteins  (e.g.  YabO from B. subtilis and YrfH from E. coli), or in
association with  other  domains  such  as  the  N-terminal  alpha  helix rich
globular domain  found  in  S4  proteins, the pseudouridine synthase catalytic
domain, the  methylase  domain,  the  tyrosyl-tRNA  synthetases  domain or the
deaminase domain.  It  has  been  proposed  that  the  S4 domain is capable of
recognizing complex, unique 3D features in highly folded RNA molecules such as
rRNAs, tRNAs, and untranslated regions of mRNAs [1].

The S4   domain   contains   a  characteristic  pattern  of  conserved  polar,
hydrophobic, and  small  residues  in its N-terminal and central parts. The C-
terminal part  does  not  show a high degree of conservation between different
families within the superfamily of S4 containing proteins and may be important
for interactions  specific to each family [1]. The S4 domain has an alpha/beta
structure consisting  of  an  antiparallel  beta  sheet  packed  against alpha
helices (see <PDB:1C05>) [2,3,4].

The profile we developed covers the entire S4 RNA-binding domain.

-Sequences known to belong to this class detected by the profile: ALL,  except
 40S ribosomal  protein S9  from Entamoeba histolytica,  Candida albicans  and
 Drosophila melanogaster.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: November 2002 / First entry.

[ 1] Aravind L., Koonin E.V.
     "Novel predicted RNA-binding domains associated with the translation
     machinery."
     J. Mol. Evol. 48:291-302(1999).
     PubMed=10093218
[ 2] Davies C., Gerstner R.B., Draper D.E., Ramakrishnan V., White S.W.
     "The crystal structure of ribosomal protein S4 reveals a two-domain
     molecule with an extensive RNA-binding surface: one domain shows
     structural homology to the ETS DNA-binding motif."
     EMBO J. 17:4545-4558(1998).
     PubMed=9707415; DOI=10.1093/emboj/17.16.4545
[ 3] Guijarro J.I., Pintar A., Prochnicka-Chalufour A., Guez V.,
     Gilquin B., Bedouelle H., Delepierre M.
     "Structure and dynamics of the anticodon arm binding domain of
     Bacillus stearothermophilus Tyrosyl-tRNA synthetase."
     Structure 10:311-317(2002).
     PubMed=12005430
[ 4] Sivaraman J., Sauve V., Larocque R., Stura E.A., Schrag J.D.,
     Cygler M., Matte A.
     "Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil
     and UMP."
     Nat. Struct. Biol. 9:353-358(2002).
     PubMed=11953756; DOI=10.1038/nsb788

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