title: A Role for the 2' OH of peptidyl-tRNA substrate in peptide release on the ribosome revealed through RF-mediated rescue.
abstract: The 2' OH of the peptidyl-tRNA substrate is thought to be important for catalysis of both peptide bond formation and peptide release in the ribosomal active site. The release reaction also specifically depends on a release factor protein (RF) to hydrolyze the ester linkage of the peptidyl-tRNA upon recognition of stop codons in the A site. Here, we demonstrate that certain amino acid substitutions (in particular those containing hydroxyl or thiol groups) in the conserved GGQ glutamine of release factor RF1 can rescue defects in the release reaction associated with peptidyl-tRNA substrates lacking a 2' OH. We explored this rescue effect through biochemical and computational approaches that support a model where the 2' OH of the P-site substrate is critical for orienting the nucleophile in a hydrogen-bonding network productive for catalysis.
authors.affiliation: Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Shaw
authors.forename: Stefan
authors.initials: S
authors.lastname: Trobro
authors.forename: Shan L
authors.initials: SL
authors.lastname: He
authors.forename: Johan
authors.initials: J
authors.lastname: Åqvist
authors.forename: Rachel
authors.initials: R
authors.lastname: Green
mesh_terms: D019943:Amino Acid Substitution; D055162:Biocatalysis; D020134:Catalytic Domain; D018388:Codon, Terminator; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D006878:Hydroxides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010454:Peptide Termination Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*; D012997:Solvents / Q000737:chemistry; D013379:Substrate Specificity
chemical_list: D018388:Codon, Terminator; D006878:Hydroxides; D010454:Peptide Termination Factors; D010455:Peptides; D012346:RNA, Transfer, Amino Acyl; D012997:Solvents; C019037:tRNA, peptidyl-