Mechanism of peptide bond formation on the ribosome.
Peptide bond formation is the fundamental reaction of ribosomal protein synthesis. The ribosome's active site--the peptidyl transferase center--is composed of rRNA, and thus the ribosome is the largest known RNA catalyst. The ribosome accelerates peptide bond formation by 10(7)-fold relative to the uncatalyzed reaction. Recent progress of structural, biochemical and computational approaches has provided a fairly detailed picture of the catalytic mechanisms employed by the ribosome. Energetically, catalysis is entirely entropic, indicating an important role of solvent reorganization, substrate positioning, and/or orientation of the reacting groups within the active site. The ribosome provides a pre-organized network of electrostatic interactions that stabilize the transition state and facilitate proton shuttling involving ribose hydroxyl groups of tRNA. The catalytic mechanism employed by the ribosome suggests how ancient RNA-world enzymes may have functioned.
Rodnina
Marina V
MV
Institute of Physical Biochemistry, University of Witten/Herdecke, Witten, Germany. rodnina@uni-wh.de
Beringer
Malte
M
Wintermeyer
Wolfgang
W
D001665:Binding Sites; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D010452:Peptide Biosynthesis; D014176:Protein Biosynthesis; D016337:RNA, Catalytic / Q000378:metabolism; D012335:RNA, Ribosomal / Q000737:chemistry / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism
D016337:RNA, Catalytic; D012335:RNA, Ribosomal; D012269:Ribosomal Proteins; D012343:RNA, Transfer