The 5S RNA binding protein from yeast (Saccharomyces cerevisiae) ribosomes. An RNA binding sequence in the carboxyl-terminal region.

The carboxyl-terminal half (CN2 fragment) of the yeast 5S RNA binding protein (YL3) retains an ability to form homogeneous ribonucleoprotein complexes with RNA although the N-terminal half (CN1) appears to confer specificity for the 5S RNA molecule [Nazar, R.N., Yaguchi, M., Willick, G.E., Rollin, C.F. and Roy, C. (1979) Eur. J. Biochem. 102, 573-582]. The nucleic acid binding site in this fragment was more clearly delineated by cleaving the CN2 fragment with a variety of enzymatic and chemical reagents and further examining the ability of the products to form RNA-peptide complexes. Hot acetic acid treatment produced a 47-residue subfragment (CN2-A1) which originated from the C terminus and continued to form stable ribonucleopeptide complexes. The amino acid sequence of this subfragment was determined to be: -Pro-Ala-Phe-Lys-Pro-Thr-Glu-Lys50-Phe-Thr-Lys-Glu-Gln-Tyr-Ala-Ala -Glu60-Ser-Ly s -Lys-Tyr-Arg-Gln-Thr-Lys-Leu-Ser70-Lys-Gln-Gln-Arg-Ala-Ala-Arg-Val -Ala-Ala80-Ly s -Ile-Ala-Ala-Leu-Ala-Gly-Gln-Gln-COOH, with 12 of the 16 basic residues in the CN2 fragment being present in this binding site. The amino acid sequence of the CN2-A1 fragment bears a limited homology in both amino acid and charge distribution with histone 2B from mammals and with one of the 5S RNA binding proteins (EL25) from Escherichia coli. The results suggest that many protein binding sites for nucleic acids may share common structural features and further support the notion that the single large eukaryotic 5S RNA protein may have evolved through a fusion of genes for the multiple 5S RNA binding proteins in prokaryotes.