title: A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding.
abstract: High-resolution structures reveal that yeast ribosomal protein L11 and its bacterial/archael homologs called L5 contain a highly conserved, basically charged internal loop that interacts with the peptidyl-transfer RNA (tRNA) T-loop. We call this the L11 'P-site loop'. Chemical protection of wild-type ribosome shows that that the P-site loop is inherently flexible, i.e. it is extended into the ribosomal P-site when this is unoccupied by tRNA, while it is retracted into the terminal loop of 25S rRNA Helix 84 when the P-site is occupied. To further analyze the function of this structure, a series of mutants within the P-site loop were created and analyzed. A mutant that favors interaction of the P-site loop with the terminal loop of Helix 84 promoted increased affinity for peptidyl-tRNA, while another that favors its extension into the ribosomal P-site had the opposite effect. The two mutants also had opposing effects on binding of aa-tRNA to the ribosomal A-site, and downstream functional effects were observed on translational fidelity, drug resistance/hypersensitivity, virus maintenance and overall cell growth. These analyses suggest that the L11 P-site loop normally helps to optimize ribosome function by monitoring the occupancy status of the ribosomal P-site.
authors: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
authors: Michael H J
authors: MH
authors: Rhodin
authors: Jonathan D
authors: JD
authors: Dinman
mesh_terms: D000483:Alleles; D025141:Drug Resistance, Fungal; D008958:Models, Molecular; D009154:Mutation; D010641:Phenotype; D011485:Protein Binding; D014176:Protein Biosynthesis; D011487:Protein Conformation; D012343:RNA, Transfer / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000737:chemistry* / Q000235:genetics; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics / Q000254:growth & development; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics; D013696:Temperature
chemical_list: D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins; C027624:ribosomal protein L11; D012343:RNA, Transfer