Science · 2000 · 2.3K citations · 46 references
Life SciencesBiochemistryMolecular BiologyEnzyme MechanismStructural BiochemistryStructural BiologyPeptide Bond ChemistryProtein StructureRibosome FunctionRibosome StructureRna StructureTranslation In ProkaryotesNascent Peptide Exit TunnelPeptide Bond TautomerismPolypeptide Exit TunnelRibosomal CatalysisRibosomal Rna FunctionRibosomal RnasRibosomally Synthesized Peptide BiosynthesisRibosomally Synthesized Peptides
Ribosomal RNA residues in domain V of 23S rRNA exclusively contact substrate analogs, and the polypeptide exit tunnel is largely RNA‑derived with key protein contributions. The study uses atomic structures of the Haloarcula marismortui ribosome to demonstrate its ribozyme nature and investigate the catalytic properties of its all‑RNA active site. The ribosome catalyzes peptide bond formation via a mechanism analogous to the reverse acylation step of serine proteases, with A2486 acting as a general base and its pKa modulated by hydrogen bonding to G2482 and a buried phosphate that stabilizes unusual tautomers.
Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23 S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coli ) playing the same general base role as histidine-57 in chymotrypsin. The unusual p K a (where K a is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli ), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e.
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The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution
Nenad Ban, Poul Nissen, J.L. Hansen et al. · Science · 2000 · 3.3K citations
The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
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The origin of the genetic code
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