Determination of the amino acids in yeast ribosomal protein YS11 essential for the recognition of nucleotides in 18 S ribosomal RNA.
The nucleotides in domain I of 18 S rRNA that are important for the binding of the essential yeast ribosomal protein YS11 are mainly in a kink-turn motif and the terminal loop of helix 11 (H11). In the atomic structure of the Thermus thermophilus 30 S subunit, 16 amino acids in S17, the homolog of YS11, are within hydrogen bonding distance of nucleotides in 16 S rRNA. The homologous or analogous 16 amino acids in YS11 were replaced with alanine; nine of the substitutions slowed the growth of yeast cells. The most severe effects were caused by mutations R103A, N106A, K133A, T134A, and K151A. The T. thermophilus analogs of Arg103, Asn106, Thr134, and Lys151 contact nucleotides in the kink-turn motif of 16 S rRNA, whereas Lys133 contacts nucleotides in the terminal loop of H11. These contacts are predominantly with backbone phosphate and sugar oxygens in regions that deviate from A-form geometry, suggesting that YS11 recognizes the shape of its rRNA-binding site rather than reading the sequence of nucleotides. The effect of the mutations on the binding of YS11 to a domain I fragment of 18 S rRNA accorded, in general, with their effect on growth. Mutations of seven YS11 amino acids (Ser77, Met80, Arg88, Tyr97, Pro130, Ser132, and Arg136) whose homologs or analogs in S17 are within hydrogen bonding distance of nucleotides in 16 S rRNA did not affect binding. Apparently, proximities alone do not define either the amino acids or the nucleotides that are important for recognition.
Dresios
John
J
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637.
Chan
Yuen-Ling
YL
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637.
Wool
Ira G
IG
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637. Electronic address: irawool@uchicago.edu.
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000596:Amino Acids; D001483:Base Sequence; D001665:Binding Sites; D015966:Gene Expression Regulation, Fungal; D008967:Molecular Biology; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D012337:RNA, Ribosomal, 18S / Q000737:chemistry / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
D000596:Amino Acids; D012337:RNA, Ribosomal, 18S; D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins; C511612:YS11 protein, S cerevisiae