PROSITE documentation PDOC50889 [for PROSITE entry PS50889]
S4 RNA-binding domain profile


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 α 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 α/β structure consisting of an antiparallel β sheet packed against α helices (see <PDB:1C05>) [2,3,4].

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

Last update:

November 2002 / First entry.


Technical section

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

S4, PS50889; S4 RNA-binding domain profile  (MATRIX)


1AuthorsAravind L. Koonin E.V.
TitleNovel predicted RNA-binding domains associated with the translation machinery.
SourceJ. Mol. Evol. 48:291-302(1999).
PubMed ID10093218

2AuthorsDavies C. Gerstner R.B. Draper D.E. Ramakrishnan V. White S.W.
TitleThe 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.
SourceEMBO J. 17:4545-4558(1998).
PubMed ID9707415

3AuthorsGuijarro J.I. Pintar A. Prochnicka-Chalufour A. Guez V. Gilquin B. Bedouelle H. Delepierre M.
TitleStructure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase.
SourceStructure 10:311-317(2002).
PubMed ID12005430

4AuthorsSivaraman J. Sauve V. Larocque R. Stura E.A. Schrag J.D. Cygler M. Matte A.
TitleStructure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP.
SourceNat. Struct. Biol. 9:353-358(2002).
PubMed ID11953756

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