Ribosomal catalysis: the evolution of mechanistic concepts for peptide bond formation and peptidyl-tRNA hydrolysis. 2008

Matthias D Erlacher, and Norbert Polacek
Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Innsbruck, Austria.

Over time the mechanistic concepts to describe the two principal chemical reactions that are catalyzed by the ribosome, peptide bond formation and peptidyl-tRNA hydrolysis, have undergone dramatic changes. While the initial models were based on a ribosomal protein-based mechanism, evidence for a direct functional contribution of ribosomal RNA for catalysis has accumulated over the past years. The presentation of high resolution crystallographic structures of the large ribosomal subunit at the beginning of the new millennium dramatically increased our molecular insight into the organization of the active center and finally placed the ribosome amongst the list of RNA enzymes. Combined with elaborate biochemical and biophysical approaches the translation field has made significant progress in understanding mechanistic details of ribosomal catalysis. While it seems that the mechanism of ribosome-catalyzed peptidyl-tRNA hydrolysis is just emerging, the knowledge on transpeptidation is already very advanced. It has been realized that intricate interactions between ribosomal RNA and the transfer RNA substrate are crucial for proton shuttling that is required for efficient amide bond formation.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D010443 Peptide Chain Termination, Translational A process of GENETIC TRANSLATION whereby the terminal amino acid is added to a lengthening polypeptide. This termination process is signaled from the MESSENGER RNA, by one of three termination codons (CODON, TERMINATOR) that immediately follows the last amino acid-specifying CODON. Chain Termination, Peptide, Translational,Protein Biosynthesis Termination,Protein Chain Termination, Translational,Protein Translation Termination,Translation Termination, Genetic,Translation Termination, Protein,Translational Peptide Chain Termination,Translational Termination, Protein,Biosynthesis Termination, Protein,Genetic Translation Termination,Protein Translational Termination,Termination, Genetic Translation,Termination, Protein Biosynthesis,Termination, Protein Translation,Termination, Protein Translational
D002384 Catalysis The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction. Catalyses
D006868 Hydrolysis The process of cleaving a chemical compound by the addition of a molecule of water.
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D012269 Ribosomal Proteins Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits. Proteins, Ribosomal,Ribosomal Protein,Protein, Ribosomal
D012270 Ribosomes Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION. Ribosome
D012335 RNA, Ribosomal The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed) Ribosomal RNA,15S RNA,RNA, 15S
D012346 RNA, Transfer, Amino Acyl Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process. Amino Acyl tRNA,Transfer RNA, Amino Acyl,tRNA-Amino Acyl,Amino Acyl T RNA,Acyl tRNA, Amino,Acyl, tRNA-Amino,tRNA Amino Acyl,tRNA, Amino Acyl
D016337 RNA, Catalytic RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate. Catalytic RNA,Ribozyme,Ribozymes

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