PROSITE documentation PDOC00556 [for PROSITE entry PS00646]

Ribosomal protein S13 signature and profile




Description

Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues [1,2].

The crystal structure of the S13 protein has been solved as part of the small ribosomal subunit (see <PDB:1J5E; M>) [3]. It consists of two separated domains, an approximately 60-residue N-terminal domain which forms a small helical domain consisting of two-turn helices and two α-turn structure, and a C-terminal long straight α helix followed by a region devoid of secondary structure. The N-terminal domain makes several base specific interactions with the 16S RNA. Several lysine residues in the C-terminal helix also contact RNA.

Proteins known to belong to this family are listed below.

  • Eubacterial S13.
  • Plant chloroplast S13 (nuclear encoded).
  • Red algal chloroplast S13.
  • Cyanelle S13.
  • Archaebacterial S13.
  • Plant mitochondrial S13.
  • Mammalian and plant S18.

As a signature pattern, we selected the best conserved regions located at the C-terminal end of the long straight α helix. We also developed a profile which covers the N-terminal domain and the long straight α helix.

Last update:

December 2004 / Pattern and text revised.

Technical section

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

RIBOSOMAL_S13_1, PS00646; Ribosomal protein S13 signature  (PATTERN)

RIBOSOMAL_S13_2, PS50159; Ribosomal protein S13 family profile  (MATRIX)


References

1AuthorsChan Y.-L., Paz V., Wool I.G.
TitleThe primary structure of rat ribosomal protein S18.
SourceBiochem. Biophys. Res. Commun. 178:1212-1218(1991).
PubMed ID1872840

2AuthorsOtaka E., Hashimoto T., Mizuta K.
SourceProtein Seq. Data Anal. 5:285-300(1993).

3AuthorsBrodersen D.E., Clemons W.M. Jr., Carter A.P., Wimberly B.T., Ramakrishnan V.
TitleCrystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA.
SourceJ. Mol. Biol. 316:725-768(2002).
PubMed ID11866529
DOI10.1006/jmbi.2001.5359



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