PROSITE documentation PDOC00556

Ribosomal protein S13 signature and profile

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.