Peptide bond formation on the ribosome takes place in an active site composed of RNA. Recent progress of structural, biochemical, and computational approaches has provided a fairly detailed picture of the catalytic mechanism of the reaction. The ribosome accelerates peptide bond formation by lowering the activation entropy of the reaction due to positioning the two substrates, ordering water in...

Peptidyl-tRNA hydrolases (Pths) are essential enzymes found in bacteria, archaea, and eukaryotes. Pths cleave the peptide:tRNA ester bond of peptidyl-tRNAs generated from premature termination of protein synthesis and the expression of short ORFs or minigenes. Accumulation of peptidyl-tRNAs is toxic presumably due to impaired translational initiation or slowed protein synthesis caused by specif...

The 3'-peptidyl-tRNA conjugates that possess a hydrolysis-resistant ribose-3'-amide linkage instead of the natural ester linkage would represent valuable substrates for ribosomal studies. Up to date, access to these derivatives is severely limited. Here, we present a novel approach for the reliable synthesis of non-hydrolyzable 3'-peptidyl-tRNAs that contain all the respective genuine nucleosid...

3-(4'-Benzoylphenyl)propionyl[3H] Phe-tRNA bound to the peptidyl site of the ribosome is photo-crosslinked exclusively to 23S RNA on irradiation at 320 nm. The site of reaction has been identified both by hybridization and primer-extension experiments as uridine-2584 and uridine-2585, located within the central loop of domain V according to the secondary structure model of 23S RNA. The fact tha...

The main enzymatic reaction of the large ribosomal subunit is peptide bond formation. Ribosome crystallography showed that A2451 of 23S rRNA makes the closest approach to the attacking amino group of aminoacyl-tRNA. Mutations of A2451 had relatively small effects on transpeptidation and failed to unequivocally identify the crucial functional group(s). Here, we employed an in vitro reconstitutio...

Peptidyl-prolyl cis/trans isomerases (PPIases) are an enzyme family which catalyse the isomerisation of proline peptide bonds to promote folding and re-folding peptides proteins. Three subfamilies have been identified: cyclophilins, FK506-binding proteins parvulins. Individual PPIases overexpressed in a number cancers [62], members targetted for immunosuppressant effects.

The synthesis of four new peptidyl nucleosides is reported. The kinetic data obtained for the transesterification of 2'/3'-O-benzyloxycarbonyl-L-p-nitrophenylalanyl 5'-O-trityl ribonucleosides which contain different substituents at C position of the purine residue indicates for different mechanisms of the transesterification reaction. The peptidyl nucleosides with an amino group at C position ...

Expression of the chloramphenicol resistance gene cat-86 is regulated by translation attenuation. Among the three ribosomally targeted antibiotics that can induce the gene, only amicetin has an unknown mode of action. Here we demonstrate that the nucleoside antibiotic amicetin is an inhibitor of bacterial peptidyl transferase. Thus, the three inducers of cat-86, chloramphenicol, erythromycin, a...

Background: The yeast histone chaperone Fpr4 harbours a peptidyl-prolyl isomerase domain of the FK506-binding protein (FKBP) family. Results: Catalytic efficiency towards three peptides from histone H3 relates to residues flanking the central proline. Conclusion: Substrate residues C-terminal to the proline dictate isomerase activity by Fpr4. Significance: The findings reveal new molecular deta...

The ability of cystamine, bis-N-aminoethyl disulfide, to inactivate cathepsin B by disulfide exchange is considerably enhanced by the addition of hydrophobic residues which apparently occupy secondary binding sites in the extended active center of the protease. For example, a peptidyl cystamine derivative such as symmetrical Gly-Phe-cystamine is substrate-like and promotes the disulfide exchang...