{PDOC00556} {PS00646; RIBOSOMAL_S13_1} {PS50159; RIBOSOMAL_S13_2} {BEGIN} *********************************************** * 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 ) [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 alpha-turn structure, and a C-terminal long straight alpha 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 alpha helix. We also developed a profile which covers the N-terminal domain and the long straight alpha helix. -Consensus pattern: [KRQSEAT]-[GS]-x-R-H-x(2)-[GSNHKLCD]-x(2)-[LIVMCT]-[RNH]- G-Q -Sequences known to belong to this class detected by the pattern: ALL, except for Chlamydia trachomatis S13. -Sequences known to belong to this class detected by the profile: ALL. -Other sequence(s) detected in Swiss-Prot: NONE. -Last update: December 2004 / Pattern and text revised. [ 1] Chan Y.-L., Paz V., Wool I.G. "The primary structure of rat ribosomal protein S18." Biochem. Biophys. Res. Commun. 178:1212-1218(1991). PubMed=1872840 [ 2] Otaka E., Hashimoto T., Mizuta K. Protein Seq. Data Anal. 5:285-300(1993). [ 3] Brodersen D.E., Clemons W.M. Jr., Carter A.P., Wimberly B.T., Ramakrishnan V. "Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA." J. Mol. Biol. 316:725-768(2002). PubMed=11866529; DOI=10.1006/jmbi.2001.5359 -------------------------------------------------------------------------------- PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html -------------------------------------------------------------------------------- {END}